Daily Papers

Traditional Chinese Medicine (TCM) has seen increasing adoption in healthcare, with specialized Large Language Models (LLMs) emerging to support clinical applications. A fundamental requirement for these models is accurate identification of TCM drug ingredients. In this paper, we evaluate how general and TCM-specialized LLMs perform when identifying ingredients of Chinese drugs. Our systematic analysis reveals consistent failure patterns: models often interpret drug names literally, overuse common herbs regardless of relevance, and exhibit erratic behaviors when faced with unfamiliar formulations. LLMs also fail to understand the verification task. These findings demonstrate that current LLMs rely primarily on drug names rather than possessing systematic pharmacological knowledge. To address these limitations, we propose a Retrieval Augmented Generation (RAG) approach focused on ingredient names. Experiments across 220 TCM formulations show our method significantly improves accuracy from approximately 50% to 82% in ingredient verification tasks. Our work highlights critical weaknesses in current TCM-specific LLMs and offers a practical solution for enhancing their clinical reliability.

Parametric verification of linear temporal properties for stochastic models can be expressed as computing the satisfaction probability of a certain property as a function of the parameters of the model. Smoothed model checking (smMC) aims at inferring the satisfaction function over the entire parameter space from a limited set of observations obtained via simulation. As observations are costly and noisy, smMC is framed as a Bayesian inference problem so that the estimates have an additional quantification of the uncertainty. In smMC the authors use Gaussian Processes (GP), inferred by means of the Expectation Propagation algorithm. This approach provides accurate reconstructions with statistically sound quantification of the uncertainty. However, it inherits the well-known scalability issues of GP. In this paper, we exploit recent advances in probabilistic machine learning to push this limitation forward, making Bayesian inference of smMC scalable to larger datasets and enabling its application to models with high dimensional parameter spaces. We propose Stochastic Variational Smoothed Model Checking (SV-smMC), a solution that exploits stochastic variational inference (SVI) to approximate the posterior distribution of the smMC problem. The strength and flexibility of SVI make SV-smMC applicable to two alternative probabilistic models: Gaussian Processes (GP) and Bayesian Neural Networks (BNN). The core ingredient of SVI is a stochastic gradient-based optimization that makes inference easily parallelizable and that enables GPU acceleration. In this paper, we compare the performances of smMC against those of SV-smMC by looking at the scalability, the computational efficiency and the accuracy of the reconstructed satisfaction function.

Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may output the correct molecule, product, or option while its reasoning violates chemical logic. Existing process-level evaluators are hard to scale because LLM judges and human step-level process annotation are costly, inconsistent, and vulnerable to hallucination. We introduce ChemCoTBench-V2, a rule-verifiable diagnostic benchmark for low-cost, auditable evaluation of structured, verifier-addressable chemical reasoning traces. It spans molecular understanding, molecule editing, molecular optimization, and reaction prediction, with 5,620 evaluation samples across 18 reporting tasks. Models must expose key intermediate steps in expert-designed templates, and those steps are checked with deterministic chemistry rules and, for closed-answer tasks, reference traces rather than another LLM judge. Open-ended molecular optimization is evaluated with oracle-verifiable state constraints rather than strict trace matching. The benchmark reports three separate signals: final-answer correctness, template adherence, and step-wise verifier correctness over expert-refined intermediate commitments. Experiments on frontier models reveal a persistent gap between final-answer success and structured-reasoning-state consistency: models often follow the requested format while failing chemical-step checks, or answer correctly with weak supporting reasoning. ChemCoTBench-V2 enables fine-grained model comparison and identifies the concrete step at which the trace first violates the verifier.

In grocery e-commerce, customers often build ingredient baskets guided by dietary preferences but lack the expertise to create complete meals. Leveraging recipe knowledge to recommend complementary ingredients based on a partial basket is essential for improving the culinary experience. Traditional recipe completion methods typically predict a single missing ingredient using a leave-one-out strategy. However, they fall short in two key aspects: (i) they do not reflect real-world scenarios where multiple ingredients are often needed, and (ii) they overlook relationships among the missing ingredients themselves. To address these limitations, we reformulate basket completion as a set-to-set (S2S) recommendation problem, where an incomplete basket is input into a system that predicts a set of complementary ingredients. We introduce S2SRec2, a set-to-set ingredient recommendation framework based on a Set Transformer and trained in a multitask learning paradigm. S2SRec2 jointly learns to (i) retrieve missing ingredients from the representation of existing ones and (ii) assess basket completeness after prediction. These tasks are optimized together, enforcing accurate retrieval and coherent basket completion. Experiments on large-scale recipe datasets and qualitative analyses show that S2SRec2 significantly outperforms single-target baselines, offering a promising approach to enhance grocery shopping and inspire culinary creativity.

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

We present Epicure, a family of three sibling skip-gram ingredient embeddings retrained from scratch on a multilingual recipe corpus. We aggregate 4.14M recipes from 11 sources spanning seven languages, English, Chinese, Russian, Vietnamese, Spanish, Turkish, Indonesian, German, and Indian-English, and normalise the raw ingredient strings to 1,790 canonical entries via an LLM-augmented pipeline. A 203,508-edge ingredient-ingredient NPMI graph and an 80,019-edge typed FlavorDB ingredient-compound graph, 2,247 typed compound nodes across 15 categories, seed three Metapath2Vec variants that share architecture and hyperparameters and differ only in the random-walk schema: Cooc walks the co-occurrence graph only, Chem walks the typed compound metapaths only, and Core blends both via injected ingredient-ingredient walks at controlled mixing, placing each model at a distinct point on the chemistry-vs-recipe-context spectrum.

Accurate nutrition estimation helps people make informed dietary choices and is essential in the prevention of serious health complications. We present NutriBench, the first publicly available natural language meal description nutrition benchmark. NutriBench consists of 11,857 meal descriptions generated from real-world global dietary intake data. The data is human-verified and annotated with macro-nutrient labels, including carbohydrates, proteins, fats, and calories. We conduct an extensive evaluation of NutriBench on the task of carbohydrate estimation, testing twelve leading Large Language Models (LLMs), including GPT-4o, Llama3.1, Qwen2, Gemma2, and OpenBioLLM models, using standard, Chain-of-Thought and Retrieval-Augmented Generation strategies. Additionally, we present a study involving professional nutritionists, finding that LLMs can provide more accurate and faster estimates. Finally, we perform a real-world risk assessment by simulating the effect of carbohydrate predictions on the blood glucose levels of individuals with diabetes. Our work highlights the opportunities and challenges of using LLMs for nutrition estimation, demonstrating their potential to aid professionals and laypersons and improve health outcomes. Our benchmark is publicly available at: https://mehak126.github.io/nutribench.html

Identifying subtle technical errors within complex scientific and technical documents, especially those requiring multimodal interpretation (e.g., formulas in images), presents a significant hurdle for Large Language Models (LLMs) whose inherent error-correction tendencies can mask inaccuracies. This exploratory proof-of-concept (PoC) study investigates structured LLM context conditioning, informed by Persistent Workflow Prompting (PWP) principles, as a methodological strategy to modulate this LLM behavior at inference time. The approach is designed to enhance the reliability of readily available, general-purpose LLMs (specifically Gemini 2.5 Pro and ChatGPT Plus o3) for precise validation tasks, crucially relying only on their standard chat interfaces without API access or model modifications. To explore this methodology, we focused on validating chemical formulas within a single, complex test paper with known textual and image-based errors. Several prompting strategies were evaluated: while basic prompts proved unreliable, an approach adapting PWP structures to rigorously condition the LLM's analytical mindset appeared to improve textual error identification with both models. Notably, this method also guided Gemini 2.5 Pro to repeatedly identify a subtle image-based formula error previously overlooked during manual review, a task where ChatGPT Plus o3 failed in our tests. These preliminary findings highlight specific LLM operational modes that impede detail-oriented validation and suggest that PWP-informed context conditioning offers a promising and highly accessible technique for developing more robust LLM-driven analytical workflows, particularly for tasks requiring meticulous error detection in scientific and technical documents. Extensive validation beyond this limited PoC is necessary to ascertain broader applicability.

Automatically constructing a food diary that tracks the ingredients consumed can help people follow a healthy diet. We tackle the problem of food ingredients recognition as a multi-label learning problem. We propose a method for adapting a highly performing state of the art CNN in order to act as a multi-label predictor for learning recipes in terms of their list of ingredients. We prove that our model is able to, given a picture, predict its list of ingredients, even if the recipe corresponding to the picture has never been seen by the model. We make public two new datasets suitable for this purpose. Furthermore, we prove that a model trained with a high variability of recipes and ingredients is able to generalize better on new data, and visualize how it specializes each of its neurons to different ingredients.

Language models (LMs) are widely used by an increasing number of users, underscoring the challenge of maintaining factuality across a broad range of topics. We first present VERIFY (Verification and Evidence RetrIeval for FactualitY evaluation), a pipeline to evaluate LMs' factuality in real-world user interactions. VERIFY considers the verifiability of LM-generated content and categorizes content units as supported, unsupported, or undecidable based on the retrieved evidence from the Web. Importantly, factuality judgment by VERIFY correlates better with human evaluations than existing methods. Using VERIFY, we identify "hallucination prompts" across diverse topics, i.e., those eliciting the highest rates of incorrect and inconclusive LM responses. These prompts form FactBench, a dataset of 1K prompts across 150 fine-grained topics. Our dataset captures emerging factuality challenges in real-world LM interactions and can be regularly updated with new prompts. We benchmark widely-used LMs from GPT, Gemini, and Llama3.1 family on FactBench, yielding the following key findings: (i) Proprietary models exhibit better factuality, with performance declining from Easy to Hard hallucination prompts. (ii) Llama3.1-405B-Instruct shows comparable or lower factual accuracy than Llama3.1-70B-Instruct across all evaluation methods due to its higher subjectivity that leads to more content labeled as undecidable. (iii) Gemini1.5-Pro shows a significantly higher refusal rate, with over-refusal in 25% of cases. Our code and data are publicly available at https://huggingface.co/spaces/launch/factbench.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

Mycotoxins, toxic secondary metabolites produced by certain fungi, pose significant threats to global food safety and public health. These compounds can contaminate a variety of crops, leading to economic losses and health risks to both humans and animals. Traditional lab analysis methods for mycotoxin detection can be time-consuming and may not always be suitable for large-scale screenings. However, in recent years, machine learning (ML) methods have gained popularity for use in the detection of mycotoxins and in the food safety industry in general, due to their accurate and timely predictions. We provide a systematic review on some of the recent ML applications for detecting/predicting the presence of mycotoxin on a variety of food ingredients, highlighting their advantages, challenges, and potential for future advancements. We address the need for reproducibility and transparency in ML research through open access to data and code. An observation from our findings is the frequent lack of detailed reporting on hyperparameters in many studies as well as a lack of open source code, which raises concerns about the reproducibility and optimisation of the ML models used. The findings reveal that while the majority of studies predominantly utilised neural networks for mycotoxin detection, there was a notable diversity in the types of neural network architectures employed, with convolutional neural networks being the most popular.

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.

Factual hallucination remains a central challenge for large language models (LLMs). Existing mitigation approaches primarily rely on either external post-hoc verification or mapping uncertainty directly to abstention during fine-tuning, often resulting in overly conservative behavior. We propose VeriFY, a training-time framework that teaches LLMs to reason about factual uncertainty through consistency-based self-verification. VeriFY augments training with structured verification traces that guide the model to produce an initial answer, generate and answer a probing verification query, issue a consistency judgment, and then decide whether to answer or abstain. To address the risk of reinforcing hallucinated content when training on augmented traces, we introduce a stage-level loss masking approach that excludes hallucinated answer stages from the training objective while preserving supervision over verification behavior. Across multiple model families and scales, VeriFY reduces factual hallucination rates by 9.7 to 53.3 percent, with only modest reductions in recall (0.4 to 5.7 percent), and generalizes across datasets when trained on a single source. The source code, training data, and trained model checkpoints will be released upon acceptance.

Large Language Models (LLMs) have shown growing potential in molecular sciences, but they often produce chemically inaccurate descriptions and struggle to recognize or justify potential errors. This raises important concerns about their robustness and reliability in scientific applications. To support more rigorous evaluation of LLMs in chemical reasoning, we present the MolErr2Fix benchmark, designed to assess LLMs on error detection and correction in molecular descriptions. Unlike existing benchmarks focused on molecule-to-text generation or property prediction, MolErr2Fix emphasizes fine-grained chemical understanding. It tasks LLMs with identifying, localizing, explaining, and revising potential structural and semantic errors in molecular descriptions. Specifically, MolErr2Fix consists of 1,193 fine-grained annotated error instances. Each instance contains quadruple annotations, i.e,. (error type, span location, the explanation, and the correction). These tasks are intended to reflect the types of reasoning and verification required in real-world chemical communication. Evaluations of current state-of-the-art LLMs reveal notable performance gaps, underscoring the need for more robust chemical reasoning capabilities. MolErr2Fix provides a focused benchmark for evaluating such capabilities and aims to support progress toward more reliable and chemically informed language models. All annotations and an accompanying evaluation API will be publicly released to facilitate future research.

