Christophe Révillion

Artadji Attoumane

Annelise Tran

come

Introduction

Material and methods

Classification results : Land cover and webmapping interface

. We used SPOT 5 satellite images (© CNES, Distribution Airbus Defense and Space) acquired between July 2013 and July 2014. The SPOT5 images used are a pair of images for each island with a panchromatic image at 2.5m resolution and a multispectral image with 4 channels (green, red, PRI and MIR) at 10m resolution.

All additional vector data come from the OSM database. These are the main roads (key=highway; values=primary; secondary; tertiary; residential) and agricultural zoning (landuse=farmland). On these agricultural areas, additional tags are used when it comes to sugar cane (crop=sugarcane) which is a dominant crop on the two largest islands studied, Réunion Island and Mauritius.

The classification algorithm is a hierarchical object-based image analysis method, implemented in eCognition® software. Each object is described by attributes related to its reflectance, texture and geometry. Our hierarchical classification process is organized into two levels. A first level of segmentation with the objective of delineating agricultural and natural objects and a second level of segmentation with a smaller scale factor to extract urban areas, isolated buildings and main roads.

All the methodology is described in a paper in the Data journal (Revillion et al., 2019). A Land Use/Land cover on the small Indian Ocean islands, an example of its use with the study of vector-borne diseases

Applications in health research

We classified the LULC of these tropical islands into 11 major classes. Helped by a good knowledge of the field the classification reached a good general accuracy with a kappa of 0.85. This high resolution land cover is available on a web portal (http://homisland.seas-oi.org/) to ensure a wider distribution to researchers and thematicians using land cover information.

Christophe Révillion (1) , Artadji Attoumane (2) , Annelise Tran (3) , Vincent Herbreteau 7.

8.

For such analysis, we use the land cover map to calculate landscape indicators (or landscape metrics). The simplest are the minimum distances between each animal and each land cover class. Despite their simplicity, they provide valuable information when it comes to interpreting, for proximity of a species to humans or to wetlands.

The analysis can also define the immediate environment of each animal within a determined radius (a buffer zone around the capture points). Each landscape element within this radius is called a patch, and the calculations focus on their surface areas, contours and shapes. The nature of the landscape (built-up, forest, agricultural, etc.), its consistency or diversity, its fragmentation and the structure of its elements can be defined from this. One metric commonly used to describe landscape fragmentation is edge density, which is calculated by measuring the length of the contours in all the patches within a buffer zone and dividing this by the surface area.

Land cover analysis provides very useful information for characterizing the environment of infectious diseases, which may be the habitat of vector species (such as mosquitoes, rodents) or the place of exposure to a disease. Studies can be based on animal samples precisely localized with a GPS, or on the location of people by their address.

Use of landscape metrics to compare rodent populations in Reunion Island

Two landscape metrics for comparing positive and negative rodents to leptospirosis, with 4 species (Rattus rattus, Rattus norvegicus, Mus musculus and Suncus murinus), in Reunion island 6.

4.

Land use/land cover (LULC) data are key information to understand the relationships between humans and their environment. So, Many small islands are located in the southwestern Indian Ocean. These islands have their own environmental specificities and very fragmented landscapes. Generic LULC products developed from low and medium resolution satellite images are not suitable for studying these small territories.

When studying the geography and ecology of vector-borne diseases in small islands, high spatial resolution is also fundamental to measure the favorable or unfavorable conditions to the presence of the vectors and pathogens or to characterize the physical environmental of the people who have contracted a disease (Tran et al., 2016). Also, the analysis of satellite imagery for use in the health field is limited by the technical difficulties inherent to remote sensing and access to remotely-sensed products.

To overcome this need, we realized a homogeneous high resolution land cover mapping of these small islands by analysing SPOT 5 satellite images. Our objective was to provide an easy accessible product with a common typology in order to allow comparative studies on several islands.

Modelling Aedes albopictus mosquito population dynamics in Mauritius

The 'Tiger' mosquito, Aedes albopictus, is a vector of viruses responsible for Chikungunya and dengue fever.

  Tran A., Kassié D. & Herbreteau V. (2016). Applications of Remote Sensing to the Epidemiology of Infectious Diseases: Some Examples. In: Land Surface Remote Sensing: Environment and Risks (eds. Baghdadi N & Zribi M). Elsevier, pp. 295-315. Révillion, C., Attoumane, A. & Herbreteau, V. (2019) Homisland-IO: Homogeneous Land Use/Land Cover over the Small Islands of the Indian Ocean. Data, 4, 82.

  La Réunion, UMR 228 Espace-Dev (IRD, UA, UG, UM, UR), 40 Avenue de Soweto 97410 Saint-Pierre, La Réunion, France 2 Institut de Recherche pour le Développement, UMR 228 Espace-Dev (IRD, UA, UG, UM, UR), 40 Avenue de Soweto 97410 Saint-Pierre, La Réunion, France 3 CIRAD, UMR TETIS (AgroParisTech, Cirad, CNRS, Irstea), 2 Rue Maxime Rivière, Sainte-Clotilde 97491, La Réunion, France 4 Institut de Recherche pour le Développement, UMR 228 Espace-Dev (IRD, UA, UG, UM, UR), 5 Preah Monivong Blvd (93), Phnom Penh 12100, Cambodge3.5.

