Daily Papers

Large language models are typically trained densely: all parameters are updated with respect to all inputs. This requires synchronization of billions of parameters across thousands of GPUs. We introduce a simple but effective method to asynchronously train large, sparse language models on arbitrary text corpora. Our method clusters a corpus into sets of related documents, trains a separate expert language model on each cluster, and combines them in a sparse ensemble for inference. This approach generalizes embarrassingly parallel training by automatically discovering the domains for each expert, and eliminates nearly all the communication overhead of existing sparse language models. Our technique outperforms dense baselines on multiple corpora and few-shot tasks, and our analysis shows that specializing experts to meaningful clusters is key to these gains. Performance also improves with the number of experts and size of training data, suggesting this is a highly efficient and accessible approach to training large language models.

Test-time computing approaches, which leverage additional computational resources during inference, have been proven effective in enhancing large language model performance. This work introduces a novel, linearly scaling approach, TestNUC, that improves test-time predictions by leveraging the local consistency of neighboring unlabeled data-it classifies an input instance by considering not only the model's prediction on that instance but also on neighboring unlabeled instances. We evaluate TestNUC across eight diverse datasets, spanning intent classification, topic mining, domain discovery, and emotion detection, demonstrating its consistent superiority over baseline methods such as standard prompting and self-consistency. Furthermore, TestNUC can be seamlessly integrated with existing test-time computing approaches, substantially boosting their performance. Our analysis reveals that TestNUC scales effectively with increasing amounts of unlabeled data and performs robustly across different embedding models, making it practical for real-world applications. Our code is available at https://github.com/HenryPengZou/TestNUC.

With the growing prominence of the Mixture of Experts (MoE) architecture in developing large-scale foundation models, we investigate the Hierarchical Mixture of Experts (HMoE), a specialized variant of MoE that excels in handling complex inputs and improving performance on targeted tasks. Our analysis highlights the advantages of using the Laplace gating function over the traditional Softmax gating within the HMoE frameworks. We theoretically demonstrate that applying the Laplace gating function at both levels of the HMoE model helps eliminate undesirable parameter interactions caused by the Softmax gating and, therefore, accelerates the expert convergence as well as enhances the expert specialization. Empirical validation across diverse scenarios supports these theoretical claims. This includes large-scale multimodal tasks, image classification, and latent domain discovery and prediction tasks, where our modified HMoE models show great performance improvements compared to the conventional HMoE models.

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject to several limitations common in LLMs such as hallucinations. In response, we present GeneAgent, a first-of-its-kind language agent featuring self-verification capability. It autonomously interacts with various biological databases and leverages relevant domain knowledge to improve accuracy and reduce hallucination occurrences. Benchmarking on 1,106 gene sets from different sources, GeneAgent consistently outperforms standard GPT-4 by a significant margin. Moreover, a detailed manual review confirms the effectiveness of the self-verification module in minimizing hallucinations and generating more reliable analytical narratives. To demonstrate its practical utility, we apply GeneAgent to seven novel gene sets derived from mouse B2905 melanoma cell lines, with expert evaluations showing that GeneAgent offers novel insights into gene functions and subsequently expedites knowledge discovery.

Hypothetical induction is recognized as the main reasoning type when scientists make observations about the world and try to propose hypotheses to explain those observations. Past research on hypothetical induction is under a constrained setting: (1) the observation annotations in the dataset are carefully manually handpicked sentences (resulting in a close-domain setting); and (2) the ground truth hypotheses are mostly commonsense knowledge, making the task less challenging. In this work, we tackle these problems by proposing the first dataset for social science academic hypotheses discovery, with the final goal to create systems that automatically generate valid, novel, and helpful scientific hypotheses, given only a pile of raw web corpus. Unlike previous settings, the new dataset requires (1) using open-domain data (raw web corpus) as observations; and (2) proposing hypotheses even new to humanity. A multi-module framework is developed for the task, including three different feedback mechanisms to boost performance, which exhibits superior performance in terms of both GPT-4 based and expert-based evaluation. To the best of our knowledge, this is the first work showing that LLMs are able to generate novel (''not existing in literature'') and valid (''reflecting reality'') scientific hypotheses.

While AI systems demonstrate exponentially improving capabilities, the pace of AI research itself remains linearly bounded by human cognitive capacity, creating an increasingly severe development bottleneck. We present ASI-Arch, the first demonstration of Artificial Superintelligence for AI research (ASI4AI) in the critical domain of neural architecture discovery--a fully autonomous system that shatters this fundamental constraint by enabling AI to conduct its own architectural innovation. Moving beyond traditional Neural Architecture Search (NAS), which is fundamentally limited to exploring human-defined spaces, we introduce a paradigm shift from automated optimization to automated innovation. ASI-Arch can conduct end-to-end scientific research in the domain of architecture discovery, autonomously hypothesizing novel architectural concepts, implementing them as executable code, training and empirically validating their performance through rigorous experimentation and past experience. ASI-Arch conducted 1,773 autonomous experiments over 20,000 GPU hours, culminating in the discovery of 106 innovative, state-of-the-art (SOTA) linear attention architectures. Like AlphaGo's Move 37 that revealed unexpected strategic insights invisible to human players, our AI-discovered architectures demonstrate emergent design principles that systematically surpass human-designed baselines and illuminate previously unknown pathways for architectural innovation. Crucially, we establish the first empirical scaling law for scientific discovery itself--demonstrating that architectural breakthroughs can be scaled computationally, transforming research progress from a human-limited to a computation-scalable process. We provide comprehensive analysis of the emergent design patterns and autonomous research capabilities that enabled these breakthroughs, establishing a blueprint for self-accelerating AI systems.

The tasks of out-of-domain (OOD) intent discovery and generalized intent discovery (GID) aim to extend a closed intent classifier to open-world intent sets, which is crucial to task-oriented dialogue (TOD) systems. Previous methods address them by fine-tuning discriminative models. Recently, although some studies have been exploring the application of large language models (LLMs) represented by ChatGPT to various downstream tasks, it is still unclear for the ability of ChatGPT to discover and incrementally extent OOD intents. In this paper, we comprehensively evaluate ChatGPT on OOD intent discovery and GID, and then outline the strengths and weaknesses of ChatGPT. Overall, ChatGPT exhibits consistent advantages under zero-shot settings, but is still at a disadvantage compared to fine-tuned models. More deeply, through a series of analytical experiments, we summarize and discuss the challenges faced by LLMs including clustering, domain-specific understanding, and cross-domain in-context learning scenarios. Finally, we provide empirical guidance for future directions to address these challenges.

Accelerating the discovery of novel and more effective therapeutics is an important pharmaceutical problem in which deep learning is playing an increasingly significant role. However, real-world drug discovery tasks are often characterized by a scarcity of labeled data and significant covariate shiftx2013x2013a setting that poses a challenge to standard deep learning methods. In this paper, we present Q-SAVI, a probabilistic model able to address these challenges by encoding explicit prior knowledge of the data-generating process into a prior distribution over functions, presenting researchers with a transparent and probabilistically principled way to encode data-driven modeling preferences. Building on a novel, gold-standard bioactivity dataset that facilitates a meaningful comparison of models in an extrapolative regime, we explore different approaches to induce data shift and construct a challenging evaluation setup. We then demonstrate that using Q-SAVI to integrate contextualized prior knowledge of drug-like chemical space into the modeling process affords substantial gains in predictive accuracy and calibration, outperforming a broad range of state-of-the-art self-supervised pre-training and domain adaptation techniques.

Perovskite solar cells (PSCs) have rapidly emerged as a leading contender in next-generation photovoltaic technologies, owing to their exceptional power conversion efficiencies and advantageous material properties. Despite these advances, challenges such as long-term stability, environmental sustainability, and scalable manufacturing continue to hinder their commercialization. Precursor additive engineering has shown promise in addressing these issues by enhancing both the performance and durability of PSCs. However, the explosive growth of scientific literature and the complex interplay of materials, processes, and device architectures make it increasingly difficult for researchers to efficiently access, organize, and utilize domain knowledge in this rapidly evolving field. To address this gap, we introduce Perovskite-R1, a specialized large language model (LLM) with advanced reasoning capabilities tailored for the discovery and design of PSC precursor additives. By systematically mining and curating 1,232 high-quality scientific publications and integrating a comprehensive library of 33,269 candidate materials, we constructed a domain-specific instruction-tuning dataset using automated question-answer generation and chain-of-thought reasoning. Fine-tuning the QwQ-32B model on this dataset resulted in Perovskite-R1, which can intelligently synthesize literature insights and generate innovative and practical solutions for defect passivation and the selection of precursor additives. Experimental validation of several model-proposed strategies confirms their effectiveness in improving material stability and performance. Our work demonstrates the potential of domain-adapted LLMs in accelerating materials discovery and provides a closed-loop framework for intelligent, data-driven advancements in perovskite photovoltaic research.

It stands to reason that the amount and the quality of data is of key importance for setting up accurate AI-driven models. Among others, a fundamental aspect to consider is the bias introduced during sample selection in database generation. This is particularly relevant when a model is trained on a specialized dataset to predict a property of interest, and then applied to forecast the same property over samples having a completely different genesis. Indeed, the resulting biased model will likely produce unreliable predictions for many of those out-of-the-box samples. Neglecting such an aspect may hinder the AI-based discovery process, even when high quality, sufficiently large and highly reputable data sources are available. In this regard, with superconducting and thermoelectric materials as two prototypical case studies in the field of energy material discovery, we present and validate a new method (based on a classification strategy) capable of detecting, quantifying and circumventing the presence of cross-domain data bias.

Qualitative insights from user experiences are critical for informing product and policy decisions, but collecting such data at scale is constrained by the time and availability of experts to conduct semi-structured interviews. Recent work has explored using large language models (LLMs) to automate interviewing, yet existing systems lack a principled mechanism for balancing systematic coverage of predefined topics with adaptive exploration, or the ability to pursue follow-ups, deep dives, and emergent themes that arise organically during conversation. In this work, we formulate adaptive semi-structured interviewing as an optimization problem over the interviewer's behavior. We define interview utility as a trade-off between coverage of a predefined interview topic guide, discovery of relevant emergent themes, and interview cost measured by length. Based on this formulation, we introduce SparkMe, a multi-agent LLM interviewer that performs deliberative planning via simulated conversation rollouts to select questions with high expected utility. We evaluate SparkMe through controlled experiments with LLM-based interviewees, showing that it achieves higher interview utility, improving topic guide coverage (+4.7% over the best baseline) and eliciting richer emergent insights while using fewer conversational turns than prior LLM interviewing approaches. We further validate SparkMe in a user study with 70 participants across 7 professions on the impact of AI on their workflows. Domain experts rate SparkMe as producing high-quality adaptive interviews that surface helpful profession-specific insights not captured by prior approaches. The code, datasets, and evaluation protocols for SparkMe are available as open-source at https://github.com/SALT-NLP/SparkMe.

Understanding causal relationships between machines is crucial for fault diagnosis and optimization in manufacturing processes. Real-world datasets frequently exhibit up to 90% missing data and high dimensionality from hundreds of sensors. These datasets also include domain-specific expert knowledge and chronological order information, reflecting the recording order across different machines, which is pivotal for discerning causal relationships within the manufacturing data. However, previous methods for handling missing data in scenarios akin to real-world conditions have not been able to effectively utilize expert knowledge. Conversely, prior methods that can incorporate expert knowledge struggle with datasets that exhibit missing values. Therefore, we propose COKE to construct causal graphs in manufacturing datasets by leveraging expert knowledge and chronological order among sensors without imputing missing data. Utilizing the characteristics of the recipe, we maximize the use of samples with missing values, derive embeddings from intersections with an initial graph that incorporates expert knowledge and chronological order, and create a sensor ordering graph. The graph-generating process has been optimized by an actor-critic architecture to obtain a final graph that has a maximum reward. Experimental evaluations in diverse settings of sensor quantities and missing proportions demonstrate that our approach compared with the benchmark methods shows an average improvement of 39.9% in the F1-score. Moreover, the F1-score improvement can reach 62.6% when considering the configuration similar to real-world datasets, and 85.0% in real-world semiconductor datasets. The source code is available at https://github.com/OuTingYun/COKE.

Unsupervised domain adaptation (UDA) has proven to be highly effective in transferring knowledge from a label-rich source domain to a label-scarce target domain. However, the presence of additional novel categories in the target domain has led to the development of open-set domain adaptation (ODA) and universal domain adaptation (UNDA). Existing ODA and UNDA methods treat all novel categories as a single, unified unknown class and attempt to detect it during training. However, we found that domain variance can lead to more significant view-noise in unsupervised data augmentation, which affects the effectiveness of contrastive learning (CL) and causes the model to be overconfident in novel category discovery. To address these issues, a framework named Soft-contrastive All-in-one Network (SAN) is proposed for ODA and UNDA tasks. SAN includes a novel data-augmentation-based soft contrastive learning (SCL) loss to fine-tune the backbone for feature transfer and a more human-intuitive classifier to improve new class discovery capability. The SCL loss weakens the adverse effects of the data augmentation view-noise problem which is amplified in domain transfer tasks. The All-in-One (AIO) classifier overcomes the overconfidence problem of current mainstream closed-set and open-set classifiers. Visualization and ablation experiments demonstrate the effectiveness of the proposed innovations. Furthermore, extensive experiment results on ODA and UNDA show that SAN outperforms existing state-of-the-art methods.