Typical fact verification models use retrieved written evidence to verify claims. Evidence sources, however, often change over time as more information is gathered and revised. In order to adapt, models must be sensitive to subtle differences in supporting evidence. We present VitaminC, a benchmark infused with challenging cases that require fact verification models to discern and adjust to slight factual changes. We collect over 100,000 Wikipedia revisions that modify an underlying fact, and leverage these revisions, together with additional synthetically constructed ones, to create a total of over 400,000 claim-evidence pairs. Unlike previous resources, the examples in VitaminC are contrastive, i.e., they contain evidence pairs that are nearly identical in language and content, with the exception that one supports a given claim while the other does not. We show that training using this design increases robustness -- improving accuracy by 10% on adversarial fact verification and 6% on adversarial natural language inference (NLI). Moreover, the structure of VitaminC leads us to define additional tasks for fact-checking resources: tagging relevant words in the evidence for verifying the claim, identifying factual revisions, and providing automatic edits via factually consistent text generation.

Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance remains limited. Existing benchmarks and metrics typically rely on published synthetic procedures and Top-K accuracy based on single ground-truth, which does not capture the open-ended nature of real-world synthesis planning. We propose a new benchmarking framework for single-step retrosynthesis that evaluates both general-purpose and chemistry-specialized LLMs using ChemCensor, a novel metric for chemical plausibility. By emphasizing plausibility over exact match, this approach better aligns with human synthesis planning practices. We also introduce CREED, a novel dataset comprising millions of ChemCensor-validated reaction records for LLM training, and use it to train a model that improves over the LLM baselines under this benchmark.

We present MM-Food-100K, a public 100,000-sample multimodal food intelligence dataset with verifiable provenance. It is a curated approximately 10% open subset of an original 1.2 million, quality-accepted corpus of food images annotated for a wide range of information (such as dish name, region of creation). The corpus was collected over six weeks from over 87,000 contributors using the Codatta contribution model, which combines community sourcing with configurable AI-assisted quality checks; each submission is linked to a wallet address in a secure off-chain ledger for traceability, with a full on-chain protocol on the roadmap. We describe the schema, pipeline, and QA, and validate utility by fine-tuning large vision-language models (ChatGPT 5, ChatGPT OSS, Qwen-Max) on image-based nutrition prediction. Fine-tuning yields consistent gains over out-of-box baselines across standard metrics; we report results primarily on the MM-Food-100K subset. We release MM-Food-100K for publicly free access and retain approximately 90% for potential commercial access with revenue sharing to contributors.

Large Language Models (LLMs) are trained on a vast amount of procedural texts, but they do not directly observe real-world phenomena. In the context of cooking recipes, this poses a challenge, as intermediate states of ingredients are often omitted, making it difficult for models to track ingredient states and understand recipes accurately. In this paper, we apply state probing, a method for evaluating a language model's understanding of the world, to the domain of cooking. We propose a new task and dataset for evaluating how well LLMs can recognize intermediate ingredient states during cooking procedures. We first construct a new Japanese recipe dataset with clear and accurate annotations of ingredient state changes, collected from well-structured and controlled recipe texts. Using this dataset, we design three novel tasks to evaluate whether LLMs can track ingredient state transitions and identify ingredients present at intermediate steps. Our experiments with widely used LLMs, such as Llama3.1-70B and Qwen2.5-72B, show that learning ingredient state knowledge improves their understanding of cooking processes, achieving performance comparable to commercial LLMs.

As LLM-powered agents have been used for high-stakes decision-making, such as clinical diagnosis, it becomes critical to develop reliable verification of their decisions to facilitate trustworthy deployment. Yet, existing verifiers usually underperform owing to a lack of domain knowledge and limited calibration. To address this, we establish GLEAN, an agent verification framework with Guideline-grounded Evidence Accumulation that compiles expert-curated protocols into trajectory-informed, well-calibrated correctness signals. GLEAN evaluates the step-wise alignment with domain guidelines and aggregates multi-guideline ratings into surrogate features, which are accumulated along the trajectory and calibrated into correctness probabilities using Bayesian logistic regression. Moreover, the estimated uncertainty triggers active verification, which selectively collects additional evidence for uncertain cases via expanding guideline coverage and performing differential checks. We empirically validate GLEAN with agentic clinical diagnosis across three diseases from the MIMIC-IV dataset, surpassing the best baseline by 12% in AUROC and 50% in Brier score reduction, which confirms the effectiveness in both discrimination and calibration. In addition, the expert study with clinicians recognizes GLEAN's utility in practice.

Deep learning and language models are increasingly dominating automated program repair research. While previous generate-and-validate approaches were able to find and use fix ingredients on a file or even project level, neural language models are limited to the code that fits their input window. In this work we investigate how important identifier ingredients are in neural program repair and present ScanFix, an approach that leverages an additional scanner model to extract identifiers from a bug's file and potentially project-level context. We find that lack of knowledge of far-away identifiers is an important cause of failed repairs. Augmenting repair model input with scanner-extracted identifiers yields relative improvements of up to 31%. However, ScanFix is outperformed by a model with a large input window (> 5k tokens). When passing ingredients from the ground-truth fix, improvements are even higher. This shows that, with refined extraction techniques, ingredient scanning, similar to fix candidate ranking, could have the potential to become an important subtask of future automated repair systems. At the same time, it also demonstrates that this idea is subject to Sutton's bitter lesson and may be rendered unnecessary by new code models with ever-increasing context windows.

Artificial Intelligence (AI)-generated images have become increasingly realistic and readily adaptable to concrete real-world claims, creating new challenges for verifying visual evidence. A concrete emerging risk is AI-generated refund fraud, in which manipulated or synthetic images are used to support claims about damaged products, poor delivery conditions, or service-related defects. Existing AI-generated image detection benchmarks mainly evaluate standalone authenticity classification, cross-generator transfer, or forensic localization, leaving claim-conditioned fraudulent evidence detection underexplored. To bridge this gap, we introduce FraudBench, a multimodal benchmark for detecting AI-generated fraudulent refund evidence. FraudBench is constructed from real-world user-review evidence across e-commerce, food delivery, and travel-service scenarios. We curate real evidence images together with their associated review and product metadata, identify genuine damaged and undamaged evidence through MLLM-assisted filtering and human annotation, and synthesize fake-damaged evidence from genuine undamaged reference images using six state-of-the-art image editing and generation models. Using FraudBench, we evaluate MLLMs, specialized AI-generated image detectors, and human participants under the same settings. Experiments show that current MLLMs often recognize real-damaged evidence but fail on many fake-damaged subsets, with fake-damage detection rates (TPR) far below the 50% baseline on most generator subsets. Specialized detectors generally perform better but remain inconsistent across generators and can produce false positives on real-damaged samples, revealing a clear gap between generic AI image detection and reliable claim-conditioned refund-evidence verification.

The rapid expansion of chemistry literature poses significant challenges for researchers seeking to efficiently access domain-specific knowledge. To support advancements in chemistry-focused natural language processing (NLP), we present ChemRxivQuest, a curated dataset of 970 high-quality question-answer (QA) pairs derived from 155 ChemRxiv preprints across 17 subfields of chemistry. Each QA pair is explicitly linked to its source text segment to ensure traceability and contextual accuracy. ChemRxivQuest was constructed using an automated pipeline that combines optical character recognition (OCR), GPT-4o-based QA generation, and a fuzzy matching technique for answer verification. The dataset emphasizes conceptual, mechanistic, applied, and experimental questions, enabling applications in retrieval-based QA systems, search engine development, and fine-tuning of domain-adapted large language models. We analyze the dataset's structure, coverage, and limitations, and outline future directions for expansion and expert validation. ChemRxivQuest provides a foundational resource for chemistry NLP research, education, and tool development.

Monitoring frying oil degradation is critical for food safety, yet current practice relies on destructive wet-chemistry assays that provide no spatial information and are unsuitable for real-time use. We identify a fundamental obstacle in thermal-image-based inspection, the camera-fingerprint shortcut, whereby models memorize sensor-specific noise and thermal bias instead of learning oxidation chemistry, collapsing under video-disjoint evaluation. We propose FryNet, a dual-stream RGB-thermal framework that jointly performs oil-region segmentation, serviceability classification, and regression of four chemical oxidation indices (PV, p-AV, Totox, temperature) in a single forward pass. A ThermalMiT-B2 backbone with channel and spatial attention extracts thermal features, while an RGB-MAE Encoder learns chemically grounded representations via masked autoencoding and chemical alignment. Dual-Encoder DANN adversarially regularizes both streams against video identity via Gradient Reversal Layers, and FiLM fusion bridges thermal structure with RGB chemical context. On 7,226 paired frames across 28 frying videos, FryNet achieves 98.97% mIoU, 100% classification accuracy, and 2.32 mean regression MAE, outperforming all seven baselines.

Automatic food recipe generation methods provide a creative tool for chefs to explore and to create new, and interesting culinary delights. Given the recent success of large language models (LLMs), they have the potential to create new recipes that can meet individual preferences, dietary constraints, and adapt to what is in your refrigerator. Existing research on using LLMs to generate recipes has shown that LLMs can be finetuned to generate realistic-sounding recipes. However, on close examination, these generated recipes often fail to meet basic requirements like including chicken as an ingredient in chicken dishes. In this paper, we propose RecipeMC, a text generation method using GPT-2 that relies on Monte Carlo Tree Search (MCTS). RecipeMC allows us to define reward functions to put soft constraints on text generation and thus improve the credibility of the generated recipes. Our results show that human evaluators prefer recipes generated with RecipeMC more often than recipes generated with other baseline methods when compared with real recipes.

Scientific texts often convey authority due to their technical language and complex data. However, this complexity can sometimes lead to the spread of misinformation. Non-experts are particularly susceptible to misleading claims based on scientific tables due to their high information density and perceived credibility. Existing table claim verification models, including state-of-the-art large language models (LLMs), often struggle with precise fine-grained reasoning, resulting in errors and a lack of precision in verifying scientific claims. Inspired by Cognitive Load Theory, we propose that enhancing a model's ability to interpret table-based claims involves reducing cognitive load by developing modular, reusable reasoning components (i.e., atomic skills). We introduce a skill-chaining schema that dynamically composes these skills to facilitate more accurate and generalizable reasoning with a reduced cognitive load. To evaluate this, we create SciAtomicBench, a cross-domain benchmark with fine-grained reasoning annotations. With only 350 fine-tuning examples, our model trained by atomic reasoning outperforms GPT-4o's chain-of-thought method, achieving state-of-the-art results with far less training data.

Large language models (LLMs) increasingly rely on reinforcement learning (RL) to enhance their reasoning capabilities through feedback. A critical challenge is verifying the consistency of model-generated responses and reference answers, since these responses are often lengthy, diverse, and nuanced. Rule-based verifiers struggle with complexity, prompting the use of model-based verifiers. However, specialized verifiers lack flexibility, while general LLM judges can be inconsistent. Existing research primarily focuses on building better verifiers, yet a systematic evaluation of different types of verifiers' performance across domains remains lacking, severely constraining the reliable development of Reinforcement Learning with Verifiable Reward (RLVR). To address this, we propose VerifyBench--a cross-domain comprehensive benchmark for systematically evaluating verifiers. We construct 4,000 expert-level questions covering mathematics, physics, chemistry, and biology. Each question is equipped with reference answers and diverse responses. The reliability of the evaluation is ensured through a rigorous annotation process conducted by a multidisciplinary expert team. We design a four-dimensional experimental framework to comprehensively compare the performance boundaries of specialized verifiers and general LLMs under combined conditions of extracted answers vs. complete responses, and short vs. long outputs. Our evaluation uncovers fundamental trade-offs in verifiers: while specialized verifiers achieve leading accuracy, they exhibit deficiencies in recall; general models show stronger inclusivity but unstable precision. More importantly, we discover verifiers' high sensitivity to input structure and inherent limitations in cross-domain generalization, providing critical insights into the bottlenecks of current verifier technology.

"Pasta alla Cacio e pepe" is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio and pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the "Mozzarella Phase" and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish.

Without accurate transcription of numerical data in scientific documents, a scientist cannot draw accurate conclusions. Unfortunately, the process of copying numerical data from one paper to another is prone to human error. In this paper, we propose to meet this challenge through the novel task of automatic table verification (AutoTV), in which the objective is to verify the accuracy of numerical data in tables by cross-referencing cited sources. To support this task, we propose a new benchmark, arXiVeri, which comprises tabular data drawn from open-access academic papers on arXiv. We introduce metrics to evaluate the performance of a table verifier in two key areas: (i) table matching, which aims to identify the source table in a cited document that corresponds to a target table, and (ii) cell matching, which aims to locate shared cells between a target and source table and identify their row and column indices accurately. By leveraging the flexible capabilities of modern large language models (LLMs), we propose simple baselines for table verification. Our findings highlight the complexity of this task, even for state-of-the-art LLMs like OpenAI's GPT-4. The code and benchmark will be made publicly available.

Fact verification has attracted a lot of attention in the machine learning and natural language processing communities, as it is one of the key methods for detecting misinformation. Existing large-scale benchmarks for this task have focused mostly on textual sources, i.e. unstructured information, and thus ignored the wealth of information available in structured formats, such as tables. In this paper we introduce a novel dataset and benchmark, Fact Extraction and VERification Over Unstructured and Structured information (FEVEROUS), which consists of 87,026 verified claims. Each claim is annotated with evidence in the form of sentences and/or cells from tables in Wikipedia, as well as a label indicating whether this evidence supports, refutes, or does not provide enough information to reach a verdict. Furthermore, we detail our efforts to track and minimize the biases present in the dataset and could be exploited by models, e.g. being able to predict the label without using evidence. Finally, we develop a baseline for verifying claims against text and tables which predicts both the correct evidence and verdict for 18% of the claims.