  Calculation of the minimum distances from one animal to each land cover class Characterization of the surrounding landscape (heterogeneous / homogeneous)

For

  This simulation tool is adapted for supporting decisionmaking in the surveillance and control of mosquitoborne diseases. rainfall data. Land cover information is used to estimate the environmental suitability for Aedes albopictus breeding sites (from built-up areas classes) for each 1km² square cell.

Acknowledgements

The authors would like to thank :

The SEAS-OI platform for the distribution of SPOT5 images;

The 3Liz (3liz.com) company for its remarkable free and opensource webmapping tool, lizmap for QGIS.

Funding -LeptOI project (FEDER POCT 31569); -ISSE-Mayotte project (French Ministry of Outremer, MOM 2012); -IRD for the funding of a PhD thesis (ARTS) in the Comoros; -TROI project (FEDER InterReg V).


domain: info sde

text:
Hervé Goëau
email: herve.goeau@cirad.fr

Stefan Kahl

Hervé Glotin
email: herve.glotin@univ-tln.fr

Robert Planqué

Willem-Pier Vellinga

Alexis Joly
email: alexis.joly@inria.fr

Overview of BirdCLEF 2018: monospecies vs. soundscape bird identification

Keywords: LifeCLEF, bird, song, call, species, retrieval, audio, collection, identification, fine-grained classification, evaluation, benchmark, bioacoustics, ecological monitoring

The BirdCLEF challenge offers a large-scale proving ground for system-oriented evaluation of bird species identification based on audio recordings of their sounds. One of its strengths is that it uses data collected through Xeno-canto, the worldwide community of bird sound recordists. This ensures that BirdCLEF is close to the conditions of realworld application, in particular with regard to the number of species in the training set (1500). Two main scenarios are evaluated: (i) the identification of a particular bird species in a recording, and (ii), the recognition of all species vocalising in a long sequence (up to one hour) of raw soundscapes that can contain tens of birds singing more or less simultaneously. This paper reports an overview of the systems developed by the six participating research groups, the methodology of the evaluation of their performance, and an analysis and discussion of the results obtained.

Introduction

Accurate knowledge of the identity, the geographic distribution and the evolution of bird species is essential for a sustainable development of humanity as well as for biodiversity conservation. The general public, especially so-called "birders" as well as professionals such as park rangers, ecological consultants and of course ornithologists are potential users of an automated bird sound identifying system, typically in the context of wider initiatives related to ecological surveillance or biodiversity conservation. The BirdCLEF challenge evaluates the state-of-the-art of audio-based bird identification systems at a very large scale. Before BirdCLEF started in 2014, three previous initiatives on the evaluation of acoustic bird species identification took place, including two from the SABIOD 6 group [START_REF] Glotin | Overview of the 2nd challenge on acoustic bird classification[END_REF][START_REF] Glotin | Bioacoustic challenges in icml4b[END_REF][START_REF] Briggs | The 9th mlsp competition: New methods for acoustic classification of multiple simultaneous bird species in noisy environment[END_REF]. In collaboration with the organizers of these previous challenges, the BirdCLEF 2014BirdCLEF , 2015BirdCLEF , 2016 and 2017 challenges went one step further by (i) significantly increasing the species number by an order of magnitude, (ii) working on real-world social data built from thousands of recordists, and (iii) moving to a more usage-driven and system-oriented benchmark by allowing the use of metadata and defining information retrieval oriented metrics. Overall, these tasks were much more difficult than previous benchmarks because of the higher confusion risk between the classes, the higher background noise and the higher diversity in the acquisition conditions (different recording devices, contexts diversity, etc.). The main novelty of the 2017 edition of the challenge with respect to the previous years was the inclusion of soundscape recordings containing time-coded bird species annotations. Usually xeno-canto recordings focus on a single foreground species and result from using mono-directional recording devices. Soundscapes, on the other hand, are generally based on omnidirectional recording devices that monitor a specific environment continuously over a long period. This new kind of recording reflects (possibly crowdsourced) passive acoustic monitoring scenarios that could soon augment the number of collected sound recordings by several orders of magnitude. For the 2018-th edition of the BirdCLEF challenge, we continued evaluating both scenarios as two different tasks: (i) the identification of a particular bird specimen in a recording of it, and (ii), the recognition of all specimens singing in a long sequence (up to one hour) of raw soundscapes that can contain tens of birds singing simultaneously. In this paper, we report the methodology of the conducted evaluation as well as an analysis and a discussion of the results achieved by the six participating groups.