Light curves describe temporal variations in the brightness of celestial objects. Learning robust representations of light curves is essential for large-scale automatic discovery in the dynamic universe, but existing time-series foundation models often struggle with the uneven sampling, complex noise, and wide range of physical timescales that characterize astronomical observations. We propose a domain-informed representation learning framework for irregular astronomical time series with Joint-Embedding predictive architecture (JEPA), combining semantics-preserving views, uncertainty-aware tokenization, and multi-view self-distillation. The encoders are trained with multi-view self-distillation using LeJEPA regularization on the LEAVES dataset and evaluated on the StarEmbed classification benchmark. On StarEmbed, our model outperforms hand-crafted features on 15 of 16 classification metrics. In few-shot linear probing, it achieves macro-F1 scores of 42.56 pm 7.21 with one sample per class and 63.58 pm 1.20 with 100 samples per class, consistently improving over hand-crafted features. Beyond variable-star classification, the learned representation supports similarity search, parameter estimation, and photometric zero-point drift detection. We further evaluate cross-domain adaptation on 12 heterogeneous irregular time-series datasets from PYRREGULAR, where the adapted variant matches or exceeds previous state-of-the-art performance on 5 datasets, compared with at most 3 wins by any single prior baseline. These results demonstrate that domain-informed multi-view self-distillation is an effective strategy for learning representations of irregular time series, while also highlighting that successful time-series representation learning requires domain-specific inductive biases rather than a universally optimal architecture.

Causal representation learning (CRL) seeks to recover latent variables with identifiability guarantees, typically up to permutation and component-wise reparameterization under appropriate assumptions. However, identifiability does not imply interpretability: latent semantics are typically assigned post hoc by alignment with known ground-truth factors. This limitation is particularly acute in scientific time series, where underlying mechanisms are unknown and discovering interpretable structure is a primary goal. In contrast, scientific observations (such as residue-pair distances, climate indices, or process sensors) are inherently semantic, as they correspond to named physical quantities. This raises a key question: can the interpretability of observations be transferred to the identifiable latent space? We propose MOSAIC (Module discovery via Sparse Additive Identifiable Causal learning), a sparse temporal VAE that integrates temporal CRL identifiability with support recovery over observed variables. MOSAIC identifies latent variables via regime-conditioned temporal variation, and recovers for each latent a sparse set of associated observations through an additive decoder, yielding module-level interpretability. We show that ANOVA main-effect supports are identifiable under general smooth mixing functions, and provide finite-sample recovery guarantees for a tractable sparse-additive variant. Empirically, MOSAIC recovers domain-consistent variable groups across RNA molecular dynamics, solar wind, ENSO climate, the Tennessee Eastman process, and a synthetic tokamak benchmark, enabling interpretable discovery of latent mechanisms in scientific time series.

Modern neural networks rely on generic activation functions (ReLU, GELU, SiLU) that ignore the mathematical structure inherent in scientific data. We propose Neuro-Symbolic Activation Discovery, a framework that uses Genetic Programming to extract interpretable mathematical formulas from data and inject them as custom activation functions. Our key contribution is the discovery of a Geometric Transfer phenomenon: activation functions learned from particle physics data successfully generalize to ecological classification, outperforming standard activations (ReLU, GELU, SiLU) in both accuracy and parameter efficiency. On the Forest Cover dataset, our Hybrid Transfer model achieves 82.4% accuracy with only 5,825 parameters, compared to 83.4% accuracy requiring 31,801 parameters for a conventional heavy network -- a 5.5x parameter reduction with only 1% accuracy loss. We introduce a Parameter Efficiency Score (E_{param} = AUC / log_{10}(Params)) and demonstrate that lightweight hybrid architectures consistently achieve 18-21% higher efficiency than over-parameterized baselines. Crucially, we establish boundary conditions: while Physics to Ecology transfer succeeds (both involve continuous Euclidean measurements), Physics to Text transfer fails (discrete word frequencies require different mathematical structures). Our work opens pathways toward domain-specific activation libraries for efficient scientific machine learning.

Matbench Discovery simulates the deployment of machine learning (ML) energy models in a high-throughput search for stable inorganic crystals. We address the disconnect between (i) thermodynamic stability and formation energy and (ii) in-domain vs out-of-distribution performance. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with further insights into trade-offs between various performance metrics. To answer the question which ML methodology performs best at materials discovery, our initial release explores a variety of models including random forests, graph neural networks (GNN), one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials (UIP). Ranked best-to-worst by their test set F1 score on thermodynamic stability prediction, we find CHGNet > M3GNet > MACE > ALIGNN > MEGNet > CGCNN > CGCNN+P > Wrenformer > BOWSR > Voronoi tessellation fingerprints with random forest. The top 3 models are UIPs, the winning methodology for ML-guided materials discovery, achieving F1 scores of ~0.6 for crystal stability classification and discovery acceleration factors (DAF) of up to 5x on the first 10k most stable predictions compared to dummy selection from our test set. We also highlight a sharp disconnect between commonly used global regression metrics and more task-relevant classification metrics. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV/atom above the convex hull where most materials are. Our results highlight the need to focus on classification metrics that actually correlate with improved stability hit rate.

Efficient discovery of precursor additives is essential for improving the performance of perovskite solar cells, yet the large chemical space makes conventional trial-and-error screening inefficient. We develop LEAP(LLM-driven Exploration via Active Learning for Perovskites), an expert-in-the-loop closed framework that couples a domain-specialized large language model(LLM) with active learning for iterative additive prioritization. The LLM is trained to extract mechanism-relevant knowledge from the perovskite additive literature and to represent candidate molecules through interpretable descriptors, which are further integrated into a Bayesian optimization workflow for uncertainty-aware prioritization under low-data conditions. Benchmark results on unseen literature show that the domain-specialized model outperforms general-purpose models in mechanism-consistent reasoning. Experimental validation in an expert-in-the-loop proof-of-concept study suggests improved additive prioritization across three screening rounds, leading to average device PCEs of 20.13% and 20.87% for the later-round 6-CDQ- and 2-CNA-treated devices, respectively, compared with 19.25% for the control, with a champion PCE of 21.32%. These results provide preliminary evidence that literature-grounded mechanistic descriptors, when coupled with Bayesian optimization and expert feasibility review, can support mechanism-aware additive prioritization in perovskite photovoltaics.

A fundamental bottleneck in human-AI collaboration is the "intention expression gap," the difficulty for humans to effectively convey complex, high-dimensional thoughts to AI. This challenge often traps users in inefficient trial-and-error loops and is exacerbated by the diverse expertise levels of users. We reframe this problem from passive instruction following to a Socratic collaboration paradigm, proposing an agent that actively probes for information to resolve its uncertainty about user intent. we name the proposed agent Nous, trained to acquire proficiency in this inquiry policy. The core mechanism of Nous is a training framework grounded in the first principles of information theory. Within this framework, we define the information gain from dialogue as an intrinsic reward signal, which is fundamentally equivalent to the reduction of Shannon entropy over a structured task space. This reward design enables us to avoid reliance on costly human preference annotations or external reward models. To validate our framework, we develop an automated simulation pipeline to generate a large-scale, preference-based dataset for the challenging task of scientific diagram generation. Comprehensive experiments, including ablations, subjective and objective evaluations, and tests across user expertise levels, demonstrate the effectiveness of our proposed framework. Nous achieves leading efficiency and output quality, while remaining robust to varying user expertise. Moreover, its design is domain-agnostic, and we show evidence of generalization beyond diagram generation. Experimental results prove that our work offers a principled, scalable, and adaptive paradigm for resolving uncertainty about user intent in complex human-AI collaboration.

While the capabilities of generative models heavily improved in different domains (images, text, graphs, molecules, etc.), their evaluation metrics largely remain based on simplified quantities or manual inspection with limited practicality. To this end, we propose a framework for Multi-level Performance Evaluation of Generative mOdels (MPEGO), which could be employed across different domains. MPEGO aims to quantify generation performance hierarchically, starting from a sub-feature-based low-level evaluation to a global features-based high-level evaluation. MPEGO offers great customizability as the employed features are entirely user-driven and can thus be highly domain/problem-specific while being arbitrarily complex (e.g., outcomes of experimental procedures). We validate MPEGO using multiple generative models across several datasets from the material discovery domain. An ablation study is conducted to study the plausibility of intermediate steps in MPEGO. Results demonstrate that MPEGO provides a flexible, user-driven, and multi-level evaluation framework, with practical insights on the generation quality. The framework, source code, and experiments will be available at https://github.com/GT4SD/mpego.

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

Many disciplines pose natural-language research questions over large document collections whose answers typically require structured evidence, traditionally obtained by manually designing an annotation schema and exhaustively labeling the corpus, a slow and error-prone process. We introduce ScheMatiQ, which leverages calls to a backbone LLM to take a question and a corpus to produce a schema and a grounded database, with a web interface that lets steer and revise the extraction. In collaboration with domain experts, we show that ScheMatiQ yields outputs that support real-world analysis in law and computational biology. We release ScheMatiQ as open source with a public web interface, and invite experts across disciplines to use it with their own data. All resources, including the website, source code, and demonstration video, are available at: www.ScheMatiQ-ai.com

Theory of Mind (ToM), the ability to understand people's mental variables based on their behavior, is key to developing socially intelligent agents. Current approaches to Theory of Mind reasoning either rely on prompting Large Language Models (LLMs), which are prone to systematic errors, or use rigid, handcrafted Bayesian Theory of Mind (BToM) models, which are more robust but cannot generalize across different domains. In this work, we introduce AutoToM, an automated Bayesian Theory of Mind method for achieving open-ended machine Theory of Mind. AutoToM can operate in any domain, infer any mental variable, and conduct robust Theory of Mind reasoning of any order. Given a Theory of Mind inference problem, AutoToM first proposes an initial BToM model. It then conducts automated Bayesian inverse planning based on the proposed model, leveraging an LLM as the backend. Based on the uncertainty of the inference, it iteratively refines the model, by introducing additional mental variables and/or incorporating more timesteps in the context. Empirical evaluations across multiple Theory of Mind benchmarks demonstrate that AutoToM consistently achieves state-of-the-art performance, offering a scalable, robust, and interpretable approach to machine Theory of Mind.

Ask a pretrained biomedical language model whether "cortisol 28 ug/dL" and "stock-market volatility" are related, and it returns a cosine similarity of 0.83 on a scale where 1.0 means identical. The two share no mechanism. This is not a corner case: every off-the-shelf biomedical encoder we tested (BioBERT, PubMedBERT, BioM-ELECTRA) scores unrelated cross-domain pairs between 0.76 and 0.92 when the answer should be near zero. Accuracy on cross-domain discrimination is 0%. Retrieval systems survive this, because a language model downstream filters the noise. A Large Behavioural Model (LBM), a foundation model whose subject is a person rather than a sentence, does not: it reasons over a graph of a user's life and treats embedding proximity as evidence that two events are causally linked. False proximity writes a false causal edge, and everything downstream inherits the error. Here, embedding geometry is not a tuning knob; it is correctness. We report the fix. A contrastive pass over 72,034 pairs raises PubMedBERT BIOSSES correlation from 0.633 to 0.828 and within-vs-across-domain separation from 1.05x to 1.63x. A second pass, BODHI, mines hard negatives from edges absent in a biomedical knowledge graph and lifts separation to 2.30x and the discrimination gap to +0.392, at a 4.5% BIOSSES cost. On an Intel Xeon 6737P with AMX, OpenVINO cuts single-query latency from 1367 ms to 10 ms (133x) and reaches 555 sentences/sec. One finding contradicts standard advice: FP16 beats INT8 on this silicon at every serving batch size, and we explain why. The same model on a no-AMX Ice Lake instance runs 13-27x slower. We release the benchmark suite, training corpora, the BODHI generator, and the OpenVINO scripts.

Understanding the brain increasingly depends on integrating evidence across scales, modalities, and disciplines. Addressing a single research question therefore requires a coordinated sequence of operations, from surveying prior work to executing analyses and interpreting results in light of domain knowledge. AI agents promise to accelerate this process, but current agents lack domain expertise in brain science, may fabricate claims, drift during multi-step reasoning, and offer few defined points for expert intervention. These failures are especially costly in brain science, where conclusions feed into downstream scientific claims and depend on laboratory-specific expertise and careful human judgment. We present BrainPilot a fully open-source multi-agent system that accelerates brain science research with traceable logs and agent-verified results. A principal investigator (PI) agent coordinates specialist agents grounded in curated domain knowledge: a unified brain science knowledge base containing 7{,}233 indexed items and a skill library of 72 reusable methodology units across seven research domains. Every major step is recorded in the Graph of Trace, an auditable record that links subgoals, tool use, evidence, and claims and allows researchers to follow and inspect the workflow. An Auditor agent further integrates fabrication checking into the workflow. For evaluation, we run three brain science tasks from Agents' Last Exam, introduce our own benchmark, BrainPilotBench-v0, and present additional end-to-end case studies. Across these evaluations, BrainPilot with an open-source backbone model attains performance comparable to state-of-the-art agent framework with less costs.