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address these issues, we introduce SUPERChem, a benchmark of 500 expert-curated reasoning-intensive chemistry problems, covering diverse subfields and provided in both multimodal and text-only formats. Original content and an iterative curation pipeline eliminate flawed items and mitigate data contamination. Each problem is paired with an expert-authored solution path, enabling Reasoning Path Fidelity (RPF) scoring to evaluate reasoning quality beyond final-answer accuracy. Evaluations against a human baseline of 40.3% accuracy show that even the best-performing model, GPT-5 (High), reaches only 38.5%, followed closely by Gemini 2.5 Pro (37.9%) and DeepSeek-V3.1-Think (37.3%). SUPERChem elicits multi-step, multimodal reasoning, reveals model-dependent effects of visual information, and distinguishes high-fidelity reasoners from heuristic ones. By providing a challenging benchmark and a reliable evaluation framework, SUPERChem aims to facilitate the advancement of LLMs toward expert-level chemical intelligence. The dataset of the benchmark is available at https://huggingface.co/datasets/ZehuaZhao/SUPERChem.

Nutrition estimation of meals from visual data is an important problem for dietary monitoring and computational health, but existing approaches largely rely on single images of the finally completed dish. This setting is fundamentally limited because many nutritionally relevant ingredients and transformations, such as oils, sauces, and mixed components, become visually ambiguous after cooking, making accurate calorie and macronutrient estimation difficult. In this paper, we investigate whether the cooking process information from egocentric cooking videos can contribute to dish-level nutrition estimation. First, we further manually annotated the HD-EPIC dataset and established the first benchmark for video-based nutrition estimation. Most importantly, we propose V-Nutri, a staged framework that combines Nutrition5K-pretrained visual backbones with a lightweight fusion module that aggregates features from the final dish frame and cooking process keyframes extracted from the egocentric videos. V-Nutri also includes a cooking keyframes selection module, a VideoMamba-based event-detection model that targets ingredient-addition moments. Experiments on the HD-EPIC dataset show that process cues can provide complementary nutritional evidence, improving nutrition estimation under controlled conditions. Our results further indicate that the benefit of process keyframes depends strongly on backbone representation capacity and event detection quality. Our code and annotated dataset is available at https://github.com/K624-YCK/V-Nutri.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.

People enjoy food photography because they appreciate food. Behind each meal there is a story described in a complex recipe and, unfortunately, by simply looking at a food image we do not have access to its preparation process. Therefore, in this paper we introduce an inverse cooking system that recreates cooking recipes given food images. Our system predicts ingredients as sets by means of a novel architecture, modeling their dependencies without imposing any order, and then generates cooking instructions by attending to both image and its inferred ingredients simultaneously. We extensively evaluate the whole system on the large-scale Recipe1M dataset and show that (1) we improve performance w.r.t. previous baselines for ingredient prediction; (2) we are able to obtain high quality recipes by leveraging both image and ingredients; (3) our system is able to produce more compelling recipes than retrieval-based approaches according to human judgment. We make code and models publicly available.

Question Answering (QA) effectively evaluates language models' reasoning and knowledge depth. While QA datasets are plentiful in areas like general domain and biomedicine, academic chemistry is less explored. Chemical QA plays a crucial role in both education and research by effectively translating complex chemical information into readily understandable format. Addressing this gap, we introduce ScholarChemQA, a large-scale QA dataset constructed from chemical papers. This dataset reflects typical real-world challenges, including an imbalanced data distribution and a substantial amount of unlabeled data that can be potentially useful. Correspondingly, we introduce a QAMatch model, specifically designed to effectively answer chemical questions by fully leveraging our collected data. We first address the issue of imbalanced label distribution by re-weighting the instance-wise loss based on the inverse frequency of each class, ensuring minority classes are not dominated by majority ones during optimization. Next, we utilize the unlabeled data to enrich the learning process, generating a variety of augmentations based on a SoftMix operation and ensuring their predictions align with the same target, i.e., pseudo-labels. To ensure the quality of the pseudo-labels, we propose a calibration procedure aimed at closely aligning the pseudo-label estimates of individual samples with a desired ground truth distribution. Experiments show that our QAMatch significantly outperforms the recent similar-scale baselines and Large Language Models (LLMs) not only on our ScholarChemQA dataset but also on four benchmark datasets. We hope our benchmark and model can facilitate and promote more research on chemical QA.

The identification of bitter peptides is crucial in various domains, including food science, drug discovery, and biochemical research. These peptides not only contribute to the undesirable taste of hydrolyzed proteins but also play key roles in physiological and pharmacological processes. However, experimental methods for identifying bitter peptides are time-consuming and expensive. With the rapid expansion of peptide sequence databases in the post-genomic era, the demand for efficient computational approaches to distinguish bitter from non-bitter peptides has become increasingly significant. In this study, we propose a novel stacking-based ensemble learning framework aimed at enhancing the accuracy and reliability of bitter peptide classification. Our method integrates diverse sequence-based feature representations and leverages a broad set of machine learning classifiers. The first stacking layer comprises multiple base classifiers, each trained on distinct feature encoding schemes, while the second layer employs logistic regression to refine predictions using an eight-dimensional probability vector. Extensive evaluations on a carefully curated dataset demonstrate that our model significantly outperforms existing predictive methods, providing a robust and reliable computational tool for bitter peptide identification. Our approach achieves an accuracy of 96.09\% and a Matthews Correlation Coefficient (MCC) of 0.9220 on the independent test set, underscoring its effectiveness and generalizability. To facilitate real-time usage and broader accessibility, we have also developed a user-friendly web server based on the proposed method, which is freely accessible at https://ibitter-stack-webserver.streamlit.app/. This tool enables researchers and practitioners to conveniently screen peptide sequences for bitterness in real-time applications.

Training models through self-play alone (without any human data) has been a longstanding goal in AI, but its effectiveness for training large language models remains unclear, particularly in code generation where rewards based on unit tests are brittle and prone to error propagation. We study self-play in the verified code generation setting, where formal verification provides reliable correctness signals. We introduce Propose, Solve, Verify (PSV) a simple self-play framework where formal verification signals are used to create a proposer capable of generating challenging synthetic problems and a solver trained via expert iteration. We use PSV to train PSV-Verus, which across three benchmarks improves pass@1 by up to 9.6x over inference-only and expert-iteration baselines. We show that performance scales with the number of generated questions and training iterations, and through ablations identify formal verification and difficulty-aware proposal as essential ingredients for successful self-play.

In the early 2000s, renowned chef Heston Blumenthal formulated his "food pairing" hypothesis, positing that if foods share many flavor compounds, then they tend to taste good when eaten together. In 2011, Ahn et al. conducted a study using a dataset of recipes, ingredients, and flavor compounds, finding that, in Western cuisine, ingredients in recipes often share more flavor compounds than expected by chance, indicating a natural tendency towards food pairing. Building upon Ahn's research, our work applies state-of-the-art collaborative filtering techniques to the dataset, providing a tool that can recommend new foods to add in recipes, retrieve missing ingredients and advise against certain combinations. We create our recommender in two ways, by taking into account ingredients appearances in recipes or shared flavor compounds between foods. While our analysis confirms the existence of food pairing, the recipe-based recommender performs significantly better than the flavor-based one, leading to the conclusion that food pairing is just one of the principles to take into account when creating recipes. Furthermore, and more interestingly, we find that food pairing in data is mostly due to trivial couplings of very similar ingredients, leading to a reconsideration of its current role in recipes, from being an already existing feature to a key to open up new scenarios in gastronomy. Our flavor-based recommender can thus leverage this novel concept and provide a new tool to lead culinary innovation.

Calorie and nutrition research has attained increased interest in recent years. But, due to the complexity of the problem, literature in this area focuses on a limited subset of ingredients or dish types and simple convolutional neural networks or traditional machine learning. Simultaneously, estimation of ingredient portions can help improve calorie estimation and meal re-production from a given image. In this paper, given a single cooking image, a pipeline for calorie estimation and meal re-production for different servings of the meal is proposed. The pipeline contains two stages. In the first stage, a set of ingredients associated with the meal in the given image are predicted. In the second stage, given image features and ingredients, portions of the ingredients and finally the total meal calorie are simultaneously estimated using a deep transformer-based model. Portion estimation introduced in the model helps improve calorie estimation and is also beneficial for meal re-production in different serving sizes. To demonstrate the benefits of the pipeline, the model can be used for meal kits generation. To evaluate the pipeline, the large scale dataset Recipe1M is used. Prior to experiments, the Recipe1M dataset is parsed and explicitly annotated with portions of ingredients. Experiments show that using ingredients and their portions significantly improves calorie estimation. Also, a visual interface is created in which a user can interact with the pipeline to reach accurate calorie estimations and generate a meal kit for cooking purposes.

We introduce FragAtlas-62M, a specialized foundation model trained on the largest fragment dataset to date. Built on the complete ZINC-22 fragment subset comprising over 62 million molecules, it achieves unprecedented coverage of fragment chemical space. Our GPT-2 based model (42.7M parameters) generates 99.90% chemically valid fragments. Validation across 12 descriptors and three fingerprint methods shows generated fragments closely match the training distribution (all effect sizes < 0.4). The model retains 53.6% of known ZINC fragments while producing 22% novel structures with practical relevance. We release FragAtlas-62M with training code, preprocessed data, documentation, and model weights to accelerate adoption.

Language models are widely used in chemistry for molecular property prediction and small-molecule generation, yet Natural Products (NPs) remain underexplored despite their importance in drug discovery. To address this gap, we develop NP-specific chemical language models (NPCLMs) by pre-training state-space models (Mamba and Mamba-2) and comparing them with transformer baselines (GPT). Using a dataset of about 1M NPs, we present the first systematic comparison of selective state-space models and transformers for NP-focused tasks, together with eight tokenization strategies including character-level, Atom-in-SMILES (AIS), byte-pair encoding (BPE), and NP-specific BPE. We evaluate molecule generation (validity, uniqueness, novelty) and property prediction (membrane permeability, taste, anti-cancer activity) using MCC and AUC-ROC. Mamba generates 1-2 percent more valid and unique molecules than Mamba-2 and GPT, with fewer long-range dependency errors, while GPT yields slightly more novel structures. For property prediction, Mamba variants outperform GPT by 0.02-0.04 MCC under random splits, while scaffold splits show comparable performance. Results demonstrate that domain-specific pre-training on about 1M NPs can match models trained on datasets over 100 times larger.

Regulatory compliance auditing across diverse industrial domains requires heightened quality assurance and traceability. Present manual and intermittent approaches to such auditing yield significant challenges, potentially leading to oversights in the monitoring process. To address these issues, we introduce a real-time, multi-modal sensing system employing 3D time-of-flight and RGB cameras, coupled with unsupervised learning techniques on edge AI devices. This enables continuous object tracking thereby enhancing efficiency in record-keeping and minimizing manual interventions. While we validate the system in a knife sanitization context within agrifood facilities, emphasizing its prowess against occlusion and low-light issues with RGB cameras, its potential spans various industrial monitoring settings.

As large language models (LLMs) are increasingly applied to scientific reasoning, the complexity of answer formats and the diversity of equivalent expressions make answer verification a critical yet challenging task. Existing verification studies in scientific domains suffer from two major limitations: (a) the absence of systematic evaluation standards and insufficient disciplinary coverage, which hinders their comprehensive assessment; and (b) heavy reliance on cumbersome rule design or prompt engineering, which reduces their effectiveness in complex reasoning scenarios or limits their cross-disciplinary generalization. To address these challenges, we propose solutions at both the data and model levels. On the data side, we construct SCI-VerifyBench, a cross-disciplinary benchmark covering mathematics, physics, biology, chemistry, and general scientific QA. The benchmark is built from real LLM responses and enhanced with domain-specific equivalence transformations that generate challenging and realistic data. Model-based and expert annotations ensure both quality and diversity, enabling rigorous evaluation of verification ability. On the model side, we emphasize the importance of reasoning for verification and introduce SCI-Verifier, a unified reasoning-augmented verifier for scientific domains. Through post-training, SCI-Verifier demonstrates strong logical reasoning and equivalence judgment capabilities while maintaining concise and stable outputs. Together, SCI-VerifyBench and SCI-Verifier provide a principled framework for scientific verification, offering both systematic evaluation and practical pathways to enhance the reliability and applicability of LLMs in scientific domains.

Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry. Most existing approaches to MS/MS identification remain tied to reference libraries or predefined candidate sets, whereas de novo methods aim to generate structures directly from spectra. A common de novo route predicts a molecular fingerprint from the spectrum and then decodes structures from it, enabling decoder pretraining on large molecule-only corpora. However, this paradigm creates a training-inference mismatch: the decoder is trained on oracle fingerprints computed from molecules, but at inference it is queried with a noisy spectrum-induced fingerprint posterior that is typically collapsed to a single thresholded fingerprint. We introduce MS-GPT, which recasts fingerprint-mediated de novo elucidation as spectrum-induced posterior querying of a conditional molecule-language model. MS-GPT conditions a molecule-language model on fingerprints and formulas, then converts the spectrum-induced posterior into a band of fingerprint queries near the oracle-fingerprint manifold through active-bit density calibration. Candidates sampled across this band are pooled and ranked by generation-frequency consensus. A lightweight LoRA adapter further mitigates domain-specific posterior bias while preserving the pretrained molecular prior. On NPLIB1 and MassSpecGym, MS-GPT sets a new state of the art, reaching Top-1/Top-10 exact-match accuracy of 29.8\%/41.1\% and 23.9\%/28.7\%, respectively. Candidate-pool scaling shows that efficient autoregressive molecular generation continues to improve recall with a little additional inference cost. The source code and model checkpoints are available at https://github.com/VIKI623/MS-GPT.

DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent from the reference set: under Conformal Risk Control's certified miss-rate constraint, a low-discrimination signal forces the threshold below the entire test-benign mass. We compose three signals derived from a synthesis order's public annotation: k-mer Jaccard similarity to known toxins, the trimmed-mean score of a five-LLM judge panel, and cosine similarity to clustered embedding centroids. Fused under a monotone logistic aggregator and calibrated by Conformal Risk Control, the resulting screener certifies E[FNR] le α. Across ten leave-one-taxonomic-family-out folds at α=0.05 on UniProt KW-0800 reviewed toxins, the calibrated screener achieves 0% test miss rate on every fold and 0% test false-flag rate on nine of ten folds. The bound's finite-sample slack 1/(n_{cal}+1) caps the certifiable miss rate at 1.77% on our 200-hazard subsample; reaching procurement-grade α=10^{-3} requires an 18times larger calibration set, which the full reviewed UniProt KW-0800 corpus is large enough to deliver. The binding constraint on certifiable DNA-synthesis screening is calibration data, not algorithms. Code: https://github.com/najmulhasan-code/crc-screen

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

Autonomous research agents produce competitive solutions and professional-looking manuscripts, yet their outputs contain verifiability failures undetectable by surface-level evaluation: fabricated citations, unreproducible scores, and method descriptions that diverge from the implementation. We address this through three contributions. First, Chain-of-Evidence (CoE), a verifiability framework requiring every claim to be traceable to its evidence source. Second, ScientistOne, an end-to-end autonomous research system that maintains evidence chains by construction throughout literature review, solution discovery, and paper writing. Third, CoE Audit, a post-hoc audit whose four integrity checks -- score verification, specification violation, reference verification, and method-code alignment -- apply uniformly to all systems. Across 75 papers spanning five systems and five frontier research tasks, every baseline exhibits at least one systematic failure mode: hallucinated reference rates reach 21%, score verification passes in as few as 42% of papers, and method-code alignment ranges from 20% to 80%. ScientistOne achieves zero hallucinated references (0/337), perfect score verification (12/12), and the highest method-code alignment (14/15), while matching or exceeding human expert performance on all five tasks. ScientistOne further generalizes to six additional tasks spanning medical imaging, fine-grained recognition, 3D perception, and language modeling, achieving state-of-the-art on Parameter Golf and gold medals on MLE-Bench tasks where baselines fail entirely.

Verification is crucial for effective mathematical reasoning. We present a new temporal consistency method where verifiers iteratively refine their judgments based on the previous assessment. Unlike one-round verification or multi-model debate approaches, our method leverages consistency in a sequence of self-reflection actions to improve verification accuracy. Empirical evaluations across diverse mathematical process error identification benchmarks (Mathcheck, ProcessBench, and PRM800K) show consistent performance improvements over baseline methods. When applied to the recent DeepSeek R1 distilled models, our method demonstrates strong performance, enabling 7B/8B distilled models to outperform all 70B/72B models and GPT-4o on ProcessBench. Notably, the distilled 14B model with our method achieves performance comparable to Deepseek-R1. Our codes are available at https://github.com/jcguo123/Temporal-Consistency

Techniques for reliable rubric-based LLM evaluation -- ensemble judging, bias mitigation, few-shot calibration -- are scattered across papers with inconsistent terminology and partial implementations. We introduce Autorubric, an open-source framework that unifies these rubric-based LLM evaluation lessons with opinionated defaults: analytic rubrics with binary, ordinal, and nominal criteria; single-judge and ensemble evaluation; few-shot calibration; bias mitigations; and psychometric reliability metrics. We validate on three benchmarks: RiceChem (college chemistry grading, 80\% accuracy with 5-shot calibration), ResearcherBench (deep research evaluation, 931 criteria, cross-judge agreement analysis), and CHARM-100, a new chatbot evaluation dataset combining all three criterion types with ground truth labels (87\% binary accuracy, moderate-to-substantial κ). Beyond measurement, per-criterion scores and explanations serve as optimization signals. We demonstrate how Autorubric's rubric-evaluation explanations raise a peer review agent's score from 0.47 to 0.85 (above the 0.82 expert-curated baseline), and its scores serve as RL rewards to produce statistically significant improvement on AdvancedIF (+0.039, Wilcoxon p = 0.032) with positive transfer to IFEval. In all of these cases, Autorubric enabled us to rapidly operationalize various rubric design choices and best practices with minimal effort.

Visual recognition of materials and their states is essential for understanding most aspects of the world, from determining whether food is cooked, metal is rusted, or a chemical reaction has occurred. However, current image recognition methods are limited to specific classes and properties and can't handle the vast number of material states in the world. To address this, we present MatSim: the first dataset and benchmark for computer vision-based recognition of similarities and transitions between materials and textures, focusing on identifying any material under any conditions using one or a few examples. The dataset contains synthetic and natural images. The synthetic images were rendered using giant collections of textures, objects, and environments generated by computer graphics artists. We use mixtures and gradual transitions between materials to allow the system to learn cases with smooth transitions between states (like gradually cooked food). We also render images with materials inside transparent containers to support beverage and chemistry lab use cases. We use this dataset to train a siamese net that identifies the same material in different objects, mixtures, and environments. The descriptor generated by this net can be used to identify the states of materials and their subclasses using a single image. We also present the first few-shot material recognition benchmark with images from a wide range of fields, including the state of foods and drinks, types of grounds, and many other use cases. We show that a net trained on the MatSim synthetic dataset outperforms state-of-the-art models like Clip on the benchmark and also achieves good results on other unsupervised material classification tasks.

We present SciClaimEval, a new scientific dataset for the claim verification task. Unlike existing resources, SciClaimEval features authentic claims, including refuted ones, directly extracted from published papers. To create refuted claims, we introduce a novel approach that modifies the supporting evidence (figures and tables), rather than altering the claims or relying on large language models (LLMs) to fabricate contradictions. The dataset provides cross-modal evidence with diverse representations: figures are available as images, while tables are provided in multiple formats, including images, LaTeX source, HTML, and JSON. SciClaimEval contains 1,664 annotated samples from 180 papers across three domains, machine learning, natural language processing, and medicine, validated through expert annotation. We benchmark 11 multimodal foundation models, both open-source and proprietary, across the dataset. Results show that figure-based verification remains particularly challenging for all models, as a substantial performance gap remains between the best system and human baseline.

Accurate thermochemical data with sub-chemical accuracy (i.e., within pm1 kcal mol^{-1} from sufficiently accurate experimental or theoretical reference data) is essential for the development and improvement of computational chemistry methods. Challenging thermochemical properties such as heats of formation and total atomization energies (TAEs) are of particular interest because they rigorously test the ability of computational chemistry methods to accurately describe complex chemical transformations involving multiple bond rearrangements. Yet, existing thermochemical datasets that confidently reach this level of accuracy are limited in either size or scope. Datasets with highly accurate reference values include a small number of data points, and larger datasets provide less accurate data or only cover a narrow portion of the chemical space. The existing datasets are therefore insufficient for developing data-driven methods with predictive accuracy over a large chemical space. The Microsoft Research Accurate Chemistry Collection (MSR-ACC) will address this challenge. Here, it offers the MSR-ACC/TAE25 dataset of 76,879 total atomization energies obtained at the CCSD(T)/CBS level via the W1-F12 thermochemical protocol. The dataset is constructed to exhaustively cover chemical space for all elements up to argon by enumerating and sampling chemical graphs, thus avoiding bias towards any particular subspace of the chemical space (such as drug-like, organic, or experimentally observed molecules). With this first dataset in MSR-ACC, we enable data-driven approaches for developing predictive computational chemistry methods with unprecedented accuracy and scope.

Chemical reasoning inherently integrates visual, textual, and symbolic modalities, yet existing benchmarks rarely capture this complexity, often relying on simple image-text pairs with limited chemical semantics. As a result, the actual ability of Multimodal Large Language Models (MLLMs) to process and integrate chemically meaningful information across modalities remains unclear. We introduce ChemVTS-Bench, a domain-authentic benchmark designed to systematically evaluate the Visual-Textual-Symbolic (VTS) reasoning abilities of MLLMs. ChemVTS-Bench contains diverse and challenging chemical problems spanning organic molecules, inorganic materials, and 3D crystal structures, with each task presented in three complementary input modes: (1) visual-only, (2) visual-text hybrid, and (3) SMILES-based symbolic input. This design enables fine-grained analysis of modality-dependent reasoning behaviors and cross-modal integration. To ensure rigorous and reproducible evaluation, we further develop an automated agent-based workflow that standardizes inference, verifies answers, and diagnoses failure modes. Extensive experiments on state-of-the-art MLLMs reveal that visual-only inputs remain challenging, structural chemistry is the hardest domain, and multimodal fusion mitigates but does not eliminate visual, knowledge-based, or logical errors, highlighting ChemVTS-Bench as a rigorous, domain-faithful testbed for advancing multimodal chemical reasoning. All data and code will be released to support future research.

Dietary intake estimation plays a crucial role in understanding the nutritional habits of individuals and populations, aiding in the prevention and management of diet-related health issues. Accurate estimation requires comprehensive datasets of food scenes, including images, segmentation masks, and accompanying dietary intake metadata. In this paper, we introduce NutritionVerse-Real, an open access manually collected 2D food scene dataset for dietary intake estimation with 889 images of 251 distinct dishes and 45 unique food types. The NutritionVerse-Real dataset was created by manually collecting images of food scenes in real life, measuring the weight of every ingredient and computing the associated dietary content of each dish using the ingredient weights and nutritional information from the food packaging or the Canada Nutrient File. Segmentation masks were then generated through human labelling of the images. We provide further analysis on the data diversity to highlight potential biases when using this data to develop models for dietary intake estimation. NutritionVerse-Real is publicly available at https://www.kaggle.com/datasets/nutritionverse/nutritionverse-real as part of an open initiative to accelerate machine learning for dietary sensing.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

Fact verification aims to verify a claim using evidence from a trustworthy knowledge base. To address this challenge, algorithms must produce features for every claim that are both semantically meaningful, and compact enough to find a semantic alignment with the source information. In contrast to previous work, which tackled the alignment problem by learning over annotated corpora of claims and their corresponding labels, we propose SFAVEL (Self-supervised Fact Verification via Language Model Distillation), a novel unsupervised pretraining framework that leverages pre-trained language models to distil self-supervised features into high-quality claim-fact alignments without the need for annotations. This is enabled by a novel contrastive loss function that encourages features to attain high-quality claim and evidence alignments whilst preserving the semantic relationships across the corpora. Notably, we present results that achieve a new state-of-the-art on FB15k-237 (+5.3% Hits@1) and FEVER (+8% accuracy) with linear evaluation.

Advances in training, post-training, and inference-time methods have enabled frontier reasoning models to win gold medals in math competitions and settle challenging open problems. Gaining trust in the responses of these models requires that natural language proofs be checked for errors. LLM judges are increasingly being adopted to meet the growing demand for evaluating such proofs. While verification is considered easier than generation, what model capability does reliable verification actually require? We systematically evaluate four open-source and two frontier LLMs on datasets of human-graded natural language proofs of competition-level problems. We consider two key metrics: verifier accuracy and self-consistency (the rate of agreement across repeated judgments on the same proof). We observe that smaller open-source models are only up to ~10% behind frontier models in accuracy but they are up to ~25% more inconsistent. Furthermore, we see that verifier accuracy is sensitive to prompt choice across all models. We then demonstrate that the smaller models, in fact, do possess the mathematical capabilities to verify proofs at the level of frontier models, but they struggle to reliably elicit these capabilities with general judging prompts. Through an LLM-guided prompt search, we synthesize an ensemble of specialized prompts that overcome the specific failure modes of smaller models, boosting their performance by up to 9.1% in accuracy and 15.9% in self-consistency. These gains are realized across models and datasets, allowing models like Qwen3.5-35B to perform on par with frontier models such as Gemini 3.1 Pro for proof verification.

Seeking health-related advice on the internet has become a common practice in the digital era. Determining the trustworthiness of medical claims found online and finding appropriate evidence for this information is increasingly challenging. Fact-checking has emerged as an approach to assess the veracity of factual claims using evidence from credible knowledge sources. To help advance the automation of this task, in this paper, we introduce a novel dataset of 750 health-related claims, labeled for veracity by medical experts and backed with evidence from appropriate clinical studies. We provide an analysis of the dataset, highlighting its characteristics and challenges. The dataset can be used for Machine Learning tasks related to automated fact-checking such as evidence retrieval, veracity prediction, and explanation generation. For this purpose, we provide baseline models based on different approaches, examine their performance, and discuss the findings.

Despite substantial progress in fact-verification benchmarks, claims grounded in large-scale structured data remain underexplored. In this work, we introduce ClaimDB, the first fact-verification benchmark where the evidence for claims is derived from compositions of millions of records and multiple tables. ClaimDB consists of 80 unique real-life databases covering a wide range of domains, from governance and healthcare to media, education and the natural sciences. At this scale, verification approaches that rely on "reading" the evidence break down, forcing a timely shift toward reasoning in executable programs. We conduct extensive experiments with 30 state-of-the-art proprietary and open-source (below 70B) LLMs and find that none exceed 83% accuracy, with more than half below 55%. Our analysis also reveals that both closed- and open-source models struggle with abstention -- the ability to admit that there is no evidence to decide -- raising doubts about their reliability in high-stakes data analysis. We release the benchmark, code, and the LLM leaderboard at https://claimdb.github.io .