Tasks description

Task1: monospecies (monophone) recordings

The goal of the task is to identify the species of the most audible bird (i.e. the one that was intended to be recorded) in each of the provided test recordings. Therefore, the evaluated systems have to return a ranked list of possible species for each of the 12,347 test recordings. Each prediction item (i.e. each line of the file to be submitted) has to respect the following format: <MediaId;ClassId;Probability;Rank> Each participating group was allowed to submit up to 4 run files providing the predictions made from 4 different methods. The use of any of the provided metadata complementary to the audio content was authorized. It was also allowed to use any external training data but at the condition that (i) the experiment is entirely re-producible, i.e. that the used external resource is clearly referenced and accessible to any other research group in the world, (ii) participants submit at least one run without external training data so that we can study the contribution of such resources, (iii) the additional resource does not contain any of the test observations. It was in particular strictly forbidden to crawl training data from: www.xeno-canto.org.

The dataset was the same as the one used for BirdCLEF 2017 [START_REF] Goëau | Lifeclef bird identification task 2017[END_REF], mostly based on the contributions of the Xeno-Canto network. The training set contains 36,496 recordings covering 1500 species of central and south America (the largest bioacoustic dataset in the literature). It has a massive class imbalance with a minimum of four recordings for Laniocera rufescens and a maximum of 160 recordings for Henicorhina leucophrys. Recordings are associated to various metadata such as the type of sound (call, song, alarm, flight, etc.), the date, the location, textual comments of the authors, multilingual common names and collaborative quality ratings. The test set contains 12,347 recordings of the same type (mono-phone recordings). More details about that data can be found in the overview working note of BirdCLEF 2017 [START_REF] Goëau | Lifeclef bird identification task 2017[END_REF].

The used evaluation metric is the Mean Reciprocal Rank (MRR). The MRR is a statistic measure for evaluating any process that produces a list of possible responses to a sample of queries ordered by probability of correctness. The reciprocal rank of a query response is the multiplicative inverse of the rank of the first correct answer. The MRR is the average of the reciprocal ranks for the whole test set:

M RR = 1 |Q| Q i=1 1 rank i
where |Q| is the total number of query occurrences in the test set.

Mean Average Precision was used as a secondary metric to take into account the background species, considering each audio file of the test set as a query and computed as:

mAP = |Q| q=1 AveP (q) Q ,
where AveP (q) for a given test file q is computed as

AveP (q) = n k=1 (P (k) × rel(k)) number of relevant documents .
Here k is the rank in the sequence of returned species, n is the total number of returned species, P (k) is the precision at cut-off k in the list and rel(k) is an indicator function equaling 1 if the item at rank k is a relevant species (i.e. one of the species in the ground truth).

Task2: soundscape recordings

The goal of the task was to localize and identify all audible birds within the provided soundscape recordings. Therefore, each soundscape was divided into segments of 5 seconds, and a list of species accomapnied by probability scores had to be returned for each segment. Each prediction item (i.e. each line of the run file) had to respect the following format:

<MediaId;TC1-TC2;ClassId;Probability> where probability is a real value in [0;1] decreasing with the confidence in the prediction, and where TC1-TC2 is a timecode interval with the format of hh:mm:ss with a length of 5 seconds (e.g.: 00:00:00-00:00:05, then 00:00:05-00:00:10).

Each participating group was allowed to submit up to 4 run files built from different methods. As for the monophone task, participants were allowed to use the provided metadata and to use external training data at the condition that the experiment is entirely re-producible and not biased.

The training set provided for this task was the same as that for the monophone task, i.e. 36,496 monophone recordings coming from Xeno-canto and covering 1500 species of Central and South America. Complementary to that data, a validation set of soundscapes with time-coded labels was provided as training data. It contained about 20 minutes of soundscapes representing 240 segments of 5 seconds and with a total of 385 bird species annotations. The test set used for the final blind evaluation contained about 6 hours of soundscapes split into 4382 segments of 5 seconds (to be processed as separate queries). Some of them were stereophonic, offering possibilities of source separation to enhance the recognition. More details about the soundscape data (locations, authors, etc.) can be found in the overview working note of BirdCLEF 2017 [START_REF] Goëau | Lifeclef bird identification task 2017[END_REF]. In a nutshell, 2 hours of soundscapes were recorded in Peru (with the support of Amazon Explorama Lodges within the BRILAAM STIC-AmSud 17-STIC-01 and SABIOD.org project) and 4,5 hours were recorded in Columbia by Paula Caycedo Rosales, ornithologist from the Biodiversa Foundation of Colombia and an active Xenocanto recordist.

In order to assist participants in the development of their system, a baseline code repository and a validation dataset were shared with the participants. The validation package contained 20 minutes of annotated soundscapes split into 5 recordings taken from last year's test dataset. The baseline repository7 was developed by Chemnitz University of Technology and offered tools and an example workflow covering all required topics such as spectrogram extraction, deep neural network training, audio classification on field recordings and local validation (more details can be found in [START_REF] Kahl | Recognizing birds from sound-the 2018 birdclef baseline system[END_REF]).