Agentic systems enable the intelligent use of research tooling, augmenting a researcher's ability to investigate and propose novel solutions to existing problems. Within Additive Manufacturing (AM), alloy discovery remains a complex challenge, often requiring expertise in the various domains of materials science, thermodynamic simulations, and experimental analysis. Large Language Model (LLM) enabled agents can facilitate this endeavor by utilizing their extensive knowledge base to dispatch tool calls via Model Context Protocol (MCP) to perform actions such as Thermo-Calc property diagram calculations and lack of fusion process map generation. In addition, the multi-agent system developed in this work is able to effectively reason through complex user prompts and provide analysis on the printability of proposed alloys. These agents can dynamically adjust their task trajectory to the outcomes of tool call results, effectively enabling autonomous decision-making in practical environments. This work aims to utilize LLM enabled agents to automate and accelerate the task of alloy discovery within the field of additive manufacturing and showcase the benefits of adopting this multi-agent system.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

Equation discovery aims to automate the discovery of scientific models in the form of mathematical equations from data. Technically, equation discovery is implemented by symbolic regression algorithms. Performance of symbolic regression for equation discovery is measured along two dimensions: Prediction accuracy on test data, and recovery of known groundtruth formulas. For standard regression, accuracy is typically measured on in-domain test data, for instance, by splitting a data set randomly into training and test data. While this makes sense for in-domain interpolation, which is the common goal in ordinary regression, it can be a misleading proxy for true model discovery and generalization. The obvious alternative is to measure out-of-domain accuracy. However, obtaining challenging out-of-domain test data is a non-trivial problem. Therefore, we focus on equation recovery for evaluating symbolic regression algorithms for equation discovery. The rationale is that symbolic regression algorithms that perform well in recovering known groundtruth formulas are good candidates to perform well in unknown equation discovery. Existing benchmarks for symbolic regression include equation recovery tasks, however, with only a small number of groundtruth formulas that are publicly known. Moreover, these benchmarks place less emphasis on evaluating the robustness of algorithms in terms of their behavior under changing dimensionality, sampling size, sampling distribution and sampling domain. This, however, is of central importance to practitioners wanting to discover equations for modeling natural phenomena, since data is almost certainly noisy and comes from diverse domains, distributions, and sample sizes. To fill this gap, we introduce the Equation Recovery Benchmark (ERBench), a new evaluation framework designed to rigorously assess algorithms explicitly targeting the task of equation discovery.

The discovery of novel methodologies for emerging problems is a continuing cycle in ML, often driven by the migration of techniques across domains. Building on this observation, we ask whether current LLM ideation systems benefit from targeted cross-domain retrieval or simply from exposure to diverse mechanisms. We study this question through PaperGym, a three-stage pipeline: (1) tool-augmented seed extraction via read, grep, and bash over an isolated paper environment, (2) cross-domain seed retrieval via paraphrasing across seven ML domains, and (3) method synthesis from retrieved seeds, each scored by rubric-based judges. Tool-augmented extraction improves specificity, and paraphrase-based retrieval broadens domain coverage. In synthesis, cross-domain retrieval receives more pairwise novelty wins than no-retrieval and same-domain baselines, but shows no significant difference from a random diverse-seed control. These findings suggest LLM ideation systems benefit from diverse seed exposure, but do not yet reliably exploit the semantic reason particular seeds were retrieved. We release the seed library, rubric prompts, and run scripts at https://github.com/yunjoochoi/PaperGym

*Automated circuit discovery* is a central tool in mechanistic interpretability for identifying the internal components of neural networks responsible for specific behaviors. While prior methods have made significant progress, they typically depend on heuristics or approximations and do not offer provable guarantees over continuous input domains for the resulting circuits. In this work, we leverage recent advances in neural network verification to propose a suite of automated algorithms that yield circuits with *provable guarantees*. We focus on three types of guarantees: (1) *input domain robustness*, ensuring the circuit agrees with the model across a continuous input region; (2) *robust patching*, certifying circuit alignment under continuous patching perturbations; and (3) *minimality*, formalizing and capturing a wide array of various notions of succinctness. Interestingly, we uncover a diverse set of novel theoretical connections among these three families of guarantees, with critical implications for the convergence of our algorithms. Finally, we conduct experiments with state-of-the-art verifiers on various vision models, showing that our algorithms yield circuits with substantially stronger robustness guarantees than standard circuit discovery methods, establishing a principled foundation for provable circuit discovery.

In this paper, we introduce Auto-Intent, a method to adapt a pre-trained large language model (LLM) as an agent for a target domain without direct fine-tuning, where we empirically focus on web navigation tasks. Our approach first discovers the underlying intents from target domain demonstrations unsupervisedly, in a highly compact form (up to three words). With the extracted intents, we train our intent predictor to predict the next intent given the agent's past observations and actions. In particular, we propose a self-exploration approach where top-k probable intent predictions are provided as a hint to the pre-trained LLM agent, which leads to enhanced decision-making capabilities. Auto-Intent substantially improves the performance of GPT-{3.5, 4} and Llama-3.1-{70B, 405B} agents on the large-scale real-website navigation benchmarks from Mind2Web and online navigation tasks from WebArena with its cross-benchmark generalization from Mind2Web.

While Large Language Models (LLMs) demonstrate impressive generation abilities, they frequently struggle when it comes to specialized domains due to their limited domain-specific knowledge. Studies on domain-specific LLMs resort to expanding the vocabulary before fine-tuning on domain-specific corpus, aiming to decrease the sequence length and enhance efficiency during decoding, without thoroughly investigating the results of vocabulary expansion to LLMs over different domains. Our pilot study reveals that expansion with only a subset of the entire vocabulary may lead to superior performance. Guided by the discovery, this paper explores how to identify a vocabulary subset to achieve the optimal results. We introduce VEGAD, an adaptive method that automatically identifies valuable words from a given domain vocabulary. Our method has been validated through experiments on three Chinese datasets, demonstrating its effectiveness. Additionally, we have undertaken comprehensive analyses of the method. The selection of a optimal subset for expansion has shown to enhance performance on both domain-specific tasks and general tasks, showcasing the potential of VEGAD.

Answering counterfactual queries has many important applications such as knowledge discovery and explainability, but is challenging when causal variables are unobserved and we only see a projection onto an observation space, for instance, image pixels. One approach is to recover the latent Structural Causal Model (SCM), but this typically needs unrealistic assumptions, such as linearity of the causal mechanisms. Another approach is to use na\"ive ML approximations, such as generative models, to generate counterfactual samples; however, these lack guarantees of accuracy. In this work, we strive to strike a balance between practicality and theoretical guarantees by focusing on a specific type of causal query called domain counterfactuals, which hypothesizes what a sample would have looked like if it had been generated in a different domain (or environment). Concretely, by only assuming invertibility, sparse domain interventions and access to observational data from different domains, we aim to improve domain counterfactual estimation both theoretically and practically with less restrictive assumptions. We define domain counterfactually equivalent models and prove necessary and sufficient properties for equivalent models that provide a tight characterization of the domain counterfactual equivalence classes. Building upon this result, we prove that every equivalence class contains a model where all intervened variables are at the end when topologically sorted by the causal DAG. This surprising result suggests that a model design that only allows intervention in the last k latent variables may improve model estimation for counterfactuals. We then test this model design on extensive simulated and image-based experiments which show the sparse canonical model indeed improves counterfactual estimation over baseline non-sparse models.

The discovery of novel Ionic Liquids (ILs) is hindered by critical challenges in property prediction, including limited data, poor model accuracy, and fragmented workflows. Leveraging the power of Large Language Models (LLMs), we introduce AIonopedia, to the best of our knowledge, the first LLM agent for IL discovery. Powered by an LLM-augmented multimodal domain foundation model for ILs, AIonopedia enables accurate property predictions and incorporates a hierarchical search architecture for molecular screening and design. Trained and evaluated on a newly curated and comprehensive IL dataset, our model delivers superior performance. Complementing these results, evaluations on literature-reported systems indicate that the agent can perform effective IL modification. Moving beyond offline tests, the practical efficacy was further confirmed through real-world wet-lab validation, in which the agent demonstrated exceptional generalization capabilities on challenging out-of-distribution tasks, underscoring its ability to accelerate real-world IL discovery.

Recent attempts to combine large language models (LLMs) with causal discovery ask models to infer pairwise directions, propose graph structures, or inject language-model outputs as priors and constraints. These approaches promise faster analysis, but they also obscure whether a causal evidence is supported by data and assumptions or by textual associations, prompt artifacts and hallucinated mechanisms. We argue for a different role for agents in causal discovery. Agents should inspect data, retrieve context, explain method assumptions and clarify graph outputs, but they should not supply edges, orientations, priors, constraints or causal conclusions. We propose the principle that agents assist the workflow, while causal claims remain grounded in data, explicit assumptions, formal algorithms, diagnostics and user or domain-expert decisions. We instantiate this principle in causal-learn+, an online platform that coordinates data analysis, preprocessing, method recommendation, expert-knowledge incorporation, formal discovery and interpretation around the algorithmic ecosystem of causal-learn. A case study on Big Five personality data illustrates agent-assisted pipeline of causal discovery without turning language-model unreliability into causal evidence. The platform is available at causallearn.com.

Model cards describe model behavior through a mixture of textual descriptions and structured artifacts, including performance, configuration, and dataset tables. Existing model search systems rely predominantly on semantic similarity over text, which can produce homogeneous result sets and limit exploration of alternatives. We argue that model search is inherently comparative: users want models that are task-aligned yet differentiated in measurable ways. We hypothesize that this balance requires retrieval over condensed, high-quality evidence rather than verbose descriptions, and much of that evidence is concentrated in structured tables. We present StructuredSemanticSearch, a table-driven model search framework built on the ModelTables benchmark. Given a query, StructuredSemanticSearch combines a semantic baseline for task alignment with a structure-aware pipeline that discovers query-related model-card tables using table discovery operators such as unionability, joinability, and keyword search. Retrieved tables are mapped back to model cards under a controlled top-k budget, enabling fair comparison between text-based and table-based retrieval. Beyond retrieval, StructuredSemanticSearch adapts table integration to the model-table domain through orientation-aware integration, producing compact integrated views of tables from partially overlapping and sometimes transposed evidence tables. For evaluation, we introduce a nugget-based, auditable protocol that extracts compact evidence items from model cards, matches queries to condition- or intent-specific nuggets, and measures evidence coverage and diversity over retrieved model-card candidate sets. This protocol also provides a scalable path toward approximate, evidence-based labeling in dynamic model lakes. Experiments on 597 model-recommendation queries show improved nugget coverage for the structure-aware pipeline than semantic baseline

We introduce Aster, an AI agent for autonomous scientific discovery capable of operating over 20 times faster than existing frameworks. Given a task, an initial program, and a script to evaluate the performance of the program, Aster iteratively improves the program, often leading to new state-of-the-art performances. Aster's significant reduction in the number of iterations required for novel discovery expands the domain of tractable problems to include tasks with long evaluation durations, such as multi-hour machine learning training runs. We applied Aster to problems in mathematics, GPU kernel engineering, biology, neuroscience, and language model training. More specifically: the Erdos minimum overlap problem, optimizing the TriMul kernel, a single-cell analysis denoising problem, training a neural activity prediction model to perform well on ZAPBench, and the NanoGPT Speedrun Competition. Aster attains SOTA results in every task, except for ZAPBench, where it matches the performance of the best human solution with less than 1/190th of the compute. Aster is accessible via a web interface and API at asterlab.ai.

Large Language Models (LLMs) promise to accelerate discovery by reasoning across the expanding scientific landscape. Yet, the challenge is no longer access to information but connecting it in meaningful, domain-spanning ways. In materials science, where innovation demands integrating concepts from molecular chemistry to mechanical performance, this is especially acute. Neither humans nor single-agent LLMs can fully contend with this torrent of information, with the latter often prone to hallucinations. To address this bottleneck, we introduce a multi-agent framework guided by large-scale knowledge graphs to find sustainable substitutes for per- and polyfluoroalkyl substances (PFAS)-chemicals currently under intense regulatory scrutiny. Agents in the framework specialize in problem decomposition, evidence retrieval, design parameter extraction, and graph traversal, uncovering latent connections across distinct knowledge pockets to support hypothesis generation. Ablation studies show that the full multi-agent pipeline outperforms single-shot prompting, underscoring the value of distributed specialization and relational reasoning. We demonstrate that by tailoring graph traversal strategies, the system alternates between exploitative searches focusing on domain-critical outcomes and exploratory searches surfacing emergent cross-connections. Illustrated through the exemplar of biomedical tubing, the framework generates sustainable PFAS-free alternatives that balance tribological performance, thermal stability, chemical resistance, and biocompatibility. This work establishes a framework combining knowledge graphs with multi-agent reasoning to expand the materials design space, showcasing several initial design candidates to demonstrate the approach.