Fact-checking is the task of verifying the veracity of claims by assessing their assertions against credible evidence. The vast majority of fact-checking studies focus exclusively on political claims. Very little research explores fact-checking for other topics, specifically subject matters for which expertise is required. We present the first study of explainable fact-checking for claims which require specific expertise. For our case study we choose the setting of public health. To support this case study we construct a new dataset PUBHEALTH of 11.8K claims accompanied by journalist crafted, gold standard explanations (i.e., judgments) to support the fact-check labels for claims. We explore two tasks: veracity prediction and explanation generation. We also define and evaluate, with humans and computationally, three coherence properties of explanation quality. Our results indicate that, by training on in-domain data, gains can be made in explainable, automated fact-checking for claims which require specific expertise.

AI coding agents produce code faster than humans can review it. In our approach, the prover is the judge of whether the code is correct. Under a verifier-driven loop, AI agents wrote and verified bare-metal security software in Ada/SPARK spanning classical and post-quantum cryptography, TLS 1.3, IKEv2, X.509, and a Matrix client. GNATprove discharged 49,280 proof obligations, established functional correctness for selected primitives, and proved the absence of run-time errors for the rest, at roughly 20-40 times lower supervision cost than comparable hand verification. GNATprove alone was insufficient: some defects could not be detected and were resolved using known-answer tests, interoperability, or human review of specifications. Given weak checks, the agent tried to bypass them and reported success. We report where each layer caught faults and draw the central lesson: what an agent can be trusted to establish is bounded by the strength of its feedback.

In recent years, generative artificial intelligence (GenAI) has demonstrated remarkable capabilities in high-stakes domains such as molecular science. However, challenges related to the verifiability and structural privacy of its outputs remain largely unresolved. This paper focuses on the task of molecular toxicity repair. It proposes a structure-private verification framework - ToxiEval-ZKP - which, for the first time, introduces zero-knowledge proof (ZKP) mechanisms into the evaluation process of this task. The system enables model developers to demonstrate to external verifiers that the generated molecules meet multidimensional toxicity repair criteria, without revealing the molecular structures themselves. To this end, we design a general-purpose circuit compatible with both classification and regression tasks, incorporating evaluation logic, Poseidon-based commitment hashing, and a nullifier-based replay prevention mechanism to build a complete end-to-end ZK verification system. Experimental results demonstrate that ToxiEval-ZKP facilitates adequate validation under complete structural invisibility, offering strong circuit efficiency, security, and adaptability, thereby opening up a novel paradigm for trustworthy evaluation in generative scientific tasks.

Claim verification can be a challenging task. In this paper, we present a method to enhance the robustness and reasoning capabilities of automated claim verification through the extraction of short facts from evidence. Our novel approach, FactDetect, leverages Large Language Models (LLMs) to generate concise factual statements from evidence and label these facts based on their semantic relevance to the claim and evidence. The generated facts are then combined with the claim and evidence. To train a lightweight supervised model, we incorporate a fact-detection task into the claim verification process as a multitasking approach to improve both performance and explainability. We also show that augmenting FactDetect in the claim verification prompt enhances performance in zero-shot claim verification using LLMs. Our method demonstrates competitive results in the supervised claim verification model by 15% on the F1 score when evaluated for challenging scientific claim verification datasets. We also demonstrate that FactDetect can be augmented with claim and evidence for zero-shot prompting (AugFactDetect) in LLMs for verdict prediction. We show that AugFactDetect outperforms the baseline with statistical significance on three challenging scientific claim verification datasets with an average of 17.3% performance gain compared to the best performing baselines.

Diet plays a critical role in human health, yet tailoring dietary reasoning to individual health conditions remains a major challenge. Nutrition Question Answering (QA) has emerged as a popular method for addressing this problem. However, current research faces two critical limitations. On one hand, the absence of datasets involving user-specific medical information severely limits personalization. This challenge is further compounded by the wide variability in individual health needs. On the other hand, while large language models (LLMs), a popular solution for this task, demonstrate strong reasoning abilities, they struggle with the domain-specific complexities of personalized healthy dietary reasoning, and existing benchmarks fail to capture these challenges. To address these gaps, we introduce the Nutritional Graph Question Answering (NGQA) benchmark, the first graph question answering dataset designed for personalized nutritional health reasoning. NGQA leverages data from the National Health and Nutrition Examination Survey (NHANES) and the Food and Nutrient Database for Dietary Studies (FNDDS) to evaluate whether a food is healthy for a specific user, supported by explanations of the key contributing nutrients. The benchmark incorporates three question complexity settings and evaluates reasoning across three downstream tasks. Extensive experiments with LLM backbones and baseline models demonstrate that the NGQA benchmark effectively challenges existing models. In sum, NGQA addresses a critical real-world problem while advancing GraphQA research with a novel domain-specific benchmark.

Claim verification is essential in combating misinformation, and large language models (LLMs) have recently emerged in this area as powerful tools for assessing the veracity of claims using external knowledge. Existing LLM-based methods for claim verification typically adopt a Decompose-Then-Verify paradigm, which involves decomposing complex claims into several independent sub-claims and verifying each sub-claim separately. However, this paradigm often introduces errors during the claim decomposition process. To mitigate these errors, we propose to develop the Chain-of-Thought (CoT)-Verify paradigm, which leverages LLM reasoning methods to generate CoT-verification paths for the original complex claim without requiring decompositions into sub-claims and separate verification stages. The CoT-Verify paradigm allows us to propose a natural fine-tuning method called Reasoning-CV to enhance the verification capabilities in LLMs. Reasoning-CV includes a supervised fine-tuning (SFT) stage and a self-improvement direct preference optimization (DPO) stage. Utilizing only an 8B pre-trained LLM, Reasoning-CV demonstrates superior knowledge-assisted claim verification performances compared to existing Decompose-Then-Verify methods, as well as powerful black-box LLMs such as GPT-4o+CoT and o1-preview. Our code is available.

Dataset ownership verification, the process of determining if a dataset is used in a model's training data, is necessary for detecting unauthorized data usage and data contamination. Existing approaches, such as backdoor watermarking, rely on inducing a detectable behavior into the trained model on a part of the data distribution. However, these approaches have limitations, as they can be harmful to the model's performances or require unpractical access to the model's internals. Most importantly, previous approaches lack guarantee against false positives. This paper introduces data taggants, a novel non-backdoor dataset ownership verification technique. Our method uses pairs of out-of-distribution samples and random labels as secret keys, and leverages clean-label targeted data poisoning to subtly alter a dataset, so that models trained on it respond to the key samples with the corresponding key labels. The keys are built as to allow for statistical certificates with black-box access only to the model. We validate our approach through comprehensive and realistic experiments on ImageNet1k using ViT and ResNet models with state-of-the-art training recipes. Our findings demonstrate that data taggants can reliably make models trained on the protected dataset detectable with high confidence, without compromising validation accuracy, and demonstrates superiority over backdoor watermarking. Moreover, our method shows to be stealthy and robust against various defense mechanisms.

In this paper we introduce a new publicly available dataset for verification against textual sources, FEVER: Fact Extraction and VERification. It consists of 185,445 claims generated by altering sentences extracted from Wikipedia and subsequently verified without knowledge of the sentence they were derived from. The claims are classified as Supported, Refuted or NotEnoughInfo by annotators achieving 0.6841 in Fleiss kappa. For the first two classes, the annotators also recorded the sentence(s) forming the necessary evidence for their judgment. To characterize the challenge of the dataset presented, we develop a pipeline approach and compare it to suitably designed oracles. The best accuracy we achieve on labeling a claim accompanied by the correct evidence is 31.87%, while if we ignore the evidence we achieve 50.91%. Thus we believe that FEVER is a challenging testbed that will help stimulate progress on claim verification against textual sources.

Large language models demonstrate remarkable reasoning capabilities but often produce unreliable or incorrect responses. Existing verification methods are typically model-specific or domain-restricted, requiring significant computational resources and lacking scalability across diverse reasoning tasks. To address these limitations, we propose VerifiAgent, a unified verification agent that integrates two levels of verification: meta-verification, which assesses completeness and consistency in model responses, and tool-based adaptive verification, where VerifiAgent autonomously selects appropriate verification tools based on the reasoning type, including mathematical, logical, or commonsense reasoning. This adaptive approach ensures both efficiency and robustness across different verification scenarios. Experimental results show that VerifiAgent outperforms baseline verification methods (e.g., deductive verifier, backward verifier) among all reasoning tasks. Additionally, it can further enhance reasoning accuracy by leveraging feedback from verification results. VerifiAgent can also be effectively applied to inference scaling, achieving better results with fewer generated samples and costs compared to existing process reward models in the mathematical reasoning domain. Code is available at https://github.com/Jiuzhouh/VerifiAgent

In order to properly train a machine learning model, data must be properly collected. To guarantee a proper data collection, verifying that the collected data set holds certain properties is a possible solution. For example, guaranteeing that the data set contains samples across the whole input space, or that the data set is balanced w.r.t. different classes. We present a formal approach for verifying a set of arbitrarily stated properties over a data set. The proposed approach relies on the transformation of the data set into a first order logic formula, which can be later verified w.r.t. the different properties also stated in the same logic. A prototype tool, which uses the z3 solver, has been developed; the prototype can take as an input a set of properties stated in a formal language and formally verify a given data set w.r.t. to the given set of properties. Preliminary experimental results show the feasibility and performance of the proposed approach, and furthermore the flexibility for expressing properties of interest.

We contribute the largest publicly available dataset of naturally occurring factual claims for the purpose of automatic claim verification. It is collected from 26 fact checking websites in English, paired with textual sources and rich metadata, and labelled for veracity by human expert journalists. We present an in-depth analysis of the dataset, highlighting characteristics and challenges. Further, we present results for automatic veracity prediction, both with established baselines and with a novel method for joint ranking of evidence pages and predicting veracity that outperforms all baselines. Significant performance increases are achieved by encoding evidence, and by modelling metadata. Our best-performing model achieves a Macro F1 of 49.2%, showing that this is a challenging testbed for claim veracity prediction.

Precise recognition, editing, and generation of molecules are essential prerequisites for both chemists and AI systems tackling various chemical tasks. We present MolLangBench, a comprehensive benchmark designed to evaluate fundamental molecule-language interface tasks: language-prompted molecular structure recognition, editing, and generation. To ensure high-quality, unambiguous, and deterministic outputs, we construct the recognition tasks using automated cheminformatics tools, and curate editing and generation tasks through rigorous expert annotation and validation. MolLangBench supports the evaluation of models that interface language with different molecular representations, including linear strings, molecular images, and molecular graphs. Evaluations of state-of-the-art models reveal significant limitations: the strongest model (o3) achieves 79.2% and 78.5% accuracy on recognition and editing tasks, which are intuitively simple for humans, and performs even worse on the generation task, reaching only 29.0% accuracy. These results highlight the shortcomings of current AI systems in handling even preliminary molecular recognition and manipulation tasks. We hope MolLangBench will catalyze further research toward more effective and reliable AI systems for chemical applications.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in de novo peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

Food image segmentation is a critical and indispensible task for developing health-related applications such as estimating food calories and nutrients. Existing food image segmentation models are underperforming due to two reasons: (1) there is a lack of high quality food image datasets with fine-grained ingredient labels and pixel-wise location masks -- the existing datasets either carry coarse ingredient labels or are small in size; and (2) the complex appearance of food makes it difficult to localize and recognize ingredients in food images, e.g., the ingredients may overlap one another in the same image, and the identical ingredient may appear distinctly in different food images. In this work, we build a new food image dataset FoodSeg103 (and its extension FoodSeg154) containing 9,490 images. We annotate these images with 154 ingredient classes and each image has an average of 6 ingredient labels and pixel-wise masks. In addition, we propose a multi-modality pre-training approach called ReLeM that explicitly equips a segmentation model with rich and semantic food knowledge. In experiments, we use three popular semantic segmentation methods (i.e., Dilated Convolution based, Feature Pyramid based, and Vision Transformer based) as baselines, and evaluate them as well as ReLeM on our new datasets. We believe that the FoodSeg103 (and its extension FoodSeg154) and the pre-trained models using ReLeM can serve as a benchmark to facilitate future works on fine-grained food image understanding. We make all these datasets and methods public at https://xiongweiwu.github.io/foodseg103.html.

The obesity phenomenon, known as the heavy issue, is a leading cause of preventable chronic diseases worldwide. Traditional calorie estimation tools often rely on specific data formats or complex pipelines, limiting their practicality in real-world scenarios. Recently, vision-language models (VLMs) have excelled in understanding real-world contexts and enabling conversational interactions, making them ideal for downstream tasks such as ingredient analysis. However, applying VLMs to calorie estimation requires domain-specific data and alignment strategies. To this end, we curated CalData, a 330K image-text pair dataset tailored for ingredient recognition and calorie estimation, combining a large-scale recipe dataset with detailed nutritional instructions for robust vision-language training. Built upon this dataset, we present CaLoRAify, a novel VLM framework aligning ingredient recognition and calorie estimation via training with visual-text pairs. During inference, users only need a single monocular food image to estimate calories while retaining the flexibility of agent-based conversational interaction. With Low-rank Adaptation (LoRA) and Retrieve-augmented Generation (RAG) techniques, our system enhances the performance of foundational VLMs in the vertical domain of calorie estimation. Our code and data are fully open-sourced at https://github.com/KennyYao2001/16824-CaLORAify.