The metric used for the evaluation of the soundscape task was the classification mean Average Precision (cmAP ), considering each class c of the ground truth as a query. This means that for each class c, all predictions with ClassId = c are extracted from the run file and ranked by decreasing probability in order to compute the average precision for that class. Then, the mean across all classes is computed as the main evaluation metric. More formally:

cmAP = C c=1 AveP (c) C
where C is the number of classes (species) in the ground truth and AveP (c) is the average precision for a given species c computed as:

AveP (c) = nc k=1 P (k) × rel(k) n rel (c) .
where k is the rank of an item in the list of the predicted segments containing c, n c is the total number of predicted segments containing c, P (k) is the precision at cut-off k in the list, rel(k) is an indicator function equaling 1 if the segment at rank k is a relevant one (i.e. is labeled as containing c in the ground truth) and n rel (c) is the total number of relevant segments for class c.

Participants and methods

29 research groups registered for the BirdCLEF 2018 challenge and 6 of them finally submitted a total of 45 runs (23 runs for task1: monophone recordings and 22 runs for task2: soundscape recordings). Details of the methods used and systems evaluated are collected below (by alphabetical order) and further discussed in the working notes of the participants [START_REF] Haiwei | Construction and improvements of bird songs' classification system[END_REF][START_REF] Lasseck | Audio-based bird species identification with deep convolutional neural networks[END_REF][START_REF] Schlüter | Bird identification from timestamped, geotagged audio recordings[END_REF][START_REF] Kahl | A baseline for largescale bird species identification in field recordings[END_REF][START_REF] Müller | Two bachelor students' adventures in machine learning[END_REF]:

Duke, China-USA, 8 runs [START_REF] Haiwei | Construction and improvements of bird songs' classification system[END_REF]: This participant designed a bi-modal neural network aimed at learning a joint representation space for the audio and the metadata information (latitude, longitude, elevation and time). It relies on a relatively shallow architecture with 6 convolutional layers for the audio and a few full-connected layers aimed at learning features from the meta-data and combining them with the audio features into a single representation space. A softmax is then used for the classification output. Concerning the monophone subtask, DKU SMIIP run3 uses the bi-modal model whereas DKU SMIIP run 2 uses only the audio-based part. DKU SMIIP run 3 is a fusion of both runs. DKU SMIIP run 4 relies on a ResNet model as for comparison with the proposed model. DKU SMIIP run 5 is a combination of all models. Concerning the soundscape subtask, DKU SMIIP run1 uses the bi-modal model, DKU SMIIP run2 uses an ensemble of two bi-modal models (one with data augmentation and one without data augmentation). DKU SMIIP run3 is a fusion and run1 and run2. DKU SMIIP run4 is a fusion of all models including the ResNet. ISEN, France, 4 runs: This participant used the Soundception approach presented in [START_REF] Sevilla | Audio bird classification with inception-v4 extended with time and time-frequency attention mechanisms[END_REF] and which was the best performing system of the previous edition of BirdCLEF. It is based on an Inception-v4 architecture extended with a timefrequency attention mechanism.

MfN, Germany, 8 runs [START_REF] Lasseck | Audio-based bird species identification with deep convolutional neural networks[END_REF]: This participant trained an ensemble of convolutional neural networks based on the Inception-V3 architecture applied to mel-scale spectrograms as input. The trained models mainly differ in the preprocessing that was used to extract the spectrograms (with or without high-pass filter, sampling rate value, mono vs. stereo, FFT parameters, frequency scaling parameters, etc. Another particularity of this participant is that he uses intensive data augmentation both in the temporal and frequency domain. About ten different data augmentation techniques were implemented and evaluated separately through cross-validation ablation tests. Among them, the most contributing one is indisputably the addition of background noise or sounds from other files belonging to the same bird species with random intensity, in order to simulate artificially numerous context where a given species can be recorded. Other augmentations seem not to contribute as much taken individually, but one after one, point after point, they lead to significant improvements. Data augmentation most notably included a low-quality degradation based on MP3 encoding-decoding, jitter on duration (up to 0.5 sec), random factor to signal amplitude, random cyclic shift, random time interval dropouts, global and local pitch shift and frequency stretch, as well as color jitter (brightness, contrast, saturation, hue). MfN Run 1 for each subtask included the best single model learned during preliminary evaluations. These two models mainly differ in the pre-processing of audio files and choice of FFT parameters. MfN Run 2 combines both models, MfN Run 3 added a third declination of the model with other FFT parameters, but combined the predictions of the two best snapshots per model (regarding performance on the validation set) for averaging 3x2 predictions per species. MfN Run 4 added 4 more models and earlier snapshots of them, reaching a total combination of 18 predictions per species. No additional metadata was used except for the elimination of species based on the year of introduction in the BirdCLEF challenge.