Novel intent discovery automates the process of grouping similar messages (questions) to identify previously unknown intents. However, current research focuses on publicly available datasets which have only the question field and significantly differ from real-life datasets. This paper proposes methods to improve the intent discovery pipeline deployed in a large e-commerce platform. We show the benefit of pre-training language models on in-domain data: both self-supervised and with weak supervision. We also devise the best method to utilize the conversational structure (i.e., question and answer) of real-life datasets during fine-tuning for clustering tasks, which we call Conv. All our methods combined to fully utilize real-life datasets give up to 33pp performance boost over state-of-the-art Constrained Deep Adaptive Clustering (CDAC) model for question only. By comparison CDAC model for the question data only gives only up to 13pp performance boost over the naive baseline.

A longitudinal web crawl is a sequence of partial samples of an evolving URL population. Pairwise containment between two crawls is the standard probe; under a simple urn model of the crawl -- each round samples a fraction of the URLs and replaces a fraction -- it recovers two interpretable rates, per-round survival α and coverage c, but treats the population as uniform and consumes one pair at a time. In this work, we define a formal language for talking about a crawl. We extend this analysis with the discovery curve U(s, T), the cumulative URL footprint over a sliding window of T crawls starting at s, which under the same urn model is also a closed-form function of (α, c). Containment and the discovery curve are then two projections of one process: independent fits agree on (α, c) when the urn is homogeneous, so any disagreement is itself a measurement. Applied to Common Crawl (2020--2025, domain granularity) and to the German Academic Web (GAW, URL granularity), the two projections disagree on both archives, and a two-component urn with a persistent core fraction κ alongside shell parameters (α_partial, c_partial) reconciles the disagreement. A residual on c_partial remains, signaling that the shell itself is not homogeneous; κ is recorded as the scalar entry point to a rank-resolved generalization, which is left to follow-up work. web archive \and crawl coverage \and discovery curve \and urn model \and two-component model \and URL lifetime

Clinical image interpretation is inherently multi-step and tool-centric: clinicians iteratively combine visual evidence with patient context, quantify findings, and refine their decisions through a sequence of specialized procedures. While LLM-based agents promise to orchestrate such heterogeneous medical tools, existing systems treat tool sets and invocation strategies as static after deployment. This design is brittle under real-world domain shifts, across tasks, and evolving diagnostic requirements, where predefined tool chains frequently degrade and demand costly manual re-design. We propose MACRO, a self-evolving, experience-augmented medical agent that shifts from static tool composition to experience-driven tool discovery. From verified execution trajectories, the agent autonomously identifies recurring effective multi-step tool sequences, synthesizes them into reusable composite tools, and registers these as new high-level primitives that continuously expand its behavioral repertoire. A lightweight image-feature memory grounds tool selection in a visual-clinical context, while a GRPO-like training loop reinforces reliable invocation of discovered composites, enabling closed-loop self-improvement with minimal supervision. Extensive experiments across diverse medical imaging datasets and tasks demonstrate that autonomous composite tool discovery consistently improves multi-step orchestration accuracy and cross-domain generalization over strong baselines and recent state-of-the-art agentic methods, bridging the gap between brittle static tool use and adaptive, context-aware clinical AI assistance. Code will be available upon acceptance.

Identifying effective interventions from the scientific literature is challenging due to the high volume of publications, specialized terminology, and inconsistent reporting formats, making manual curation laborious and prone to oversight. To address this challenge, this paper proposes a novel framework leveraging large language models (LLMs), which integrates a progressive ontology prompting (POP) algorithm with a dual-agent system, named LLM-Duo. On the one hand, the POP algorithm conducts a prioritized breadth-first search (BFS) across a predefined ontology, generating structured prompt templates and action sequences to guide the automatic annotation process. On the other hand, the LLM-Duo system features two specialized LLM agents, an explorer and an evaluator, working collaboratively and adversarially to continuously refine annotation quality. We showcase the real-world applicability of our framework through a case study focused on speech-language intervention discovery. Experimental results show that our approach surpasses advanced baselines, achieving more accurate and comprehensive annotations through a fully automated process. Our approach successfully identified 2,421 interventions from a corpus of 64,177 research articles in the speech-language pathology domain, culminating in the creation of a publicly accessible intervention knowledge base with great potential to benefit the speech-language pathology community.

Text-to-SQL benchmarks play a crucial role in evaluating the progress made in the field and the ranking of different models. However, accurately matching a model-generated SQL query to a reference SQL query in a benchmark fails for various reasons, such as underspecified natural language queries, inherent assumptions in both model-generated and reference queries, and the non-deterministic nature of SQL output under certain conditions. In this paper, we conduct an extensive study of several prominent cross-domain text-to-SQL benchmarks and re-evaluate some of the top-performing models within these benchmarks, by both manually evaluating the SQL queries and rewriting them in equivalent expressions. Our evaluation reveals that attaining a perfect performance on these benchmarks is unfeasible due to the multiple interpretations that can be derived from the provided samples. Furthermore, we find that the true performance of the models is underestimated and their relative performance changes after a re-evaluation. Most notably, our evaluation reveals a surprising discovery: a recent GPT4-based model surpasses the gold standard reference queries in the Spider benchmark in our human evaluation. This finding highlights the importance of interpreting benchmark evaluations cautiously, while also acknowledging the critical role of additional independent evaluations in driving advancements in the field.

False news that spreads on social media has proliferated over the past years and has led to multi-aspect threats in the real world. While there are studies of false news on specific domains (like politics or health care), little work is found comparing false news across domains. In this article, we investigate false news across nine domains on Weibo, the largest Twitter-like social media platform in China, from 2009 to 2019. The newly collected data comprise 44,728 posts in the nine domains, published by 40,215 users, and reposted over 3.4 million times. Based on the distributions and spreads of the multi-domain dataset, we observe that false news in domains that are close to daily life like health and medicine generated more posts but diffused less effectively than those in other domains like politics, and that political false news had the most effective capacity for diffusion. The widely diffused false news posts on Weibo were associated strongly with certain types of users -- by gender, age, etc. Further, these posts provoked strong emotions in the reposts and diffused further with the active engagement of false-news starters. Our findings have the potential to help design false news detection systems in suspicious news discovery, veracity prediction, and display and explanation. The comparison of the findings on Weibo with those of existing work demonstrates nuanced patterns, suggesting the need for more research on data from diverse platforms, countries, or languages to tackle the global issue of false news. The code and new anonymized dataset are available at https://github.com/ICTMCG/Characterizing-Weibo-Multi-Domain-False-News.

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and mathematical inference. Despite their effectiveness, Long-CoT reasoning models are often criticized for their limited ability and low efficiency in knowledge-intensive domains such as molecule discovery. Success in this field requires a precise understanding of domain knowledge, including molecular structures and chemical principles, which is challenging due to the inherent complexity of molecular data and the scarcity of high-quality expert annotations. To bridge this gap, we introduce Mol-R1, a novel framework designed to improve explainability and reasoning performance of R1-like Explicit Long-CoT reasoning LLMs in text-based molecule generation. Our approach begins with a high-quality reasoning dataset curated through Prior Regulation via In-context Distillation (PRID), a dedicated distillation strategy to effectively generate paired reasoning traces guided by prior regulations. Building upon this, we introduce MoIA, Molecular Iterative Adaptation, a sophisticated training strategy that iteratively combines Supervised Fine-tuning (SFT) with Reinforced Policy Optimization (RPO), tailored to boost the reasoning performance of R1-like reasoning models for molecule discovery. Finally, we examine the performance of Mol-R1 in the text-based molecule reasoning generation task, showing superior performance against existing baselines.

Real-time detection and mitigation of technical anomalies are critical for large-scale cloud-native services, where even minutes of downtime can result in massive financial losses and diminished user trust. While customer incidents serve as a vital signal for discovering risks missed by monitoring, extracting actionable intelligence from this data remains challenging due to extreme noise, high throughput, and semantic complexity of diverse business lines. In this paper, we present TingIS, an end-to-end system designed for enterprise-grade incident discovery. At the core of TingIS is a multi-stage event linking engine that synergizes efficient indexing techniques with Large Language Models (LLMs) to make informed decisions on event merging, enabling the stable extraction of actionable incidents from just a handful of diverse user descriptions. This engine is complemented by a cascaded routing mechanism for precise business attribution and a multi-dimensional noise reduction pipeline that integrates domain knowledge, statistical patterns, and behavioral filtering. Deployed in a production environment handling a peak throughput of over 2,000 messages per minute and 300,000 messages per day, TingIS achieves a P90 alert latency of 3.5 minutes and a 95\% discovery rate for high-priority incidents. Benchmarks constructed from real-world data demonstrate that TingIS significantly outperforms baseline methods in routing accuracy, clustering quality, and Signal-to-Noise Ratio.

We present Denario, an AI multi-agent system designed to serve as a scientific research assistant. Denario can perform many different tasks, such as generating ideas, checking the literature, developing research plans, writing and executing code, making plots, and drafting and reviewing a scientific paper. The system has a modular architecture, allowing it to handle specific tasks, such as generating an idea, or carrying out end-to-end scientific analysis using Cmbagent as a deep-research backend. In this work, we describe in detail Denario and its modules, and illustrate its capabilities by presenting multiple AI-generated papers generated by it in many different scientific disciplines such as astrophysics, biology, biophysics, biomedical informatics, chemistry, material science, mathematical physics, medicine, neuroscience and planetary science. Denario also excels at combining ideas from different disciplines, and we illustrate this by showing a paper that applies methods from quantum physics and machine learning to astrophysical data. We report the evaluations performed on these papers by domain experts, who provided both numerical scores and review-like feedback. We then highlight the strengths, weaknesses, and limitations of the current system. Finally, we discuss the ethical implications of AI-driven research and reflect on how such technology relates to the philosophy of science. We publicly release the code at https://github.com/AstroPilot-AI/Denario. A Denario demo can also be run directly on the web at https://huggingface.co/spaces/astropilot-ai/Denario, and the full app will be deployed on the cloud.

Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets. This combination yields strong benchmark metrics but limits transferability to domains structurally distinct from drug discovery. To overcome this limitation and drive discovery toward real, scientifically grounded targets, we introduce the Nanotechnology Molecular Optimization (NMO) Benchmark, which bridges machine learning (ML) and quantum materials science. NMO acts simultaneously as a rigorous testbed for the ML community and a discovery engine for nanotechnology research. The suite replaces proxy oracles with quantum simulations and introduces strict protocols that prioritize scientific utility over leaderboard-oriented overfitting. The physics-based NMO tasks impose hard structural constraints and rugged fitness landscapes, posing fundamentally new requirements on generative models. Notably, advanced molecular optimization methods underperform much simpler approaches on the NMO tasks. We develop a new baseline method identifying the critical components to solve the NMO tasks, including a novel representation for modeling structural constraints and a domain-agnostic pretraining strategy to eliminate pharmaceutical dataset bias. Our results surpass state-of-the-art physical properties and reveal previously unknown structural motifs, offering new insights for the nanotechnology community and demonstrating that ML can drive genuine scientific discovery.

In this work, we introduce CodeEvolve, an open-source evolutionary coding agent that unites Large Language Models (LLMs) with genetic algorithms to solve complex computational problems. Our framework adapts powerful evolutionary concepts to the LLM domain, building upon recent methods for generalized scientific discovery. CodeEvolve employs an island-based genetic algorithm to maintain population diversity and increase throughput, introduces a novel inspiration-based crossover mechanism that leverages the LLMs context window to combine features from successful solutions, and implements meta-prompting strategies for dynamic exploration of the solution space. We conduct a rigorous evaluation of CodeEvolve on a subset of the mathematical benchmarks used to evaluate Google DeepMind's closed-source AlphaEvolve. Our findings show that our method surpasses AlphaEvolve's performance on several challenging problems. To foster collaboration and accelerate progress, we release our complete framework as an open-source repository.

Recent progress in Large Language Models (LLMs) has drawn attention to their potential for accelerating drug discovery. However, a central problem remains: translating theoretical ideas into robust implementations in the highly specialized context of pharmaceutical research. This limitation prevents practitioners from making full use of the latest AI developments in drug discovery. To address this challenge, we introduce DrugAgent, a multi-agent framework that automates machine learning (ML) programming for drug discovery tasks. DrugAgent employs an LLM Planner that formulates high-level ideas and an LLM Instructor that identifies and integrates domain knowledge when implementing those ideas. We present case studies on three representative drug discovery tasks. Our results show that DrugAgent consistently outperforms leading baselines, including a relative improvement of 4.92% in ROC-AUC compared to ReAct for drug-target interaction (DTI). DrugAgent is publicly available at https://anonymous.4open.science/r/drugagent-5C42/.