When should an AI system's answer be trusted? Formal proof assistants offer certainty but cannot reach most of the problem distribution; scalar LLM judges offer coverage but produce opaque scores that cannot be audited after the fact and are subject to the same coherence issues as any LLM. We present Theoria, a verification architecture that closes this gap. A candidate solution is rewritten into a sequence of typed state transitions, each licensed by an explicit justification, whether that be a citation, computation, or problem-given fact, and every transition is independently auditable. The foundational invariant is completeness of change: every difference between consecutive proof states must be accounted for, so hidden premises surface as unlicensed mutations rather than passing silently. On HLE-Verified Gold (185 text-only expert problems), Theoria certifies 105 at 91.4% strict precision (Wilson 95% CI [84.5%, 95.4%]). Every certification produces a human readable proof trace in which each step can be independently challenged. Holistic LLM judges achieve comparable precision at matched coverage but fail on different problems (Jaccard 0.14-0.36), making the approaches complementary. On 95 adversarial poisoned proofs across 15 domains, structured judges catch 94.7% versus 83.2% for holistic judging (p= 0.0017). The overall 11.5 pp gap concentrates in hidden premises (90.6% vs. 62.5%, a 28 pp difference) and fabricated citations (100% vs. 90%), the error classes where the formal analysis predicts an advantage; performance is identical on arithmetic and theorem-misapplication errors, where no advantage is predicted. On GPQA Diamond (n= 65), certified precision is 97.1% (Wilson CI [85.1%, 99.5%]).

This paper presents a smartphone-based imaging system capable of quantifying the concentration of an assortment of biological/chemical assay samples. The main objective is to construct an image database which characterizes the relationship between color information and concentrations of the biological/chemical assay sample. For this aim, a designated optical setup combined with image processing and data analyzing techniques was implemented. A series of experiments conducted on selected assays, including fluorescein, RNA Mango, homogenized milk and yeast have demonstrated that the proposed system estimates the concentration of fluorescent materials and colloidal mixtures comparable to currently used commercial and laboratory instruments. Furthermore, by utilizing the camera and computational power of smartphones, eventual development can be directed toward extremely compact, inexpensive and portable analysis and diagnostic systems which will allow experiments and tests to be conducted in remote or impoverished areas.

The overwhelming majority of molecules remains unexplored. This is mostly due to the sheer number of them, which prohibits any enumeration of chemical space, the set of all such molecules. In practice, only subsets of chemical space are considered, but those subsets exhibit substantial bias, prohibiting data-driven characterization of chemical space itself. In this work, we provide a method produce unbiased representative random samples of chemical space without enumeration of constituent molecules and to estimate the number of molecules in any custom chemical space. The approach is applicable to molecules which can be represented as graph and runs efficiently even for molecules of 30 atoms. We use it to estimate the representativeness of current databases with respect to their underlying chemical space and to establish a necessary criterion for a lower bound of database sizes to be representative of an underlying chemical space.

Chemistry literature synthesis often requires assembling specific findings scattered across many publications, yet existing literature-search systems primarily return ranked document lists. As a result, scientists and AI agents need to locate relevant information, verify their provenance, and assemble cross-paper answers manually. We present AskChem, a claim-centered infrastructure for cross-paper chemistry search. AskChem changes the unit of retrieval from the paper to the provenance-carrying claim: each paper is converted into atomic, typed claims, each grounded by a source DOI and a verbatim quote or an explicit evidence locator. Over this shared claim store, AskChem exposes complementary structures for search and synthesis: a stabilized faceted taxonomy for hierarchical retrieval and browsing, an evidence graph linking claims through relations, and an exploratory living taxonomy that situates indexed papers under scientific principles. AskChem currently indexes 2.4M claims from 147K papers and provides a web interface, as well as REST, SDK, and MCP access for AI agents. On AskChem-Bench, grounding a GPT-5.5 reader in AskChem yields 100% resolvable DOIs, compared with 88.3% without retrieval, and the highest citation density among five tested systems. AskChem is live at https://askchem.org.

Search-augmented LLMs increasingly mediate everyday consumer recommendations by retrieving live web content. This creates a new risk: generative recommenders may consume polluted web content, such as fake reviews and promotional pages crafted to mislead recommendations. We ask: to what extent do search-augmented LLMs become unwitting promoters of fake products when consuming polluted retrieval results? To answer this, we introduce FORGE (Fake Online Recommendations in Generative Environments), a benchmark for measuring fake-product promotion under controlled web-content pollution. Given an upstream search result, FORGE locally rewrites real products in retrieved web pages into fake ones to simulate web-content pollution, and measures how often the LLM recommends the fake product. FORGE covers 225 real-world products across 15 categories and 5 consumer scenarios. Across 12 commercial and open-weights LLMs, all models are vulnerable: a single polluted page yields fooled rates of up to 27%, while the full top-3 replacement raises this to 73.8%. Vulnerability varies substantially across categories, increasing when models lack stable prior knowledge of the relevant products. Reasoning does not mitigate this vulnerability; instead, it often generates spurious social proof to justify false recommendations. We evaluate three defenses: skepticism prompting and consensus filtering (over model priors or cross-document evidence). Skepticism can exacerbate vulnerability, much like reasoning, while filtering risks suppressing legitimate products. We release FORGE at https://github.com/leoluolol/forge-benchmark.

The AM-DeepSeek-R1-Distilled is a large-scale dataset with thinking traces for general reasoning tasks, composed of high-quality and challenging reasoning problems. These problems are collected from a multitude of open-source datasets, subjected to semantic deduplication and meticulous cleaning to eliminate test set contamination. All responses within the dataset are distilled from reasoning models (predominantly DeepSeek-R1) and have undergone rigorous verification procedures. Mathematical problems are validated by checking against reference answers, code problems are verified using test cases, and other tasks are evaluated with the aid of a reward model. The AM-Distill-Qwen-32B model, which was trained through only simple Supervised Fine-Tuning (SFT) using this batch of data, outperformed the DeepSeek-R1-Distill-Qwen-32B model on four benchmarks: AIME2024, MATH-500, GPQA-Diamond, and LiveCodeBench. Additionally, the AM-Distill-Qwen-72B model surpassed the DeepSeek-R1-Distill-Llama-70B model on all benchmarks as well. We are releasing these 1.4 million problems and their corresponding responses to the research community with the objective of fostering the development of powerful reasoning-oriented Large Language Models (LLMs). The dataset was published in https://huggingface.co/datasets/a-m-team/AM-DeepSeek-R1-Distilled-1.4M{https://huggingface.co/datasets/a-m-team/AM-DeepSeek-R1-Distilled-1.4M}.

The main issue with most evaluation schemes today is their "static" nature: the same problems are reused repeatedly, allowing for memorization, format exploitation, and eventual saturation. To measure genuine AI progress, we need evaluation that is robust by construction, not by post-hoc detection. In response, we propose VeRA (Verified Reasoning Data Augmentation), a framework that converts benchmark problems into executable specifications, comprising (i) a natural language template with placeholder slots, (ii) a coherent generator that samples valid configurations, and (iii) a deterministic verifier that validates parameters and calculates the corresponding correct answers for each configuration. From a single seed problem, VeRA automatically creates unlimited verified variants with reliable labels at near-zero marginal cost without human involvement. VeRA operates in two complementary modes. VeRA-E (equivalent) rewrites problems while keeping the underlying logic intact, useful for detecting memorization versus genuine reasoning. VeRA-H (hardened) systematically increases complexity while remaining verifiable, enabling reliable creation and labelling of fresh difficult tasks at the boundary of intelligence. Evaluating 16 frontier models with VeRA, we find: (i) VeRA-E improves evaluation quality and reveals contamination patterns. (ii) VeRA-H enables human-free generation of hard tasks with reliable labels. (iii) VeRA establishes verified benchmarks as a general paradigm. VeRA reconceptualizes benchmarks from static objects used until exhausted, to executable specifications generating fresh, verified instances on demand, enhancing robustness and cost-effectiveness for evaluation. With VeRA, we envision that evaluation in any verifiable domain can scale indefinitely without sacrificing label integrity. To stimulate future research, we have open-sourced all code and datasets.

Every year, millions of pounds of medicines remain unused in the U.S. and are subject to an in-home disposal, i.e., kept in medicine cabinets, flushed in toilet or thrown in regular trash. In-home disposal, however, can negatively impact the environment and public health. The drug take-back programs (drug take-backs) sponsored by the Drug Enforcement Administration (DEA) and its state and industry partners collect unused consumer medications and provide the best alternative to in-home disposal of medicines. However, the drug take-backs are expensive to operate and not widely available. In this paper, we show that artificial intelligence (AI) can be applied to drug take-backs to render them operationally more efficient. Since identification of any waste is crucial to a proper disposal, we showed that it is possible to accurately identify loose consumer medications solely based on the physical features and visual appearance. We have developed an automatic technique that uses deep neural networks and computer vision to identify and segregate solid medicines. We applied the technique to images of about one thousand loose pills and succeeded in correctly identifying the pills with an accuracy of 0.912 and top-5 accuracy of 0.984. We also showed that hazardous pills could be distinguished from non-hazardous pills within the dataset with an accuracy of 0.984. We believe that the power of artificial intelligence could be harnessed in products that would facilitate the operation of the drug take-backs more efficiently and help them become widely available throughout the country.

Metrics like FactScore and VeriScore that evaluate long-form factuality operate by decomposing an input response into atomic claims and then individually verifying each claim. While effective and interpretable, these methods incur numerous LLM calls and can take upwards of 100 seconds to evaluate a single response, limiting their practicality in large-scale evaluation and training scenarios. To address this, we propose VeriFastScore, which leverages synthetic data to fine-tune Llama3.1 8B for simultaneously extracting and verifying all verifiable claims within a given text based on evidence from Google Search. We show that this task cannot be solved via few-shot prompting with closed LLMs due to its complexity: the model receives ~4K tokens of evidence on average and needs to concurrently decompose claims, judge their verifiability, and verify them against noisy evidence. However, our fine-tuned VeriFastScore model demonstrates strong correlation with the original VeriScore pipeline at both the example level (r=0.80) and system level (r=0.94) while achieving an overall speedup of 6.6x (9.9x excluding evidence retrieval) over VeriScore. To facilitate future factuality research, we publicly release our VeriFastScore model and synthetic datasets.

Detecting an ingestion environment is an important aspect of monitoring dietary intake. It provides insightful information for dietary assessment. However, it is a challenging problem where human-based reviewing can be tedious, and algorithm-based review suffers from data imbalance and perceptual aliasing problems. To address these issues, we propose a neural network-based method with a two-stage training framework that tactfully combines fine-tuning and transfer learning techniques. Our method is evaluated on a newly collected dataset called ``UA Free Living Study", which uses an egocentric wearable camera, AIM-2 sensor, to simulate food consumption in free-living conditions. The proposed training framework is applied to common neural network backbones, combined with approaches in the general imbalanced classification field. Experimental results on the collected dataset show that our proposed method for automatic ingestion environment recognition successfully addresses the challenging data imbalance problem in the dataset and achieves a promising overall classification accuracy of 96.63%.

Personalized nutrition intervention for patients with multimorbidity is critical for improving health outcomes, yet remains challenging because it requires the simultaneous integration of heterogeneous clinical conditions, medications, and dietary guidelines. Single-agent large language models (LLMs) often suffer from context overload and attention dilution when processing such high-dimensional patient profiles. We introduce NutriOrion, a hierarchical multi-agent framework with a parallel-then-sequential reasoning topology. NutriOrion decomposes nutrition planning into specialized domain agents with isolated contexts to mitigate anchoring bias, followed by a conditional refinement stage. The framework includes a multi-objective prioritization algorithm to resolve conflicting dietary requirements and a safety constraint mechanism that injects pharmacological contraindications as hard negative constraints during synthesis, ensuring clinical validity by construction rather than post-hoc filtering. For clinical interoperability, NutriOrion maps synthesized insights into the ADIME standard and FHIR R4 resources. Evaluated on 330 stroke patients with multimorbidity, NutriOrion outperforms multiple baselines, including GPT-4.1 and alternative multi-agent architectures. It achieves a 12.1 percent drug-food interaction violation rate, demonstrates strong personalization with negative correlations (-0.26 to -0.35) between patient biomarkers and recommended risk nutrients, and yields clinically meaningful dietary improvements, including a 167 percent increase in fiber and a 27 percent increase in potassium, alongside reductions in sodium (9 percent) and sugars (12 percent).

This study presents a collection of physical devices and software services that fully automate Raman spectra measurements for liquid samples within a robotic facility. This method is applicable to various fields, with demonstrated efficacy in biotechnology, where Raman spectroscopy monitors substrates, metabolites, and product-related concentrations. Our system specifically measures 50 micro L samples using a liquid handling robot capable of taking 8 samples simultaneously. We record multiple Raman spectra for 10s each. Furthermore, our system takes around 20s for sample handling, cleaning, and preparation of the next measurement. All spectra and metadata are stored in a database, and we use a machine learning model to estimate concentrations from the spectra. This automated approach enables gathering spectra for various applications under uniform conditions in high-throughput fermentation processes, calibration procedures, and offline evaluations. This allows data to be combined to train sophisticated machine learning models with improved generalization. Consequently, we can develop accurate models more quickly for new applications by reusing data from prior applications, thereby reducing the need for extensive calibration data.