OFAI, Austria, 7 runs [START_REF] Schlüter | Bird identification from timestamped, geotagged audio recordings[END_REF]: This participant carefully designed a CNN architecture dedicated to birds sounds analysis in the continuity of its previous work described in [START_REF] Grill | Two convolutional neural networks for bird detection in audio signals[END_REF] (the sparrow model). The main architecture is quite shallow with a first block of 6 convolutional layers aimed at extracting features from mel-spectrograms, a species prediction block aimed at computing local predictions every 9 frames, and a temporal pooling block aimed at combining the local predictions into a single classification for the whole audio excerpt. Several variants of this base architecture were then used to train a total of 17 models (with or without ResNet blocks instead of classical convolutional layers, different temporal pooling settings, with or without background species prediction). Complementary to audio-based models, this participant also studied the use of metadata-based models. In total, 24 MLPs were trained and based on four main variables: date, elevation, localization and time. The different MLPs mainly dif-fer in the used variables (all, only one, all except one, etc.) and various parameter settings.

TUC MI, Germany, 10 runs [START_REF] Kahl | A baseline for largescale bird species identification in field recordings[END_REF]: All runs by this participant were conducted thanks to the baseline BirdCLEF package provided by Chemnitz University [START_REF] Kahl | Recognizing birds from sound-the 2018 birdclef baseline system[END_REF]. They ensemble different learning and testing strategies as well as different model architectures. Classical deep learning techniques were used, covering audio-only and metadata assisted predictions. Three different model architectures were employed: First, a shallow, strictly sequential model with only a few layers. Secondly, a custom variation of the WideResNet architecture with multiple tens of layers and thirdly a very slim and shallow model which is suited for inference on low-power devices such as the Raspberry Pi. The inputs for all three models are 256 x 128 pixel mel-scale log-amplitude spectrograms with a frequency range from 500 Hz to 15 kHz. The dataset is pre-processed using a bird activity estimator based on median thresholds similar to previous attempts of this participant [START_REF] Kahl | Large-scale bird sound classification using convolutional neural networks[END_REF]. The most successful run for the monospecies task was an ensemble consisting of multiple trained nets covering different architectures and dataset splits.

The participant tried to estimate the species list for the soundscape task based on time of the year and location using the eBird database. Despite the success of this approach in last year's attempt, the pre-selection of species did not improve the results compared to a large ensemble. Finally, the participant tried to establish a baseline for real-time deployments of neural networks for long-term biodiversity monitoring using cost-efficient platforms. The participant proposes a promising approach to shrinking model size and reducing computational costs using model distillation. The results of those runs using the slim architecture are only a fraction behind the scores of large ensembles. All additional metadata and code are published online, complementing the baseline BirdCLEF package.

ZHAW, Switzerland, 8 runs [START_REF] Müller | Two bachelor students' adventures in machine learning[END_REF]: In contrast to every other submission, the participants evaluated the use of recurrent neural networks (RNN). Using time-series as inputs for recurrent network topologies seems to be the most intuitive approach for bird sound classification. Yet, this method did not receive much attention in past years. Despite the limitations of time and computational resources, the experiments showed that bidirectional LSTMs are capable of classifying bird species based on two-dimensional inputs. Tuning RNNs to improve the overall performance seems to be challenging, although works from other sound domains showed promising results. The participants noted that not every design decision from other CNN implementations carry their benefit over to a RNN-based approach. Especially dataset augmentation methods like noise samples did not improve the results as expected. The results of the submitted runs suggest that an increased number of hidden LSTM units has significant impact on the overall performance. Additionally, data pre-processing and detection post-filtering impacts the prediction quality. Longer input segments and LSTMs with variable input length should be subject to future research.

The results achieved by all the evaluated system are displayed on Figure 1 for the monospecies recordings and on Figure 2 for the soundscape recordings. The main conclusion we can draw from that results are the following:

The overall performance improved significantly over last year for the mono-species recordings but not for the soundscapes: The best evaluated system achieves an impressive MRR score of 0.83 this year whereas the best system evaluated on the same dataset last year [START_REF] Sevilla | Audio bird classification with inception-v4 extended with time and time-frequency attention mechanisms[END_REF] achieved a MRR of 0.71. On the other side, we do not measured any strong progress on the soundscapes. The best system of MfN this year actually reaches a c-mAP of 0.193 whereas the best system of last year on the same test dataset [START_REF] Sevilla | Audio bird classification with inception-v4 extended with time and time-frequency attention mechanisms[END_REF] achieved a c-mAP of 0.182.

Inception-based architectures perform very well: As previous year, the best performing system of the challenge is based on an Inception architecture, in particular the Inception v3 model used by MfN. In their working note [START_REF] Lasseck | Audio-based bird species identification with deep convolutional neural networks[END_REF], the authors report that they also tested (for a few training epochs) more recent or larger architectures that are superior in other image classification tasks (ResNet152, DualPathNet92, InceptionV4, DensNet, InceptionResNetV2, Xception, NasNet). But none of them could meet the performance of the InceptionV3 network with attention branch.

Intensive data augmentation provides strong improvement: All the runs of MfN (which performed the best within the challenge) made use of intensive data augmentation, both in the temporal and frequency domain (see section 3 for more details). According to the cross-validation experiments of the authors [START_REF] Lasseck | Audio-based bird species identification with deep convolutional neural networks[END_REF], such intensive data augmentation allows the MRR score to be increased from 0.65 to 0.74 for a standalone Inception V3 model.