The central problem in biomedical imaging are batch effects: systematic technical variations unrelated to the biological signal of interest. These batch effects critically undermine experimental reproducibility and are the primary cause of failure of deep learning systems on new experimental batches, preventing their practical use in the real world. Despite years of research, no method has succeeded in closing this performance gap for deep learning models. We propose Control-Stabilized Adaptive Risk Minimization via Batch Normalization (CS-ARM-BN), a meta-learning adaptation method that exploits negative control samples. Such unperturbed reference images are present in every experimental batch by design and serve as stable context for adaptation. We validate our novel method on Mechanism-of-Action (MoA) classification, a crucial task for drug discovery, on the large-scale JUMP-CP dataset. The accuracy of standard ResNets drops from 0.939 pm 0.005, on the training domain, to 0.862 pm 0.060 on data from new experimental batches. Foundation models, even after Typical Variation Normalization, fail to close this gap. We are the first to show that meta-learning approaches close the domain gap by achieving 0.935 pm 0.018. If the new experimental batches exhibit strong domain shifts, such as being generated in a different lab, meta-learning approaches can be stabilized with control samples, which are always available in biomedical experiments. Our work shows that batch effects in bioimaging data can be effectively neutralized through principled in-context adaptation, which also makes them practically usable and efficient.

Protein scientific discovery is bottlenecked by the manual orchestration of information and algorithms, while general agents are insufficient in complex domain projects. VenusFactory2 provides an autonomous framework that shifts from static tool usage to dynamic workflow synthesis via a self-evolving multi-agent infrastructure to address protein-related demands. It outperforms a set of well-known agents on the VenusAgentEval benchmark, and autonomously organizes the discovery and optimization of proteins from a single natural language prompt.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

Financial metrics like the Sharpe ratio are pivotal in evaluating investment performance by balancing risk and return. However, traditional metrics often struggle with robustness and generalization, particularly in dynamic and volatile market conditions. This paper introduces AlphaSharpe, a novel framework leveraging large language models (LLMs) to iteratively evolve and optimize financial metrics to discover enhanced risk-return metrics that outperform traditional approaches in robustness and correlation with future performance metrics by employing iterative crossover, mutation, and evaluation. Key contributions of this work include: (1) a novel use of LLMs to generate and refine financial metrics with implicit domain-specific knowledge, (2) a scoring mechanism to ensure that evolved metrics generalize effectively to unseen data, and (3) an empirical demonstration of 3x predictive power for future risk-returns, and 2x portfolio performance. Experimental results in a real-world dataset highlight the superiority of discovered metrics, making them highly relevant to portfolio managers and financial decision-makers. This framework not only addresses the limitations of existing metrics but also showcases the potential of LLMs in advancing financial analytics, paving the way for informed and robust investment strategies.

Compound AI systems (CASs) that employ LLMs as agents to accomplish knowledge-intensive tasks via interactions with tools and data retrievers have garnered significant interest within database and AI communities. While these systems have the potential to supplement typical analysis workflows of data analysts in enterprise data platforms, unfortunately, CASs are subject to the same data discovery challenges that analysts have encountered over the years -- silos of multimodal data sources, created across teams and departments within an organization, make it difficult to identify appropriate data sources for accomplishing the task at hand. Existing data discovery benchmarks do not model such multimodality and multiplicity of data sources. Moreover, benchmarks of CASs prioritize only evaluating end-to-end task performance. To catalyze research on evaluating the data discovery performance of multimodal data retrievers in CASs within a real-world setting, we propose CMDBench, a benchmark modeling the complexity of enterprise data platforms. We adapt existing datasets and benchmarks in open-domain -- from question answering and complex reasoning tasks to natural language querying over structured data -- to evaluate coarse- and fine-grained data discovery and task execution performance. Our experiments reveal the impact of data retriever design on downstream task performance -- a 46% drop in task accuracy on average -- across various modalities, data sources, and task difficulty. The results indicate the need to develop optimization strategies to identify appropriate LLM agents and retrievers for efficient execution of CASs over enterprise data.

The practical utility of machine learning models in the sciences often hinges on their interpretability. It is common to assess a model's merit for scientific discovery, and thus novel insights, by how well it aligns with already available domain knowledge--a dimension that is currently largely disregarded in the comparison of neural network models. While pruning can simplify deep neural network architectures and excels in identifying sparse models, as we show in the context of gene regulatory network inference, state-of-the-art techniques struggle with biologically meaningful structure learning. To address this issue, we propose DASH, a generalizable framework that guides network pruning by using domain-specific structural information in model fitting and leads to sparser, better interpretable models that are more robust to noise. Using both synthetic data with ground truth information, as well as real-world gene expression data, we show that DASH, using knowledge about gene interaction partners within the putative regulatory network, outperforms general pruning methods by a large margin and yields deeper insights into the biological systems being studied.

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data -- natural vibrational frequencies -- via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM-based multi-agent environment on the other hand, unleashes great potentials of LLMs in addressing multi-objective materials problems and opens up new avenues for autonomous materials discovery and design.

Novel Class Discovery (NCD) is the problem of trying to discover novel classes in an unlabeled set, given a labeled set of different but related classes. The majority of NCD methods proposed so far only deal with image data, despite tabular data being among the most widely used type of data in practical applications. To interpret the results of clustering or NCD algorithms, data scientists need to understand the domain- and application-specific attributes of tabular data. This task is difficult and can often only be performed by a domain expert. Therefore, this interface allows a domain expert to easily run state-of-the-art algorithms for NCD in tabular data. With minimal knowledge in data science, interpretable results can be generated.

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.

As the capability frontier of autonomous agents continues to expand, they are increasingly able to complete specialized tasks through plug-and-play external skills. Yet current benchmarks mostly test whether models can use provided skills, leaving open whether they can discover skills from experience, repair them after failure, and maintain a coherent library over time. We introduce SkillFlow, a benchmark of 166 tasks across 20 families in which task construction within each family follows a Domain-Agnostic Execution Flow (DAEF) that defines an agent workflow framework, allowing these tasks to share a consistent workflow. Agents are evaluated under an Agentic Lifelong Learning protocol in which they begin without skills, solve tasks sequentially within each family, externalize lessons through trajectory- and rubric-driven skill patches, and carry the updated library forward. Experiments reveal a substantial capability gap. For Claude Opus 4.6, lifelong skill evolution improves task success from 62.65% to 71.08% (+8.43 points). However, high skill usage does not necessarily imply high utility: Kimi K2.5 gains only +0.60 points despite 66.87% skill usage, while Qwen-Coder-Next reaches only a 44.58% task completion rate and still regresses relative to the vanilla setting. SkillFlow contributes a structured testbed for this direction and an in-depth empirical analysis of skill discovery, patching, transfer, and their failure modes under lifelong evaluation.

We present ScienceClaw + Infinite, a framework for autonomous scientific investigation in which independent agents conduct research without central coordination, and any contributor can deploy new agents into a shared ecosystem. The system is built around three components: an extensible registry of over 300 interoperable scientific skills, an artifact layer that preserves full computational lineage as a directed acyclic graph (DAG), and a structured platform for agent-based scientific discourse with provenance-aware governance. Agents select and chain tools based on their scientific profiles, produce immutable artifacts with typed metadata and parent lineage, and broadcast unsatisfied information needs to a shared global index. The ArtifactReactor enables plannerless coordination: peer agents discover and fulfill open needs through pressure-based scoring, while schema-overlap matching triggers multi-parent synthesis across independent analyses. An autonomous mutation layer actively prunes the expanding artifact DAG to resolve conflicting or redundant workflows, while persistent memory allows agents to continuously build upon complex epistemic states across multiple cycles. Infinite converts these outputs into auditable scientific records through structured posts, provenance views, and machine-readable discourse relations, with community feedback steering subsequent investigation cycles. Across four autonomous investigations, peptide design for the somatostatin receptor SSTR2, lightweight impact-resistant ceramic screening, cross-domain resonance bridging biology, materials, and music, and formal analogy construction between urban morphology and grain-boundary evolution, the framework demonstrates heterogeneous tool chaining, emergent convergence among independently operating agents, and traceable reasoning from raw computation to published finding.

Artificial intelligence promises to accelerate scientific discovery, yet its benefits remain unevenly distributed. While technical obstacles such as scarce data, fragmented standards, and unequal access to computation are significant, we argue that the primary barriers are social and institutional. Narratives that defer progress to speculative "AI scientists," the undervaluing of data and infrastructure contributions, misaligned incentives, and gaps between domain experts and machine learning researchers all constrain impact. We highlight four interconnected challenges: community dysfunction, research priorities misaligned with upstream needs, data fragmentation, and infrastructure inequities. We argue that their roots lie in cultural and organizational practices. Addressing them requires not only technical innovation but also intentional community-building, cross-disciplinary education, shared benchmarks, and accessible infrastructure. We call for reframing AI for science as a collective social project, where sustainable collaboration and equitable participation are treated as prerequisites for technical progress.

Recently, Large Language Models (LLMs) have been applied to scientific equation discovery, leveraging their embedded scientific knowledge for hypothesis generation. However, current methods typically confine LLMs to the role of an equation proposer within search algorithms like genetic programming. In this paper, we present SR-Scientist, a framework that elevates the LLM from a simple equation proposer to an autonomous AI scientist that writes code to analyze data, implements the equation as code, submits it for evaluation, and optimizes the equation based on experimental feedback. Specifically, we wrap the code interpreter into a set of tools for data analysis and equation evaluation. The agent is instructed to optimize the equation by utilizing these tools over a long horizon with minimal human-defined pipelines. Empirical results show that SR-Scientist outperforms baseline methods by an absolute margin of 6% to 35% on datasets covering four science disciplines. Additionally, we demonstrate our method's robustness to noise, the generalization of the discovered equations to out-of-domain data, and their symbolic accuracy. Furthermore, we develop an end-to-end reinforcement learning framework to enhance the agent's capabilities.

Coding agents are increasingly used as general-purpose problem solvers, but their flexibility does not by itself confer the domain expertise needed for specialized tasks. Recent work addresses this through agent skills: reusable workflows, and code, that augment agents with domain-specific capabilities. Most skills today are hand-crafted, and existing evolutionary approaches optimize low-level artifacts (e.g. prompts \& code) that are tightly coupled to specific models and tasks. We introduce EvoSkill, a self-evolving framework that automatically discovers and refines agent skills through iterative failure analysis. EvoSkill analyzes execution failures, proposes new skills or edits to existing ones, and materializes them into structured, reusable skill folders. A Pareto frontier of agent programs governs selection, retaining only skills that improve held-out validation performance while the underlying model remains frozen. We evaluate EvoSkill on two benchmarks: OfficeQA, a grounded reasoning benchmark over U.S.\ Treasury data, where it improves exact-match accuracy by 7.3\% (60.6\% to 67.9\%); and SealQA, a search-augmented QA benchmark with noisy retrieval, where it yields a 12.1\% gain (26.6\% to 38.7\%). We also investigate the zero-shot transfer capabilties of skills evolved on one task to the other; in particular: skills evolved from SealQA transfers zero-shot to BrowseComp, improving accuracy by 5.3\% without modification demonstrating that skill-level optimization produces transferable capabilities beyond the training task.

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate domain knowledge, limiting their usage in specialized fields \eg radiology. We propose\ladder (Language-Driven Discovery and Error Rectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent domain knowledge and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

Large language models (LLMs) have shown promise in assisting cybersecurity tasks, yet existing approaches struggle with automatic vulnerability discovery and exploitation due to limited interaction, weak execution grounding, and a lack of experience reuse. We propose Co-RedTeam, a security-aware multi-agent framework designed to mirror real-world red-teaming workflows by integrating security-domain knowledge, code-aware analysis, execution-grounded iterative reasoning, and long-term memory. Co-RedTeam decomposes vulnerability analysis into coordinated discovery and exploitation stages, enabling agents to plan, execute, validate, and refine actions based on real execution feedback while learning from prior trajectories. Extensive evaluations on challenging security benchmarks demonstrate that Co-RedTeam consistently outperforms strong baselines across diverse backbone models, achieving over 60% success rate in vulnerability exploitation and over 10% absolute improvement in vulnerability detection. Ablation and iteration studies further confirm the critical role of execution feedback, structured interaction, and memory for building robust and generalizable cybersecurity agents.

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely high-dimensional combinatorial and nonlinear hypothesis spaces. Traditional methods of equation discovery largely focus on extracting equations from data alone, often neglecting the rich domain-specific prior knowledge that scientists typically depend on. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data in an efficient manner. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeletons, drawing from its physical understanding, which are then optimized against data to estimate skeleton parameters. We demonstrate LLM-SR's effectiveness across three diverse scientific domains, where it discovers physically accurate equations that provide significantly better fits to in-domain and out-of-domain data compared to the well-established equation discovery baselines

In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across sectors from drug development to renewable energy. To answer this call, we present DeepSpeed4Science initiative (deepspeed4science.ai) which aims to build unique capabilities through AI system technology innovations to help domain experts to unlock today's biggest science mysteries. By leveraging DeepSpeed's current technology pillars (training, inference and compression) as base technology enablers, DeepSpeed4Science will create a new set of AI system technologies tailored for accelerating scientific discoveries by addressing their unique complexity beyond the common technical approaches used for accelerating generic large language models (LLMs). In this paper, we showcase the early progress we made with DeepSpeed4Science in addressing two of the critical system challenges in structural biology research.