The success of drug discovery and development relies on the precise prediction of molecular activities and properties. While in silico molecular property prediction has shown remarkable potential, its use has been limited so far to assays for which large amounts of data are available. In this study, we use a fine-tuned large language model to integrate biological assays based on their textual information, coupled with Barlow Twins, a Siamese neural network using a novel self-supervised learning approach. This architecture uses both assay information and molecular fingerprints to extract the true molecular information. TwinBooster enables the prediction of properties of unseen bioassays and molecules by providing state-of-the-art zero-shot learning tasks. Remarkably, our artificial intelligence pipeline shows excellent performance on the FS-Mol benchmark. This breakthrough demonstrates the application of deep learning to critical property prediction tasks where data is typically scarce. By accelerating the early identification of active molecules in drug discovery and development, this method has the potential to help streamline the identification of novel therapeutics.

A chef's intuition about flavor, texture, and cultural identity represents tacit knowledge that is difficult to articulate yet central to culinary practice. We show that this knowledge is already encoded in FlavorGraph's 300-dimensional ingredient embeddings, trained on recipe cooccurrence and food chemistry, and that it can be systematically recovered. An LLM-augmented curation pipeline consolidates 6,653 raw FlavorGraph ingredients into 1,032 canonical entries, substantially strengthening the recoverable structure. We identify at least fifteen independently classifiable dimensions spanning taste, texture, geography, food processing, and culture.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

QDNA-ID is a trust-chain framework that links physical quantum behavior to digitally verified records. The system first executes standard quantum circuits with random shot patterns across different devices to generate entropy profiles and measurement data that reveal device-specific behavior. A Bell or CHSH test is then used to confirm that correlations originate from genuine non classical processes rather than classical simulation. The verified outcomes are converted into statistical fingerprints using entropy, divergence, and bias features to characterize each device. These features and metadata for device, session, and random seed parameters are digitally signed and time stamped to ensure integrity and traceability. Authenticated artifacts are stored in a hierarchical index for reproducible retrieval and long term auditing. A visualization and analytics interface monitors drift, policy enforcement, and device behavior logs. A machine learning engine tracks entropy drift, detects anomalies, and classifies devices based on evolving patterns. An external verification API supports independent recomputation of hashes, signatures, and CHSH evidence. QDNA-ID operates as a continuous feedback loop that maintains a persistent chain of trust for quantum computing environments.

Fact verification is essential for ensuring the reliability of LLM applications. In this study, we evaluate 12 pre-trained LLMs and one specialized fact-verifier, including frontier LLMs and open-weight reasoning LLMs, using a collection of examples from 14 fact-checking benchmarks. We share three findings intended to guide future development of more robust fact verifiers. First, we highlight the importance of addressing annotation errors and ambiguity in datasets, demonstrating that approximately 16\% of ambiguous or incorrectly labeled data substantially influences model rankings. Neglecting this issue may result in misleading conclusions during comparative evaluations, and we suggest using a systematic pipeline utilizing LLM-as-a-judge to help identify these issues at scale. Second, we discover that frontier LLMs with few-shot in-context examples, often overlooked in previous works, achieve top-tier performance. We therefore recommend future studies include comparisons with these simple yet highly effective baselines. Lastly, despite their effectiveness, frontier LLMs incur substantial costs, motivating the development of small, fine-tuned fact verifiers. We show that these small models still have room for improvement, particularly on instances that require complex reasoning. Encouragingly, we demonstrate that augmenting training with synthetic multi-hop reasoning data significantly enhances their capabilities in such instances. We release our code, model, and dataset at https://github.com/just1nseo/verifying-the-verifiers

Recent large language models often answer factual questions correctly. But users can't trust any given claim a model makes without fact-checking, because language models can hallucinate convincing nonsense. In this work we use reinforcement learning from human preferences (RLHP) to train "open-book" QA models that generate answers whilst also citing specific evidence for their claims, which aids in the appraisal of correctness. Supporting evidence is drawn from multiple documents found via a search engine, or from a single user-provided document. Our 280 billion parameter model, GopherCite, is able to produce answers with high quality supporting evidence and abstain from answering when unsure. We measure the performance of GopherCite by conducting human evaluation of answers to questions in a subset of the NaturalQuestions and ELI5 datasets. The model's response is found to be high-quality 80\% of the time on this Natural Questions subset, and 67\% of the time on the ELI5 subset. Abstaining from the third of questions for which it is most unsure improves performance to 90\% and 80\% respectively, approaching human baselines. However, analysis on the adversarial TruthfulQA dataset shows why citation is only one part of an overall strategy for safety and trustworthiness: not all claims supported by evidence are true.

Large language models (LLMs) are now available in various sizes and configurations from cloud API providers. While this diversity offers a broad spectrum of choices, effectively leveraging the options to optimize computational cost and performance remains challenging. In this work, we present AutoMix, an approach that strategically routes queries to larger LMs, based on the approximate correctness of outputs from a smaller LM. Central to AutoMix is a few-shot self-verification mechanism, which estimates the reliability of its own outputs without requiring training. Given that verifications can be noisy, we employ a meta verifier in AutoMix to refine the accuracy of these assessments. Our experiments using LLAMA2-13/70B, on five context-grounded reasoning datasets demonstrate that AutoMix surpasses established baselines, improving the incremental benefit per cost by up to 89%. Our code and data are available at https://github.com/automix-llm/automix.

The pretraining data mixture of Large Language Models (LLMs) constitutes their "digital DNA", shaping model behaviors, capabilities, and failure modes. Yet this composition is rarely disclosed, making post-hoc auditing of data combination or provenance difficult. In this work, we formalize Data Mixture Surgery (DMS): given only generated text from a target LLM, estimate the domain-level distribution of its pretraining corpus under a predefined taxonomy. We propose LLMSurgeon, a strong framework that casts DMS as an inverse problem under the label-shift assumption. Rather than directly aggregating classifier outputs, LLMSurgeon estimates a calibrated soft confusion matrix and solves a constrained inverse problem to correct systematic domain confusion and recover the latent mixture prior. To evaluate, we introduce LLMScan, a recipe-verifiable evaluation suite built from open-source LLMs with transparent pretraining mixtures. Across LLMScan, LLMSurgeon recovers domain mixtures with high fidelity under fixed protocols. Our work presents a practical, post-hoc approach for auditing the digital DNA of foundation models without access to their training data.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

Current research on the Decompose-Then-Verify paradigm for evaluating the factuality of long-form text typically treats decomposition and verification in isolation, overlooking their interactions and potential misalignment. We find that existing decomposition policies, typically hand-crafted demonstrations, do not align well with downstream verifiers in terms of atomicity -- a novel metric quantifying information density -- leading to suboptimal verification results. We formulate finding the optimal decomposition policy for optimal verification as a bilevel optimization problem. To approximate a solution for this strongly NP-hard problem, we propose dynamic decomposition, a reinforcement learning framework that leverages verifier feedback to learn a policy for dynamically decomposing claims to verifier-preferred atomicity. Experimental results show that dynamic decomposition outperforms existing decomposition policies, improving verification confidence by 0.07 and accuracy by 0.12 (on a 0-1 scale) on average across varying verifiers, datasets, and atomcities of input claims.

In an era of increasing pressure to achieve sustainable agriculture, the optimization of livestock feed for enhancing yield and minimizing environmental impact is a paramount objective. This study presents a pioneering approach towards this goal, using rumen microbiome data to predict the efficacy of feed additives in dairy cattle. We collected an extensive dataset that includes methane emissions from 2,190 Holstein cows distributed across 34 distinct sites. The cows were divided into control and experimental groups in a double-blind, unbiased manner, accounting for variables such as age, days in lactation, and average milk yield. The experimental groups were administered one of four leading commercial feed additives: Agolin, Kexxtone, Allimax, and Relyon. Methane emissions were measured individually both before the administration of additives and over a subsequent 12-week period. To develop our predictive model for additive efficacy, rumen microbiome samples were collected from 510 cows from the same herds prior to the study's onset. These samples underwent deep metagenomic shotgun sequencing, yielding an average of 15.7 million reads per sample. Utilizing innovative artificial intelligence techniques we successfully estimated the efficacy of these feed additives across different farms. The model's robustness was further confirmed through validation with independent cohorts, affirming its generalizability and reliability. Our results underscore the transformative capability of using targeted feed additive strategies to both optimize dairy yield and milk composition, and to significantly reduce methane emissions. Specifically, our predictive model demonstrates a scenario where its application could guide the assignment of additives to farms where they are most effective. In doing so, we could achieve an average potential reduction of over 27\% in overall emissions.

Verifying the success of computer use agent (CUA) trajectories is a critical challenge: without reliable verification, neither evaluation nor training signal can be trusted. In this paper, we present lessons learned from building a best-in-class verifier for web tasks we call the Universal Verifier. We design the Universal Verifier around four key principles: 1) constructing rubrics with meaningful, non-overlapping criteria to reduce noise; 2) separating process and outcome rewards that yield complementary signals, capturing cases where an agent follows the right steps but gets blocked or succeeds through an unexpected path; 3) distinguishing between controllable and uncontrollable failures scored via a cascading-error-free strategy for finer-grained failure understanding; and 4) a divide-and-conquer context management scheme that attends to all screenshots in a trajectory, improving reliability on longer task horizons. We validate these findings on CUAVerifierBench, a new set of CUA trajectories with both process and outcome human labels, showing that our Universal Verifier agrees with humans as often as humans agree with each other. We report a reduction in false positive rates to near zero compared to baselines like WebVoyager (geq 45\%) and WebJudge (geq 22\%). We emphasize that these gains stem from the cumulative effect of the design choices above. We also find that an auto-research agent achieves 70\% of expert quality in 5\% of the time, but fails to discover all strategies required to replicate the Universal Verifier. We open-source our Universal Verifier system along with CUAVerifierBench; available at https://github.com/microsoft/fara.

Noise plagues many numerical datasets, where the recorded values in the data may fail to match the true underlying values due to reasons including: erroneous sensors, data entry/processing mistakes, or imperfect human estimates. We consider general regression settings with covariates and a potentially corrupted response whose observed values may contain errors. By accounting for various uncertainties, we introduced veracity scores that distinguish between genuine errors and natural data fluctuations, conditioned on the available covariate information in the dataset. We propose a simple yet efficient filtering procedure for eliminating potential errors, and establish theoretical guarantees for our method. We also contribute a new error detection benchmark involving 5 regression datasets with real-world numerical errors (for which the true values are also known). In this benchmark and additional simulation studies, our method identifies incorrect values with better precision/recall than other approaches.

Worldwide, in 2014, more than 1.9 billion adults, 18 years and older, were overweight. Of these, over 600 million were obese. Accurately documenting dietary caloric intake is crucial to manage weight loss, but also presents challenges because most of the current methods for dietary assessment must rely on memory to recall foods eaten. The ultimate goal of our research is to develop computer-aided technical solutions to enhance and improve the accuracy of current measurements of dietary intake. Our proposed system in this paper aims to improve the accuracy of dietary assessment by analyzing the food images captured by mobile devices (e.g., smartphone). The key technique innovation in this paper is the deep learning-based food image recognition algorithms. Substantial research has demonstrated that digital imaging accurately estimates dietary intake in many environments and it has many advantages over other methods. However, how to derive the food information (e.g., food type and portion size) from food image effectively and efficiently remains a challenging and open research problem. We propose a new Convolutional Neural Network (CNN)-based food image recognition algorithm to address this problem. We applied our proposed approach to two real-world food image data sets (UEC-256 and Food-101) and achieved impressive results. To the best of our knowledge, these results outperformed all other reported work using these two data sets. Our experiments have demonstrated that the proposed approach is a promising solution for addressing the food image recognition problem. Our future work includes further improving the performance of the algorithms and integrating our system into a real-world mobile and cloud computing-based system to enhance the accuracy of current measurements of dietary intake.

Scientific research relies on accurate citation for attribution and integrity, yet large language models (LLMs) introduce a new risk: fabricated references that appear plausible but correspond to no real publications. Such hallucinated citations have already been observed in submissions and accepted papers at major machine learning venues, exposing vulnerabilities in peer review. Meanwhile, rapidly growing reference lists make manual verification impractical, and existing automated tools remain fragile to noisy and heterogeneous citation formats and lack standardized evaluation. We present the first comprehensive benchmark and detection framework for hallucinated citations in scientific writing. Our multi-agent verification pipeline decomposes citation checking into claim extraction, evidence retrieval, passage matching, reasoning, and calibrated judgment to assess whether a cited source truly supports its claim. We construct a large-scale human-validated dataset across domains and define unified metrics for citation faithfulness and evidence alignment. Experiments with state-of-the-art LLMs reveal substantial citation errors and show that our framework significantly outperforms prior methods in both accuracy and interpretability. This work provides the first scalable infrastructure for auditing citations in the LLM era and practical tools to improve the trustworthiness of scientific references.

Fact verification aims to automatically probe the veracity of a claim based on several pieces of evidence. Existing works are always engaging in the accuracy improvement, let alone the explainability, a critical capability of fact verification system. Constructing an explainable fact verification system in a complex multi-hop scenario is consistently impeded by the absence of a relevant high-quality dataset. Previous dataset either suffer from excessive simplification or fail to incorporate essential considerations for explainability. To address this, we present EX-FEVER, a pioneering dataset for multi-hop explainable fact verification. With over 60,000 claims involving 2-hop and 3-hop reasoning, each is created by summarizing and modifying information from hyperlinked Wikipedia documents. Each instance is accompanied by a veracity label and an explanation that outlines the reasoning path supporting the veracity classification. Additionally, we demonstrate a novel baseline system on our EX-FEVER dataset, showcasing document retrieval, explanation generation, and claim verification and observe that existing fact verification models trained on previous datasets struggle to perform well on our dataset. Furthermore, we highlight the potential of utilizing Large Language Models in the fact verification task. We hope our dataset could make a significant contribution by providing ample opportunities to explore the integration of natural language explanations in the domain of fact verification.