Shallow and compact architectures can compete with very deep architectures: Even if the best runs of MfN and ISEN are based on a very deep Inception model (Inception v3), it is noteworthy that shallow and compact architectures such as the ones carefully designed by OFAI can reach very competitive results, even with a minimal number of data augmentation techniques. In particular, OFAI Run 1 that is based on an ensemble of shallow networks performs better than the runs of ISEN, based on an Inception v4 architecture.

Using metadata provides observable improvements: Contrary to all previous editions of LifeCLEF, one participant succeeded this year in improving significantly the predictions of its system by using the metadata associated to each observation (date, elevation, localization and time). More precisely, OFAI Run 2 combining CNNs and metadata-based MLPs achieves a mono-species MRR of 0.75 whereas OFAI Run 1, relying solely on the CNNs, achieves a MRR of 0.72. According to the cross-validation experiments of this participant [START_REF] Schlüter | Bird identification from timestamped, geotagged audio recordings[END_REF], the most contributing information is the localization. The elevation is the second most informative variable but as it is highly correlated to the localization, it does not provide a strong additional improvement in the end. Date and then Time are the less informative but they do contribute to the global improvement of the MRR.

The brute-force assembling of networks provides significant improvements: as for many machine learning challenges (including previous Bird-CLEF editions), the best runs are achieved by the combination of several deep neural networks (e.g. 18 CNNs for MfN Run 4). The assembling strategy differs from a participant to another. MfN rather tried to assemble as much networks as possible. MfN Run 4 actually combines the predictions of all the networks that were trained by this participant (mainly based on different pre-processing and weights initialization), as well as snapshots of these models recorded earlier

Conclusion

This paper presented the overview and the results of the LifeCLEF bird identification challenge 2018. It confirmed the results of the previous edition that inception-based convolutional neural networks on mel spectrograms provide the best performance. Moreover, the use of large ensembles of such networks and of intensive data augmentation provides significant additional improvements. The best system of this year achieved an impressive MRR score of 0.83 on the typical Xeno-Canto recordings. It could probabaly even be improved by a few points by combining it with a metadata-based prediction model, as shown by the second best participant to the challenge. This means that the technology is now mature enough for this scenario. Concerning the soundscapes recordings however, we did not observe any significant improvement over the performance of last year. Recognizing many overlapping birds remains a hard problem and none of the efforts made by the participants to tackle it provided observable improvement. In the future, we will continue investigating this scenario, in particular through the introduction of a new dataset of several hundred hours of annotated soundscapes that could be partially used as training data.

  during the training phase. The gain of the ensemble over a single model can be observed by comparing MfN Run 4 (M RR = 0.83) to MfN Run 1 (M RR = 0.78). The OFAI team rather tried to select and weight the best performing models according to their cross-validation experiments. Their best performing run (OFAI Run 3) is a weighted combination of 11 CNNs and 8 metadata-based MLPs. It allows reaching a score of M RR = 0.78 whereas the combination of the best single audio and metadata models achieves a score of M RR = 0.69 (OFAI Run 4).

Fig. 1 .

 1 Fig. 1. BirdCLEF 2018 monophone identification results -Mean Reciprocal Rank.

Fig. 2 .

 2 Fig. 2. BirdCLEF 2018 soundscape identification results -classification Mean Average Precision.

Fig. 3 .

 3 Fig. 3. BirdCLEF 2018 soundscape identification results detailed per country -classification Mean Average Precision.

Scaled Acoustic Biodiversity http://sabiod.univ-tln.fr

https://github.com/kahst/BirdCLEF-Baseline

Acknowledgements The organization of the BirdCLEF task is supported by the Xeno-canto Foundation as well as by the French CNRS project SABIOD.ORG and EADM GDR CNRS MADICS, BRILAAM STIC-AmSud, and Floris'Tic. The annotations of some soundscapes were prepared by the regretted wonderful Lucio Pando of Explorama Lodges, with the support of Pam Bucur, H. Glotin and Marie Trone.


James Difrisco

ORCID Matteo Mossio

Diachronic Identity in Complex Life Cycles: An Organizational Perspective

Keywords: biological individuality, closure of constraints, development, reproduction, biological persistence, diachronic identity, genidentity, process ontology

What does it mean to be the same organism over time? This chapter develops an understanding of diachronic identity of organisms from an organizational perspective. We argue that a necessary condition for diachronic identity is organizational continuity, i.e., the presence of a continuous causal process linking successive organizational regimes, irrespective of material and functional changes. Organizational continuity is not a sufficient condition, however, because it cannot discriminate between the development of the same individual and the reproduction of a new individual. We therefore suggest that there are temporal boundaries of identity when there are changes in the number of continuous organized systems, which occurs through fission, fusion, or a combination of the two. We discuss the utility of the resulting organizational view, as well as its relations with other approaches to biological individuality.