Personalized discovery systems often train separate models for item ranking, carousel ranking, and search, even though these tasks expose complementary signals from the same viewer journey: watches shape carousel and item ranking, search queries reveal intent even when they do not lead to a catalog match, and watch history helps interpret search as rewatching, continuation, or new discovery. We introduce the user story, a serialized representation that turns a user's cross-surface history - attributes, sessions, watch events with surface and carousel context, and search events - into a single token sequence. By interleaving pretrained language tokens with domain-specific event tokens, user stories let heterogeneous recommendation and search tasks be expressed as prompted next-token prediction over a shared grammar. TubiFM is one instantiation of this approach: a Llama 3.2 1B-based model trained on user stories and prompted to rank items, carousels, or search results without task-specific architectures. In offline evaluation, this single model outperforms specialist baselines across item, carousel, and search ranking. In online A/B tests, TubiFM significantly improves search total viewing time (TVT) by +3.9% and carousel TVT by +0.30%. Item ranking is statistically neutral on TVT (+0.14%), but matches a mature production stack; across all three tasks, TubiFM serves on L40S GPUs and reduces p99 ranking latency from 500ms to 200ms. These results show that shared user stories can improve discovery while simplifying ranking systems.

Visible-infrared person re-identification (VIReID) primarily deals with matching identities across person images from different modalities. Due to the modality gap between visible and infrared images, cross-modality identity matching poses significant challenges. Recognizing that high-level semantics of pedestrian appearance, such as gender, shape, and clothing style, remain consistent across modalities, this paper intends to bridge the modality gap by infusing visual features with high-level semantics. Given the capability of CLIP to sense high-level semantic information corresponding to visual representations, we explore the application of CLIP within the domain of VIReID. Consequently, we propose a CLIP-Driven Semantic Discovery Network (CSDN) that consists of Modality-specific Prompt Learner, Semantic Information Integration (SII), and High-level Semantic Embedding (HSE). Specifically, considering the diversity stemming from modality discrepancies in language descriptions, we devise bimodal learnable text tokens to capture modality-private semantic information for visible and infrared images, respectively. Additionally, acknowledging the complementary nature of semantic details across different modalities, we integrate text features from the bimodal language descriptions to achieve comprehensive semantics. Finally, we establish a connection between the integrated text features and the visual features across modalities. This process embed rich high-level semantic information into visual representations, thereby promoting the modality invariance of visual representations. The effectiveness and superiority of our proposed CSDN over existing methods have been substantiated through experimental evaluations on multiple widely used benchmarks. The code will be released at https://github.com/nengdong96/CSDN.

Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery.

An overwhelmingly large amount of knowledge in the materials domain is generated and stored as text published in peer-reviewed scientific literature. Recent developments in natural language processing, such as bidirectional encoder representations from transformers (BERT) models, provide promising tools to extract information from these texts. However, direct application of these models in the materials domain may yield suboptimal results as the models themselves may not be trained on notations and jargon that are specific to the domain. Here, we present a materials-aware language model, namely, MatSciBERT, which is trained on a large corpus of scientific literature published in the materials domain. We further evaluate the performance of MatSciBERT on three downstream tasks, namely, abstract classification, named entity recognition, and relation extraction, on different materials datasets. We show that MatSciBERT outperforms SciBERT, a language model trained on science corpus, on all the tasks. Further, we discuss some of the applications of MatSciBERT in the materials domain for extracting information, which can, in turn, contribute to materials discovery or optimization. Finally, to make the work accessible to the larger materials community, we make the pretrained and finetuned weights and the models of MatSciBERT freely accessible.

Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and behaviour. Moreover, these hidden features can be directly manipulated to steer model behaviour. However, it remains an open question whether this phenomenon is unique to models trained on inherently structured data (ie. language, images) or if it is a general property of foundation models. In this work, we investigate the internal representations of a large physics-focused foundation model. Inspired by recent work identifying single directions in activation space for complex behaviours in LLMs, we extract activation vectors from the model during forward passes over simulation datasets for different physical regimes. We then compute "delta" representations between the two regimes. These delta tensors act as concept directions in activation space, encoding specific physical features. By injecting these concept directions back into the model during inference, we can steer its predictions, demonstrating causal control over physical behaviours, such as inducing or removing some particular physical feature from a simulation. These results suggest that scientific foundation models learn generalised representations of physical principles. They do not merely rely on superficial correlations and patterns in the simulations. Our findings open new avenues for understanding and controlling scientific foundation models and has implications for AI-enabled scientific discovery.

Scientific research is being reshaped by AI systems that move beyond isolated assistance toward longer-horizon workflows spanning literature grounding, hypothesis generation, experimentation, validation, reporting, and revision. This shift marks a transition from task-level AI for science to workflow-level research automation. Yet current systems remain fragmented, differing in autonomy, domain scope, execution environment, validation mechanism, and human oversight, while still struggling with evidence preservation, reproducibility, weak-direction rejection, provenance tracking, cross-domain robustness, and accountable scientific closure. This survey examines these developments through AutoResearch, defined as the developmental spectrum of AI-powered scientific workflow automation. Within it, Vibe Research denotes the human-steered region of prompt-based assistance and human-verified execution, whereas emerging AI-led systems coordinate larger portions of the discovery loop without achieving robust autonomy. We analyze how research systems redistribute control, evidence, execution, validation, and accountability across workflows and organize the field around five workflow conditions: literature and research grounding; hypothesis formation and planning; experimentation and tool use; feedback, validation, and review; and reporting and knowledge communication. We further synthesize AI scientist systems, mixed-initiative co-research frameworks, benchmarks, domain deployments, and open-source infrastructures. Finally, we propose five evaluation dimensions--novelty, validity, impact, reliability, and provenance--and show that AutoResearch autonomy is domain-conditioned, being more credible in structured, executable, and rapidly verifiable settings but limited in embodied, delayed, heterogeneous, ethical, or institutionally accountable contexts.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30times speedup in data preparation.

Large language models (LLMs) have shown potential as tools for scientific discovery. This has engendered growing interest in their use in humanistic disciplines, such as historical linguistics and literary studies. These fields often construct arguments on the basis of delineations like genre, or more inflexibly, time period. Although efforts have been made to restrict inference to specific domains via fine-tuning or model editing, we posit that the only true guarantee is domain-restricted pretraining -- typically, a data- and compute-expensive proposition. We show that efficient pretraining techniques can produce useful models over corpora too large for easy manual inspection but too small for "typical" LLM approaches. We employ a novel date-attribution pipeline in order to obtain a temporally-segmented dataset of five 10-million-word slices. We train two corresponding five-model batteries over these corpus segments, efficient pretraining and Llama3-8B parameter efficiently finetuned. We find that the pretrained models are faster to train than the finetuned baselines and that they better respect the historical divisions of our corpus. Emphasizing speed and precision over a-historical comprehensiveness enables a number of novel approaches to hypothesis discovery and testing in our target fields. Taking up diachronic linguistics as a testbed, we show that our method enables the detection of a diverse set of phenomena, including en masse lexical change, non-lexical (grammatical and morphological) change, and word sense introduction/obsolescence. We provide a ready-to-use pipeline that allows extension of our approach to other target fields with only minimal adaptation.

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Recent LLM-based agents have closed substantial portions of the scientific discovery loop in software-only machine-learning research, in chemistry, and in biology. Extending the same loop to high-fidelity physical simulators is harder, because solver completion does not imply physical validity and many failure modes appear only in field-level imagery rather than in solver logs. We present AI CFD Scientist, an open-source AI scientist for computational fluid dynamics (CFD) that, to our knowledge, is the first to span literature-grounded ideation, validated execution, vision-based physics verification, source-code modification, and figure-grounded writing within a single inspectable workflow. Three coupled pathways cover parameter sweeps within a fixed solver, case-local C++ library compilation for new physical models, and open-ended hypothesis search against a reference comparator, all running on OpenFOAM through Foam-Agent. At the center of the framework is a vision-language physics-verification gate that inspects rendered flow fields before any result is accepted, rerun, or written into a manuscript. On five tasks under a shared GPT-5.5 backbone, AI CFD Scientist autonomously discovers a Spalart-Allmaras runtime correction that reduces lower-wall Cf RMSE against DNS by 7.89% on the periodic hill at Reh=5600; under matched LLM cost, two strong general AI-scientist baselines (ARIS, DeepScientist) execute partial CFD workflows but lack the domain-specific validity gates needed to convert runs into defensible scientific claims; and a controlled planted-failure ablation shows that the vision-language gate detects 14 of 16 silent failures missed by solver-level checks. Code, prompts, and run artifacts are released at https://github.com/csml-rpi/cfd-scientist.

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

The rapid advancement of large language models has fundamentally shifted the bottleneck in AI development from computational power to data availability-with countless valuable datasets remaining hidden across specialized repositories, research appendices, and domain platforms. As reasoning capabilities and deep research methodologies continue to evolve, a critical question emerges: can AI agents transcend conventional search to systematically discover any dataset that meets specific user requirements, enabling truly autonomous demand-driven data curation? We introduce DatasetResearch, the first comprehensive benchmark evaluating AI agents' ability to discover and synthesize datasets from 208 real-world demands across knowledge-intensive and reasoning-intensive tasks. Our tri-dimensional evaluation framework reveals a stark reality: even advanced deep research systems achieve only 22% score on our challenging DatasetResearch-pro subset, exposing the vast gap between current capabilities and perfect dataset discovery. Our analysis uncovers a fundamental dichotomy-search agents excel at knowledge tasks through retrieval breadth, while synthesis agents dominate reasoning challenges via structured generation-yet both catastrophically fail on "corner cases" outside existing distributions. These findings establish the first rigorous baseline for dataset discovery agents and illuminate the path toward AI systems capable of finding any dataset in the digital universe. Our benchmark and comprehensive analysis provide the foundation for the next generation of self-improving AI systems and are publicly available at https://github.com/GAIR-NLP/DatasetResearch.

Causal discovery aims to recover directed causal relations from observational and interventional data, providing a basis for mechanistic understanding and reliable decision-making. Causal discovery foundation models (CDFMs) seek to amortize this problem by mapping a dataset directly to a causal graph in a single forward pass, avoiding per-dataset testing, search, or optimization. However, existing CDFMs remain limited, often failing to consistently match strong classical methods, and we find that a key bottleneck is how causal pretraining tasks are constructed. Based on this observation, we propose TabCausal, a data-driven CDFM trained with broad causal pretraining over diverse graph priors, structural mechanisms, noise models, dimensions, sample sizes, and intervention regimes. A dynamic task construction strategy composes these causal environments into varied discovery tasks, enabling more transferable structural learning from observational and mixed-interventional data. On large-scale synthetic benchmarks, TabCausal achieves better macro-averaged performance than a diverse set of causal discovery baselines. To further bridge abstract synthetic generators and realistic causal reasoning scenarios, we introduce a protocol-guided and LLM-audited semantic causal environment benchmark, where domain-grounded SCMs generate interpretable observational and interventional datasets for out-of-distribution analysis. Across both synthetic and semantic environments, TabCausal demonstrates robust structure recovery, especially under interventional evidence, highlighting broad causal pretraining as a key ingredient for transferable amortized causal discovery.

Ancient manuscripts are the primary source of ancient linguistic corpora. However, many ancient manuscripts exhibit duplications due to unintentional repeated publication or deliberate forgery. The Dead Sea Scrolls, for example, include counterfeit fragments, whereas Oracle Bones (OB) contain both republished materials and fabricated specimens. Identifying ancient manuscript duplicates is of great significance for both archaeological curation and ancient history study. In this work, we design a progressive OB duplicate discovery framework that combines unsupervised low-level keypoints matching with high-level text-centric content-based matching to refine and rank the candidate OB duplicates with semantic awareness and interpretability. We compare our model with state-of-the-art content-based image retrieval and image matching methods, showing that our model yields comparable recall performance and the highest simplified mean reciprocal rank scores for both Top-5 and Top-15 retrieval results, and with significantly accelerated computation efficiency. We have discovered over 60 pairs of new OB duplicates in real-world deployment, which were missed by domain experts for decades. Code, model and real-world results are available at: https://github.com/cszhangLMU/OBD-Finder/.

The massive and large-scale design of foundational semiconductor integrated circuits (ICs) is crucial to sustaining the advancement of many emerging and future technologies, such as generative AI, 5G/6G, and quantum computing. Excitingly, recent studies have shown the great capabilities of foundational models in expediting the design of digital ICs. Yet, applying generative AI techniques to accelerate the design of analog ICs remains a significant challenge due to critical domain-specific issues, such as the lack of a comprehensive dataset and effective representation methods for analog circuits. This paper proposes, AnalogGenie, a textbf{Gen}erattextbf{i}ve textbf{e}ngine for automatic design/discovery of textbf{Analog} circuit topologies--the most challenging and creative task in the conventional manual design flow of analog ICs. AnalogGenie addresses two key gaps in the field: building a foundational comprehensive dataset of analog circuit topology and developing a scalable sequence-based graph representation universal to analog circuits. Experimental results show the remarkable generation performance of AnalogGenie in broadening the variety of analog ICs, increasing the number of devices within a single design, and discovering unseen circuit topologies far beyond any prior arts. Our work paves the way to transform the longstanding time-consuming manual design flow of analog ICs to an automatic and massive manner powered by generative AI. Our source code is available at https://github.com/xz-group/AnalogGenie.