Current approaches to chemical map generation from hyperspectral images are based on models such as partial least squares (PLS) regression, generating pixel-wise predictions that do not consider spatial context and suffer from a high degree of noise. This study proposes an end-to-end deep learning approach using a modified version of U-Net and a custom loss function to directly obtain chemical maps from hyperspectral images, skipping all intermediate steps required for traditional pixel-wise analysis. We compare the U-Net with the traditional PLS regression on a real dataset of pork belly samples with associated mean fat reference values. The U-Net obtains a test set root mean squared error of between 9% and 13% lower than that of PLS regression on the task of mean fat prediction. At the same time, U-Net generates fine detail chemical maps where 99.91% of the variance is spatially correlated. Conversely, only 2.53% of the variance in the PLS-generated chemical maps is spatially correlated, indicating that each pixel-wise prediction is largely independent of neighboring pixels. Additionally, while the PLS-generated chemical maps contain predictions far beyond the physically possible range of 0-100%, U-Net learns to stay inside this range. Thus, the findings of this study indicate that U-Net is superior to PLS for chemical map generation.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Maintaining a balanced diet is essential for overall health, yet many individuals struggle with meal planning due to nutritional complexity, time constraints, and lack of dietary knowledge. Personalized food recommendations can help address these challenges by tailoring meal plans to individual preferences, habits, and dietary restrictions. However, existing dietary recommendation systems often lack adaptability, fail to consider real-world constraints such as food ingredient availability, and require extensive user input, making them impractical for sustainable and scalable daily use. To address these limitations, we introduce NutriGen, a framework based on large language models (LLM) designed to generate personalized meal plans that align with user-defined dietary preferences and constraints. By building a personalized nutrition database and leveraging prompt engineering, our approach enables LLMs to incorporate reliable nutritional references like the USDA nutrition database while maintaining flexibility and ease-of-use. We demonstrate that LLMs have strong potential in generating accurate and user-friendly food recommendations, addressing key limitations in existing dietary recommendation systems by providing structured, practical, and scalable meal plans. Our evaluation shows that Llama 3.1 8B and GPT-3.5 Turbo achieve the lowest percentage errors of 1.55\% and 3.68\%, respectively, producing meal plans that closely align with user-defined caloric targets while minimizing deviation and improving precision. Additionally, we compared the performance of DeepSeek V3 against several established models to evaluate its potential in personalized nutrition planning.

In this work, we propose a novel method named Automated Process-Supervised Verifier (\textsc{AutoPSV}) to enhance the reasoning capabilities of large language models (LLMs) by automatically annotating the reasoning steps. AutoPSV begins by training a verification model on the correctness of final answers, enabling it to generate automatic process annotations. This verification model assigns a confidence score to each reasoning step, indicating the probability of arriving at the correct final answer from that point onward. We detect relative changes in the verification's confidence scores across reasoning steps to automatically annotate the reasoning process, enabling error detection even in scenarios where ground truth answers are unavailable. This alleviates the need for numerous manual annotations or the high computational costs associated with model-induced annotation approaches. We experimentally validate that the step-level confidence changes learned by the verification model trained on the final answer correctness can effectively identify errors in the reasoning steps. We demonstrate that the verification model, when trained on process annotations generated by AutoPSV, exhibits improved performance in selecting correct answers from multiple LLM-generated outputs. Notably, we achieve substantial improvements across five datasets in mathematics and commonsense reasoning. The source code of AutoPSV is available at https://github.com/rookie-joe/AutoPSV.

Claim verification is critical for enhancing digital literacy. However, the state-of-the-art single-LLM methods struggle with complex claim verification that involves multi-faceted evidences. Inspired by real-world fact-checking practices, we propose DebateCV, the first claim verification framework that adopts a debate-driven methodology using multiple LLM agents. In our framework, two Debaters take opposing stances on a claim and engage in multi-round argumentation, while a Moderator evaluates the arguments and renders a verdict with justifications. To further improve the performance of the Moderator, we introduce a novel post-training strategy that leverages synthetic debate data generated by the zero-shot DebateCV, effectively addressing the scarcity of real-world debate-driven claim verification data. Experimental results show that our method outperforms existing claim verification methods under varying levels of evidence quality. Our code and dataset are publicly available at https://anonymous.4open.science/r/DebateCV-6781.

This research proposes a new recommender system algorithm for online grocery shopping. The algorithm is based on the perspective that, since the grocery items are usually bought in bulk, a grocery recommender system should be capable of recommending the items in bulk. The algorithm figures out the possible dishes a user may cook based on the items added to the basket and recommends the ingredients accordingly. Our algorithm does not depend on the user ratings. Customers usually do not have the patience to rate the groceries they purchase. Therefore, algorithms that are not dependent on user ratings need to be designed. Instead of using a brute force search, this algorithm limits the search space to a set of only a few probably food categories. Each food category consists of several food subcategories. For example, "fried rice" and "biryani" are food subcategories that belong to the food category "rice". For each food category, items are ranked according to how well they can differentiate a food subcategory. To each food subcategory in the activated search space, this algorithm attaches a score. The score is calculated based on the rank of the items added to the basket. Once the score exceeds a threshold value, its corresponding subcategory gets activated. The algorithm then uses a basket-to-recipe similarity measure to identify the best recipe matches within the activated subcategories only. This reduces the search space to a great extent. We may argue that this algorithm is similar to the content-based recommender system in some sense, but it does not suffer from the limitations like limited content, over-specialization, or the new user problem.

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in molecular chemistry. This study presents the most extensive comparison of such models to date, evaluating 25 models across 25 datasets. Under a fair comparison framework, we assess models spanning various modalities, architectures, and pretraining strategies. Using a dedicated hierarchical Bayesian statistical testing model, we arrive at a surprising result: nearly all neural models show negligible or no improvement over the baseline ECFP molecular fingerprint. Only the CLAMP model, which is also based on molecular fingerprints, performs statistically significantly better than the alternatives. These findings raise concerns about the evaluation rigor in existing studies. We discuss potential causes, propose solutions, and offer practical recommendations.

Medical knowledge is context-dependent and requires consistent reasoning across various natural language expressions of semantically equivalent phrases. This is particularly crucial for drug names, where patients often use brand names like Advil or Tylenol instead of their generic equivalents. To study this, we create a new robustness dataset, RABBITS, to evaluate performance differences on medical benchmarks after swapping brand and generic drug names using physician expert annotations. We assess both open-source and API-based LLMs on MedQA and MedMCQA, revealing a consistent performance drop ranging from 1-10\%. Furthermore, we identify a potential source of this fragility as the contamination of test data in widely used pre-training datasets. All code is accessible at https://github.com/BittermanLab/RABBITS, and a HuggingFace leaderboard is available at https://huggingface.co/spaces/AIM-Harvard/rabbits-leaderboard.

It is important that consumers and regulators can verify the provenance of large neural models to evaluate their capabilities and risks. We introduce the concept of a "Proof-of-Training-Data": any protocol that allows a model trainer to convince a Verifier of the training data that produced a set of model weights. Such protocols could verify the amount and kind of data and compute used to train the model, including whether it was trained on specific harmful or beneficial data sources. We explore efficient verification strategies for Proof-of-Training-Data that are compatible with most current large-model training procedures. These include a method for the model-trainer to verifiably pre-commit to a random seed used in training, and a method that exploits models' tendency to temporarily overfit to training data in order to detect whether a given data-point was included in training. We show experimentally that our verification procedures can catch a wide variety of attacks, including all known attacks from the Proof-of-Learning literature.

Optical chemical structure recognition (OCSR) translates molecular images into machine-readable representations like SMILES strings or molecular graphs, but remains challenging in real-world documents due to inexhaustible variations in chemical structures, shorthand conventions, and visual noise. Most existing deep-learning-based approaches rely on teacher forcing with token-level Maximum Likelihood Estimation (MLE). This training paradigm suffers from exposure bias, as models are trained under ground-truth prefixes but must condition on their own previous predictions during inference. Moreover, token-level MLE objectives hinder the optimization towards molecular-level evaluation criteria such as chemical validity and structural similarity. Here we introduce Minimum Risk Training (MRT) to OCSR and propose COMO (Closed-loop Optical Molecule recOgnition), a closed-loop framework that mitigates exposure bias by directly optimizing over molecule-level, non-differentiable objectives, by iteratively sampling and evaluating the model's own predictions. Experiments on ten benchmarks including synthetic and real-world chemical diagrams from patent and scientific literature demonstrate that COMO substantially outperforms existing rule-based and learning-based methods with less training data. Ablation studies further show that MRT is architecture-agnostic, demonstrating its potential for broad application to end-to-end OCSR systems.

Same-model self-verification, prompting a model to audit its own predicted answer, is a plausible confidence signal for selective prediction, but its practical value remains unclear once strong likelihood-based baselines are taken seriously. We evaluate self-verification against two such baselines, LL-AVG and LL-SUM, on ARC-Challenge and TruthfulQA-MC across multiple model families, scales, and prompt variants. We measure not only correctness ranking, but also abstention quality through AURC and operating-point analyses. The results are sharply task- and model-dependent. On ARC-Challenge, self-verification substantially improves over LL-AVG for Phi-2 and the Qwen models, with the largest gains appearing in Qwen-7B. On TruthfulQA-MC, however, the signal is less reliable: smaller models can become prompt-sensitive, DeepSeek-R1-Distill-8B degrades relative to LL-AVG, and LL-SUM often remains the stronger practical baseline. We therefore do not treat self-verification as a general-purpose uncertainty estimator. In this setting, it is better understood as a conditional confidence signal whose value depends on task type, model family, prompt formulation, and, crucially, the baseline it must beat.

GNNs and chemical fingerprints are the predominant approaches to representing molecules for property prediction. However, in NLP, transformers have become the de-facto standard for representation learning thanks to their strong downstream task transfer. In parallel, the software ecosystem around transformers is maturing rapidly, with libraries like HuggingFace and BertViz enabling streamlined training and introspection. In this work, we make one of the first attempts to systematically evaluate transformers on molecular property prediction tasks via our ChemBERTa model. ChemBERTa scales well with pretraining dataset size, offering competitive downstream performance on MoleculeNet and useful attention-based visualization modalities. Our results suggest that transformers offer a promising avenue of future work for molecular representation learning and property prediction. To facilitate these efforts, we release a curated dataset of 77M SMILES from PubChem suitable for large-scale self-supervised pretraining.

Fact-checking long-form text is challenging, and it is therefore common practice to break it down into multiple atomic claims. The typical approach to fact-checking these atomic claims involves retrieving a fixed number of pieces of evidence, followed by a verification step. However, this method is usually not cost-effective, as it underutilizes the verification model's internal knowledge of the claim and fails to replicate the iterative reasoning process in human search strategies. To address these limitations, we propose FIRE, a novel agent-based framework that integrates evidence retrieval and claim verification in an iterative manner. Specifically, FIRE employs a unified mechanism to decide whether to provide a final answer or generate a subsequent search query, based on its confidence in the current judgment. We compare FIRE with other strong fact-checking frameworks and find that it achieves slightly better performance while reducing large language model (LLM) costs by an average of 7.6 times and search costs by 16.5 times. These results indicate that FIRE holds promise for application in large-scale fact-checking operations. Our code is available at https://github.com/mbzuai-nlp/fire.git.

Answer verification is crucial not only for evaluating large language models (LLMs) by matching their unstructured outputs against standard answers, but also serves as the reward model to guide LLM optimization. Most evaluation frameworks rely on regularized matching or employ general LLMs for answer verification, which demands extensive, repetitive customization for regex rules or evaluation prompts. Two fundamental limitations persist in current methodologies: 1) the absence of comprehensive benchmarks that systematically evaluate verification capabilities across different LLMs; and 2) the nascent stage of verifier development, where existing approaches lack both the robustness to handle complex edge cases and the generalizability across different domains. In this work, we develop CompassVerifier, an accurate and robust lightweight verifier model for evaluation and outcome reward. It demonstrates multi-domain competency spanning math, knowledge, and diverse reasoning tasks, with the capability to process various answer types, including multi-subproblems, formulas, and sequence answers, while effectively identifying abnormal/invalid responses. We introduce VerifierBench benchmark comprising model outputs collected from multiple data sources, augmented through manual analysis of metaerror patterns to enhance CompassVerifier. We anticipate that CompassVerifier and VerifierBench will facilitate answer verification, evaluation protocols, and reinforcement learning research. Code and dataset are available at https://github.com/open-compass/CompassVerifier.

Identifying prescription medications is a frequent task for patients and medical professionals; however, this is an error-prone task as many pills have similar appearances (e.g. white round pills), which increases the risk of medication errors. In this paper, we introduce ePillID, the largest public benchmark on pill image recognition, composed of 13k images representing 9804 appearance classes (two sides for 4902 pill types). For most of the appearance classes, there exists only one reference image, making it a challenging low-shot recognition setting. We present our experimental setup and evaluation results of various baseline models on the benchmark. The best baseline using a multi-head metric-learning approach with bilinear features performed remarkably well; however, our error analysis suggests that they still fail to distinguish particularly confusing classes. The code and data are available at https://github.com/usuyama/ePillID-benchmark.