Introduction

Questions about diachronic identity have sustained extensive philosophical reflection in general metaphysics and particularly in the context of personal identity. Less attention has been given to diachronic identity of organisms. This is in spite of a recent surge of work on biological individuality in philosophy of biology, which has largely focused on which sorts of parts should be included within the spatial boundaries of individuals, and not on which sorts of events should be included within the temporal boundaries of a life. However, temporal boundaries matter for some of the same reasons that spatial boundaries do.

One biological practice that requires criteria of individuation in space is counting individuals in order to measure population size and demographic change [START_REF] Clarke | The Problem of Biological Individuality[END_REF]. For these purposes, it is often not enough to single out the appropriate individuals at specific times without also connecting them across time. One needs to be able to interrupt an observation period and later return to the system under study, to re-identify the same individuals as before, and distinguish them from the ones that are new. Otherwise, one risks double-counting certain individuals and missing others completely.

Similar considerations apply to measurements of reproductive fitness in terms of the number of offspring produced. Offspring number straightforwardly depends on how we individuate offspring. But it is not always obvious whether a biological system at a given time is the beginning of a new life or just a later developmental stage of the parent. This is especially the case in life cycles involving metamorphosis, metagenesis (alternation of generations), vegetative reproduction, fusion, fission, and symbiosis, as we will see. It is also important to be able to distinguish development, growth, and reproduction because these processes connect to different dynamics of life history evolution (Stearns 1992). A model that describes trade-offs and local optima for traits such as growth rate, time to reproduction, and mortality schedules will generate different predictions and different error rates depending on which segments of a life cycle it is applied to. For purposes of comparative biology, the formation of a reliable generalization over life history patterns in different taxa demands that the patterns be genuinely comparable. Work on biological individuality can ideally provide a domain theory that identifies which intervals of organismic processes the models should apply to.

In attempting to provide diachronic criteria of identity we encounter a first difficulty that modes of development and reproduction differ markedly across different biological taxa. It is entirely possible that there are no shared criteria of identity that apply to the class of "organisms" as such, but only local criteria for different taxonomic groups. A second, related difficulty is that organisms can have very different properties at different stages of the same lifetime. In fact, many of the properties emphasized in proposed criteria of individuality are not present throughout the lifetime of the systems they are supposed to individuate (see [START_REF] Clarke | The Problem of Biological Individuality[END_REF]DiFrisco 2018b). Accounts of individuality face this difficulty when they are based on fitness (e.g., [START_REF] Folse | What is an Individual Organism? A Multilevel Selection Perspective[END_REF], the capacity to undergo selection [START_REF] Clarke | The Multiple Realizability of Biological Individuals[END_REF], and cooperation and conflict [START_REF] Queller | Beyond Society: The Evolution of Organismality[END_REF]). An organism during its post-reproductive lifespan has no fitness, its cooperation or conflict has no evolutionary effect, and it cannot undergo selection (excluding grandparenting effects). Yet post-reproductive organisms nonetheless exist, and they have effects on biological processes other than evolution. Non-evolutionary features of organisms such as histocompatibility and symbiotic interaction can also be time-variable in development. When the properties that are supposed to determine individuality change over developmental time, they need to be embedded in the context of a life cycle structure. Then we can still count something as an individual when those properties are absent.

Intra-lifetime variability sets up a general dilemma: if the criteria for continued persistence are too demanding, then developmental processes involving dramatic material and functional transformations like metamorphosis may count as a reproductive process involving the production of a new individual. If the criteria are too relaxed, then many reproductive processes will be re-cast as development of one and the same individual. This chapter examines diachronic identity conditions for organisms specifically in light of the second problem of intra-lifetime variability. We argue that a suitable necessary condition for organismic persistence can be found in spatiotemporal continuity together with the presence of a causal structure known as closure of constraints. This dual condition is called organizational continuity. Organizational continuity is sufficient for diachronic identity only when there are no changes in the number of organized systems that are organizationally continuous with one another. Such changes can occur through events of fission or fusion, which call for special analysis. In explicating this qualification of sufficient conditions, we find that one also needs to take into account the way in which different temporal boundaries can be promoted by different biological perspectives-e.g., evolutionary, developmental, or physiological-with their distinctive modeling and generalization strategies. We close by considering how the proposed organizational view can plausibly satisfy the above biological roles for diachronic identity conditions, and highlight open questions for future work.

Organizational continuity

Spatiotemporal continuity is widely considered by philosophers to be necessary for diachronic identity of objects. An object cannot pass in and out of existence, or disappear from one location and immediately re-appear in another, while remaining numerically the same object. i Spatiotemporal continuity alone does not entail contiguity of the spatial parts of an object-commonly called "unity" in philosophy and "cohesion" in perceptual psychology-but only that the spatial regions an object occupies are connected across time. For example, a biological population can be considered an object whose parts are not topologically connected, but it can nonetheless be tracked across time in virtue of the spatiotemporal continuity of its scattered parts. Unity is often considered to also be necessary for object identity, though we will remain neutral on this issue.