Global challenges such as food supply chain disruptions, public health crises, and natural hazard responses require access to and integration of diverse datasets, many of which are geospatial. Over the past few years, a growing number of (geo)portals have been developed to address this need. However, most existing (geo)portals are stacked by separated or sparsely connected data "silos" impeding effective data consolidation. A new way of sharing and reusing geospatial data is therefore urgently needed. In this work, we introduce KnowWhereGraph, a knowledge graph-based data integration, enrichment, and synthesis framework that not only includes schemas and data related to human and environmental systems but also provides a suite of supporting tools for accessing this information. The KnowWhereGraph aims to address the challenge of data integration by building a large-scale, cross-domain, pre-integrated, FAIR-principles-based, and AI-ready data warehouse rooted in knowledge graphs. We highlight the design principles of KnowWhereGraph, emphasizing the roles of space, place, and time in bridging various data "silos". Additionally, we demonstrate multiple use cases where the proposed geospatial knowledge graph and its associated tools empower decision-makers to uncover insights that are often hidden within complex and poorly interoperable datasets.

Generative models have been very popular in the recent years for their image generation capabilities. GAN-based models are highly regarded for their disentangled latent space, which is a key feature contributing to their success in controlled image editing. On the other hand, diffusion models have emerged as powerful tools for generating high-quality images. However, the latent space of diffusion models is not as thoroughly explored or understood. Existing methods that aim to explore the latent space of diffusion models usually relies on text prompts to pinpoint specific semantics. However, this approach may be restrictive in areas such as art, fashion, or specialized fields like medicine, where suitable text prompts might not be available or easy to conceive thus limiting the scope of existing work. In this paper, we propose an unsupervised method to discover latent semantics in text-to-image diffusion models without relying on text prompts. Our method takes a small set of unlabeled images from specific domains, such as faces or cats, and a pre-trained diffusion model, and discovers diverse semantics in unsupervised fashion using a contrastive learning objective. Moreover, the learned directions can be applied simultaneously, either within the same domain (such as various types of facial edits) or across different domains (such as applying cat and face edits within the same image) without interfering with each other. Our extensive experiments show that our method achieves highly disentangled edits, outperforming existing approaches in both diffusion-based and GAN-based latent space editing methods.

Large language model (LLM) agents are increasingly applied to long-horizon tasks such as scientific discovery and machine learning engineering (MLE), where sustained self-evolution becomes a key capability. However, existing MLE agents suffer from inter-branch information isolation, memoryless search, and lack of hierarchical control, which together hinder long-horizon optimization. We present MLEvolve, an LLM-based self-evolving multi-agent framework for end-to-end machine learning algorithm discovery. By extending tree search to Progressive MCGS, MLEvolve enables cross-branch information flow through graph-based reference edges and gradually shifts the search from broad exploration to focused exploitation with an entropy-inspired progressive schedule. To allow the agent to evolve with accumulated experience, we introduce Retrospective Memory, which combines a cold-start domain knowledge base with a dynamic global memory for task-specific experience retrieval and reuse. For stable long-horizon iteration, we further decouple strategic planning from code generation with adaptive coding modes. Evaluation on MLE-Bench shows that MLEvolve achieves state-of-the-art performance across multiple dimensions including average medal rate and valid submission rate under a 12-hour budget (half the standard runtime). Moreover, MLEvolve also outperforms specialized algorithm discovery methods including AlphaEvolve on mathematical algorithm optimization tasks, demonstrating strong cross-domain generalization. Our code is available at https://github.com/InternScience/MLEvolve.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Domain Generalization (DG) aims to learn representations that remain robust under out-of-distribution (OOD) shifts and generalize effectively to unseen target domains. While recent invariant learning strategies and architectural advances have achieved strong performance, explicitly discovering a structured domain-invariant subspace through second-order statistics remains underexplored. In this work, we propose CPCANet, a novel framework grounded in Common Principal Component Analysis (CPCA), which unrolls the iterative Flury-Gautschi (FG) algorithm into fully differentiable neural layers. This approach integrates the statistical properties of CPCA into an end-to-end trainable framework, enforcing the discovery of a shared subspace across diverse domains while preserving interpretability. Experiments on four standard DG benchmarks demonstrate that CPCANet achieves state-of-the-art (SOTA) performance in zero-shot transfer. Moreover, CPCANet is architecture-agnostic and requires no dataset-specific tuning, providing a simple and efficient approach to learning robust representations under distribution shift. Code is available at https://github.com/wish44165/CPCANet.

Agentic AI tools offer a promising path to automating software development bottlenecks in scientific research pipelines, particularly for stages that take domain experts days to months to build, where scientists care about correctness and robustness, not implementation details. We present an empirical study of general-purpose coding agents on a fly optogenetics data-to-discovery pipeline. We assess agents on tasks substantially larger than existing benchmarks, datasets orders of magnitude bigger, and evaluation criteria grounded in domain expert standards. We show that agents can solve several individual pipeline stages, suggesting stage-level automation is tractable. By analyzing agents' code iterations, we show that they struggle most when there is not a pre-defined criterion to iterate on, and they must instead use their scientific judgment to assess their current solution, a key open challenge. Mirroring scientific practice, they sometimes attempt visual inspection of intermediate outputs for self-evaluation, but largely fail to interpret what they see or act on it appropriately. Solving the end-to-end pipeline correctly requires stringing together successes across all pipeline stages, and this is beyond agents' current abilities. We identify challenges largely absent from existing benchmarks, including computational resource management and generalization to large held-out data collections. Finally, we distill principles for constructing scientific tasks and rigorous evaluation criteria for open-ended problems.

Despite recent progress in language models and agents for scientific data-driven discovery, further advancing their capabilities is held back by the absence of verifiable environments representing real-world scientific tasks. To fill this gap, we introduce D3-Gym, the first automatically constructed dataset with verifiable environments for scientific Data-Driven Discovery. D3-Gym comprises (1) 565 tasks sourced from 239 real scientific repositories across four disciplines where (2) each task is equipped with a natural language instruction, an executable environment with pre-installed dependencies, input dataset and artifact previews, a reference code solution, and an automatically synthesized evaluation script. Rigorous evaluation of the quality of the verification signal in D3-Gym confirms that our evaluation scripts achieve 87.5% agreement with human-annotated gold standards and strong alignment in domain-specific evaluation logic, showing their scientific soundness. Further, training on trajectories sampled from D3-Gym yields consistent and substantial gains across Qwen3 models of varying sizes on ScienceAgentBench, boosting Qwen3-32B by 7.8 absolute points and substantially shrinking the gap with strong proprietary models. All D3-Gym artifacts (environments, creation workflow, trajectories, and models) can be found at https://github.com/OSU-NLP-Group/D3-Gym.

An important recurring pattern in scientific breakthroughs is a two-stage process: an initial phase of undirected experimentation that yields an unexpected finding, followed by a retrospective phase that explains why the finding works and situates it within existing theory. We present ResearchEVO, an end-to-end framework that computationally instantiates this discover-then-explain paradigm. The Evolution Phase employs LLM-guided bi-dimensional co-evolution -- simultaneously optimizing both algorithmic logic and overall architecture -- to search the space of code implementations purely by fitness, without requiring any understanding of the solutions it produces. The Writing Phase then takes the best-performing algorithm and autonomously generates a complete, publication-ready research paper through sentence-level retrieval-augmented generation with explicit anti-hallucination verification and automated experiment design. To our knowledge, ResearchEVO is the first system to cover this full pipeline end to end: no prior work jointly performs principled algorithm evolution and literature-grounded scientific documentation. We validate the framework on two cross-disciplinary scientific problems -- Quantum Error Correction using real Google quantum hardware data, and Physics-Informed Neural Networks -- where the Evolution Phase discovered human-interpretable algorithmic mechanisms that had not been previously proposed in the respective domain literatures. In both cases, the Writing Phase autonomously produced compilable LaTeX manuscripts that correctly grounded these blind discoveries in existing theory via RAG, with zero fabricated citations.

Explaining observed phenomena through symbolic, interpretable formulas is a fundamental goal of science. Recently, large language models (LLMs) have emerged as promising tools for symbolic equation discovery, owing to their broad domain knowledge and strong reasoning capabilities. However, most existing LLM-based systems try to guess equations directly from data, without modeling the multi-step reasoning process that scientists often follow: first inferring physical properties such as symmetries, then using these as priors to restrict the space of candidate equations. We introduce KeplerAgent, an agentic framework that explicitly follows this scientific reasoning process. The agent coordinates physics-based tools to extract intermediate structure and uses these results to configure symbolic regression engines such as PySINDy and PySR, including their function libraries and structural constraints. Across a suite of physical equation benchmarks, KeplerAgent achieves substantially higher symbolic accuracy and greater robustness to noisy data than both LLM and traditional baselines.

Current evaluations of mathematical reasoning in large language models (LLMs) are dominated by static benchmarks, either derived from competition-style problems or curated through costly expert effort, resulting in limited coverage of research-level mathematics and rapid performance saturation. We propose a fully automated, theorem-grounded pipeline for evaluating frontier mathematical reasoning, which directly transforms recent peer-reviewed mathematical literature into executable and verifiable reasoning tasks. The pipeline identifies constructive or quantitative results, instantiates them into parameterized problem templates, and generates deterministic solutions through execution-based verification, enabling scalable, reproducible, and continuously updatable evaluation without reliance on large-scale expert authoring. By design, this approach supports temporal extensibility, intrinsic correctness checking, and domain-specific customization across mathematical subfields. Applying this pipeline yields EternalMath, an evolving evaluation suite derived from contemporary research papers. Experiments with state-of-the-art LLMs reveal substantial performance gaps, indicating that mathematical reasoning at the research frontier remains far from saturated and underscoring the need for evaluation methodologies that evolve in step with human mathematical discovery.

Discovering novel high-entropy alloys (HEAs) with desirable properties is challenging due to the vast compositional space and complex phase formation mechanisms. Efficient exploration of this space requires a strategic approach that integrates heterogeneous knowledge sources. Here, we propose a framework that systematically combines knowledge extracted from computational material datasets with domain knowledge distilled from scientific literature using large language models (LLMs). A central feature of this approach is the explicit consideration of element substitutability, identifying chemically similar elements that can be interchanged to potentially stabilize desired HEAs. Dempster-Shafer theory, a mathematical framework for reasoning under uncertainty, is employed to model and combine substitutabilities based on aggregated evidence from multiple sources. The framework predicts the phase stability of candidate HEA compositions and is systematically evaluated on both quaternary alloy systems, demonstrating superior performance compared to baseline machine learning models and methods reliant on single-source evidence in cross-validation experiments. By leveraging multi-source knowledge, the framework retains robust predictive power even when key elements are absent from the training data, underscoring its potential for knowledge transfer and extrapolation. Furthermore, the enhanced interpretability of the methodology offers insights into the fundamental factors governing HEA formation. Overall, this work provides a promising strategy for accelerating HEA discovery by integrating computational and textual knowledge sources, enabling efficient exploration of vast compositional spaces with improved generalization and interpretability.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

With the proliferation of open-sourced Large Language Models (LLMs) and efficient finetuning techniques, we are on the cusp of the emergence of numerous domain-specific LLMs that have been finetuned for expertise across specialized fields and applications for which the current general-purpose LLMs are unsuitable. In academia, this technology has the potential to revolutionize the way we conduct systematic literature reviews (SLRs), access knowledge and generate new insights. This paper proposes an AI-enabled methodological framework that combines the power of LLMs with the rigorous reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). By finetuning LLMs on domain-specific academic papers that have been selected as a result of a rigorous SLR process, the proposed PRISMA-DFLLM (for Domain-specific Finetuned LLMs) reporting guidelines offer the potential to achieve greater efficiency, reusability and scalability, while also opening the potential for conducting incremental living systematic reviews with the aid of LLMs. Additionally, the proposed approach for leveraging LLMs for SLRs enables the dissemination of finetuned models, empowering researchers to accelerate advancements and democratize cutting-edge research. This paper presents the case for the feasibility of finetuned LLMs to support rigorous SLRs and the technical requirements for realizing this. This work then proposes the extended PRISMA-DFLLM checklist of reporting guidelines as well as the advantages, challenges, and potential implications of implementing PRISMA-DFLLM. Finally, a future research roadmap to develop this line of AI-enabled SLRs is presented, paving the way for a new era of evidence synthesis and knowledge discovery.

Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state. We present SciForge, a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services. SciForge is built around five pillars: (i) goal-scoped scientific decision governance for goal-oriented research, with review gates and shared review surfaces; (ii) translate-then-reason for multimodal input, routing scientific objects through domain translators before the agent reasons; (iii) evidence governance for auditable traceability, linking claims to provenance chains and audit findings; (iv) collaborative team science for collaborative research, enabling multi-role decision governance, with shared team workspaces planned for future releases; and (v) real-world application scenarios for practical impact, demonstrated through eight end-to-end user cases, with flagship demonstrations including multi-day agentic research sprints for gene discovery, AI-guided de novo protein design, molecular optimization, and genome-to-BGC discovery. The system combines a thin interaction layer, contextual research capability patterns, an Agent Runtime and Workflow Engine, an Evidence-DAG audit sidecar and a Scientific Model Router. SciForge currently runs as a desktop application, with mobile supervision support; future releases will deepen team collaboration. The system is open-source and available at https://github.com/AGI4Sci/SciForge

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

The discovery of van der Waals magnets has established a new domain in the field of magnetism, opening novel pathways for the electrical control of magnetic properties. In this context, Fe3GeTe2 (FGT) emerges as an exemplary candidate owing to its intrinsic metallic properties, which facilitate the interplay of both charge and spin degrees of freedom. Here, the bidirectional voltage control of exchange bias (EB) effect in a perpendicularly magnetized all-van der Waals FGT/O-FGT/hBN heterostructure is demonstrated. The antiferromagnetic O-FGT layer is formed by naturally oxidizing the FGT surface. The observed EB magnitude reaches 1.4 kOe with a blocking temperature (150 K) reaching close to the Curie temperature of FGT. Both the exchange field and the blocking temperature values are among the highest in the context of layered materials. The EB modulation exhibits a linear dependence on the gate voltage and its polarity, observable in both positive and negative field cooling (FC) experiments. Additionally, gate voltage-controlled magnetization switching, highlighting the potential of FGT-based heterostructures is demonstrated in advanced spintronic devices. These findings display a methodology to modulate the magnetism of van der Waals magnets offering new avenues for the development of high-performance magnetic devices.

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

Data-driven scientific discovery requires the iterative integration of scientific domain knowledge, statistical expertise, and an understanding of data semantics to make nuanced analytical decisions, e.g., about which variables, transformations, and statistical models to consider. LM-based agents equipped with planning, memory, and code execution capabilities have the potential to support data-driven science. However, evaluating agents on such open-ended tasks is challenging due to multiple valid approaches, partially correct steps, and different ways to express the same decisions. To address these challenges, we present BLADE, a benchmark to automatically evaluate agents' multifaceted approaches to open-ended research questions. BLADE consists of 12 datasets and research questions drawn from existing scientific literature, with ground truth collected from independent analyses by expert data scientists and researchers. To automatically evaluate agent responses, we developed corresponding computational methods to match different representations of analyses to this ground truth. Though language models possess considerable world knowledge, our evaluation shows that they are often limited to basic analyses. However, agents capable of interacting with the underlying data demonstrate improved, but still non-optimal, diversity in their analytical decision making. Our work enables the evaluation of agents for data-driven science and provides researchers deeper insights into agents' analysis approaches.

Accelerating materials discovery requires AI systems that can generate scientifically valid hypotheses through multi-step, domain-grounded reasoning. Standard large language models often produce fluent but weakly traceable responses to open-ended materials design problems, making it difficult to determine whether final answers are supported by coherent intermediate reasoning. We develop Graph-PRefLexOR, a family of graph-native reasoning models fine-tuned with Group Relative Policy Optimization (GRPO) to organize reasoning into explicit phases for mechanism exploration, graph construction, pattern extraction, and hypothesis synthesis. This design links neural language generation with symbolic relational structure, enabling causal connections to be constructed, inspected, and reused. On 100 open-ended questions from materials science and mechanics literature, Graph-PRefLexOR achieves 40-65% improvements over corresponding base models, with the largest gains in reasoning traceability. Embedding analyses show broader semantic exploration and approximately 2-3 times greater semantic diversity than baselines. Semantic backtracking and layer-wise hidden-state analyses further show stronger alignment between structured reasoning and final answers. Finally, test-time graph expansion reveals that additional compute primarily increases long-range conceptual recombination within a bounded semantic space, rather than simply expanding semantic coverage. These results establish graph-native reinforcement learning as a pathway toward interpretable AI systems for scientific hypothesis generation in materials design and other scientific applications.

Data-driven approaches like deep learning are rapidly advancing planetary science, particularly in Mars exploration. Despite recent progress, most existing benchmarks remain confined to closed-set supervised visual tasks and do not support text-guided retrieval for geospatial discovery. We introduce MarsRetrieval, a retrieval benchmark for evaluating vision-language models for Martian geospatial discovery. MarsRetrieval includes three tasks: (1) paired image-text retrieval, (2) landform retrieval, and (3) global geo-localization, covering multiple spatial scales and diverse geomorphic origins. We propose a unified retrieval-centric protocol to benchmark multimodal embedding architectures, including contrastive dual-tower encoders and generative vision-language models. Our evaluation shows MarsRetrieval is challenging: even strong foundation models often fail to capture domain-specific geomorphic distinctions. We further show that domain-specific fine-tuning is critical for generalizable geospatial discovery in planetary settings. Our code is available at https://github.com/ml-stat-Sustech/MarsRetrieval

Smart contract vulnerabilities have led to billions in losses, yet finding actionable exploits remains challenging. Traditional fuzzers rely on rigid heuristics and struggle with complex attacks, while human auditors are thorough but slow and don't scale. Large Language Models offer a promising middle ground, combining human-like reasoning with machine speed. Early studies show that simply prompting LLMs generates unverified vulnerability speculations with high false positive rates. To address this, we present A1, an agentic system that transforms any LLM into an end-to-end exploit generator. A1 provides agents with six domain-specific tools for autonomous vulnerability discovery, from understanding contract behavior to testing strategies on real blockchain states. All outputs are concretely validated through execution, ensuring only profitable proof-of-concept exploits are reported. We evaluate A1 across 36 real-world vulnerable contracts on Ethereum and Binance Smart Chain. A1 achieves a 63% success rate on the VERITE benchmark. Across all successful cases, A1 extracts up to \8.59 million per exploit and 9.33 million total. Using Monte Carlo analysis of historical attacks, we demonstrate that immediate vulnerability detection yields 86-89% success probability, dropping to 6-21% with week-long delays. Our economic analysis reveals a troubling asymmetry: attackers achieve profitability at \6,000 exploit values while defenders require 60,000 -- raising fundamental questions about whether AI agents inevitably favor exploitation over defense.

Time-domain surveys such as the Zwicky Transient Facility (ZTF) have opened a new frontier in the discovery and characterization of transients. While photometric light curves provide broad temporal coverage, spectroscopic observations remain crucial for physical interpretation and source classification. However, existing spectral analysis methods -- often reliant on template fitting or parametric models -- are limited in their ability to capture the complex and evolving spectra characteristic of such sources, which are sometimes only available at low resolution. In this work, we introduce SpectraNet, a deep convolutional neural network designed to learn robust representations of optical spectra from transients. Our model combines multi-scale convolution kernels and multi-scale pooling to extract features from preprocessed spectra in a hierarchical and interpretable manner. We train and validate SpectraNet on low-resolution time-series spectra obtained from the Spectral Energy Distribution Machine (SEDM) and other instruments, demonstrating state-of-the-art performance in classification. Furthermore, in redshift prediction tasks, SpectraNet achieves a root mean squared relative redshift error of 0.02, highlighting its effectiveness in precise regression tasks as well.

A recent technical breakthrough in the domain of machine learning is the discovery and the multiple applications of Generative Adversarial Networks (GANs). Those generative models are computationally demanding, as a GAN is composed of two deep neural networks, and because it trains on large datasets. A GAN is generally trained on a single server. In this paper, we address the problem of distributing GANs so that they are able to train over datasets that are spread on multiple workers. MD-GAN is exposed as the first solution for this problem: we propose a novel learning procedure for GANs so that they fit this distributed setup. We then compare the performance of MD-GAN to an adapted version of Federated Learning to GANs, using the MNIST and CIFAR10 datasets. MD-GAN exhibits a reduction by a factor of two of the learning complexity on each worker node, while providing better performances than federated learning on both datasets. We finally discuss the practical implications of distributing GANs.

This project investigates the efficacy of Large Language Models (LLMs) in understanding and extracting scientific knowledge across specific domains and to create a deep learning framework: Knowledge AI. As a part of this framework, we employ pre-trained models and fine-tune them on datasets in the scientific domain. The models are adapted for four key Natural Language Processing (NLP) tasks: summarization, text generation, question answering, and named entity recognition. Our results indicate that domain-specific fine-tuning significantly enhances model performance in each of these tasks, thereby improving their applicability for scientific contexts. This adaptation enables non-experts to efficiently query and extract information within targeted scientific fields, demonstrating the potential of fine-tuned LLMs as a tool for knowledge discovery in the sciences.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Multimodal learning has revolutionized general domain tasks, yet its application in scientific discovery is hindered by the profound semantic gap between complex scientific imagery and sparse textual descriptions. We present S1-MMAlign, a large-scale, multi-disciplinary multimodal dataset comprising over 15.5 million high-quality image-text pairs derived from 2.5 million open-access scientific papers. Spanning disciplines from physics and biology to engineering, the dataset captures diverse visual modalities including experimental setups, heatmaps, and microscopic imagery. To address the pervasive issue of weak alignment in raw scientific captions, we introduce an AI-ready semantic enhancement pipeline that utilizes the Qwen-VL multimodal large model series to recaption images by synthesizing context from paper abstracts and citation contexts. Technical validation demonstrates that this enhancement significantly improves data quality: SciBERT-based pseudo-perplexity metrics show reduced semantic ambiguity, while CLIP scores indicate an 18.21% improvement in image-text alignment. S1-MMAlign provides a foundational resource for advancing scientific reasoning and cross-modal understanding in the era of AI for Science. The dataset is publicly available at https://huggingface.co/datasets/ScienceOne-AI/S1-MMAlign.

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.

We present Cryoscope--a new 50 deg^2 field-of-view, 1.2 m aperture, K_{dark} survey telescope to be located at Dome C, Antarctica. Cryoscope has an innovative optical-thermal design wherein the entire telescope is cryogenically cooled. Cryoscope also explores new detector technology to cost-effectively tile the full focal plane. Leveraging the dark Antarctic sky and minimizing telescope thermal emission, Cryoscope achieves unprecedented deep, wide, fast and red observations, matching and exceeding volumetric survey speeds from the Ultraviolet Explorer, Vera Rubin Observatory, Nancy Grace Roman Space Telescope, SPHEREx, and NEO Surveyor. By providing coverage beyond wavelengths of 2 mum, we aim to create the most comprehensive dynamic movie of the most obscured reaches of the Universe. Cryoscope will be a dedicated discovery engine for electromagnetic emission from coalescing compact binaries, Earth-like exoplanets orbiting cold stars, and multiple facets of time-domain, stellar and solar system science. In this paper, we describe the scientific drivers and technical innovations for this new discovery engine operating in the K_{dark} passband, why we choose to deploy it in Antarctica, and the status of a fifth-scale prototype designed as a Pathfinder to retire technological risks prior to full-scale implementation. We plan to deploy the Cryoscope Pathfinder to Dome C in December 2026 and the full-scale telescope by 2030.

Evaluating the performance of machine learning models under distribution shift is challenging, especially when we only have unlabeled data from the shifted (target) domain, along with labeled data from the original (source) domain. Recent work suggests that the notion of disagreement, the degree to which two models trained with different randomness differ on the same input, is a key to tackle this problem. Experimentally, disagreement and prediction error have been shown to be strongly connected, which has been used to estimate model performance. Experiments have led to the discovery of the disagreement-on-the-line phenomenon, whereby the classification error under the target domain is often a linear function of the classification error under the source domain; and whenever this property holds, disagreement under the source and target domain follow the same linear relation. In this work, we develop a theoretical foundation for analyzing disagreement in high-dimensional random features regression; and study under what conditions the disagreement-on-the-line phenomenon occurs in our setting. Experiments on CIFAR-10-C, Tiny ImageNet-C, and Camelyon17 are consistent with our theory and support the universality of the theoretical findings.

Causal analysis plays a foundational role in scientific discovery and reliable decision-making, yet it remains largely inaccessible to domain experts due to its conceptual and algorithmic complexity. This disconnect between causal methodology and practical usability presents a dual challenge: domain experts are unable to leverage recent advances in causal learning, while causal researchers lack broad, real-world deployment to test and refine their methods. To address this, we introduce Causal-Copilot, an autonomous agent that operationalizes expert-level causal analysis within a large language model framework. Causal-Copilot automates the full pipeline of causal analysis for both tabular and time-series data -- including causal discovery, causal inference, algorithm selection, hyperparameter optimization, result interpretation, and generation of actionable insights. It supports interactive refinement through natural language, lowering the barrier for non-specialists while preserving methodological rigor. By integrating over 20 state-of-the-art causal analysis techniques, our system fosters a virtuous cycle -- expanding access to advanced causal methods for domain experts while generating rich, real-world applications that inform and advance causal theory. Empirical evaluations demonstrate that Causal-Copilot achieves superior performance compared to existing baselines, offering a reliable, scalable, and extensible solution that bridges the gap between theoretical sophistication and real-world applicability in causal analysis. A live interactive demo of Causal-Copilot is available at https://causalcopilot.com/.