Mere spatiotemporal continuity however, without any specification of the relata that are supposed to stand in the relation of continuity, is not a sufficient condition for identity. This is because any object or event is spatially continuous with its immediate environment and temporally continuous with what precedes it and what succeeds it. Some background determination about the sort of item to be tracked-such as a horse, a computer, or a thunderstorm-is needed to get a grip on its spatial boundaries as well as the kinds of change it can undergo while remaining the same thing of that sort. For example, while relying on the criterion of spatiotemporal continuity, an observer may trace different paths through spacetime if she is tracking items in her perceptual field under the sortal house versus set of bricks. The application of a suitable sortal, together with the condition of spatiotemporal continuity, can be viewed as determining the identity of entities in space and time. This is the position defended in contemporary forms of substance ontology, from [START_REF] Strawson | Entity and Identity and Other Essays[END_REF]), to Wiggins (2001[START_REF] Lowe | More Kinds of Being: A Further Study of Individuation, Identity, and the Logic of Sortal Terms[END_REF]. Roughly, x and y are the same individual iff they are spatiotemporally continuous and they fall under the same sortal.

From this point of view, the problem of organism identity can be framed as a problem of finding an adequate definition for the sortal organism or for specific kinds of organisms. We propose to approach the issue of organism identity in a different way, by first shifting from the descriptive question to a more basic explanatory one. Rather than asking which concept of the organism determines the organism's persistence, we take a step back and ask which causal structure determines its survival. If we can understand the sorts of physical features and interactions that explain, from the bottom up, how organisms survive-taking "organisms" or "individuals" in an initially loose sense-then we gain insight into how organism identity ought ultimately to be conceptualized.

Biological organisms are physical systems that exhibit a type of macroscopic order based primarily on the energy provided by chemical reactions. In order to maintain their internal structure and energetic functioning against the global thermodynamic tendency toward entropic dissipation, organisms must continually occupy states far from chemical equilibrium by absorbing chemical or radiant energy (Ruiz-Mirazo and Moreno 2004). Unlike other macroscopic dissipative structures, however, organisms exhibit not only physical order but also functional organization. We use here 'organization' in a theoretical specific sense, to refer to a specific causal regime in which groups of differentiated parts collectively maintain each other through their reciprocal interactions. The survival of organized systems as wholes depends on the overall activity of their parts. Hence, these systems can be said to be selfmaintaining in a given environment [START_REF] Moreno | Biological Autonomy: A Philosophical and Theoretical Enquiry[END_REF].

As thermodynamically open systems, organisms are traversed by flows of matter and energy in the form of complex chemical and physical transformations (processes or reactions). These transformations are controlled through the coordinated activity of system components, which are theoretically characterized as constraints. Constraints are material structures that asymmetrically act on transformations without being directly affected by them, and that remain conserved during the course of those transformations. For instance, the developed cardiovascular system of vertebrates constrains blood flow without being altered by it. ii At smaller spatial scales, enzymes change the kinetics of chemical reactions without being consumed in the process (see [START_REF] Montévil | Biological organisation as closure of constraints[END_REF] for further details).

In order to constrain a transformation, the constraint must be conserved at the time scale of the transformation it constrains. Yet on longer time scales, biological constraints also degrade and must be replaced or repaired. The cells that compose the vascular system must be nourished, and enzymes undergo degradation and denaturation over time and must be replaced. In general, the repair or replacement of a constraint occurs by means of another metabolic process or complex of processes, which is itself channeled under other constraints. For example, lipid membranes constrain the diffusion of enzymes and metabolites in such a way that the appropriate intracellular concentrations are maintained, but new lipids are also produced through the chemical reactions controlled by enzymes. Once we have reciprocally maintaining effects of a group of constraints, the notion of organization enters the picture. A system is "organized" in the relevant sense when the continued existence of a set of constraints depends on the effects that they collectively produce on the overall thermodynamic flow. If this occurs, the set of mutually dependent constraints can be said to realize closure. The mutual dependence between constraints, theoretically designated as "closure of constraints," is what allows organized systems to maintain themselves over time. iii From the organizational perspective, we can view organisms or biological individuals as being organized systems (as a necessary condition), while recognizing that not all conceptions of the organism will have this feature.

Closure of constraints plays a central role in explaining the survival of organisms, viewed as organized systems, as it explains how their parts are functionally arranged in such a way that the system can maintain itself dynamically over time. Accordingly, it seems reasonable to hold that, conceptually, closure of constraints is necessary for organism identity, since any organism that lost this property would quickly perish. Let us propose, then, that a necessary condition for diachronic identity of organisms is that they continually exhibit closure of constraints. Any temporal interval where this property of organizational continuity is not present then marks a temporal boundary of an organism's life, either due to death or nonexistence before life.

What does it mean for a system to continually exhibit closure of constraints? A first interpretation might be that the particular material structures that act as constraints in the system-i.e., membranes, enzymes, vascular systems-are conserved over time. This would be a problematic requirement on organismic persistence, however. The material composition of organized systems changes over time-indeed, it must change if the systems are to survive, because functional constraints degrade and must be repaired or replaced.

A second interpretation might be that continually exhibiting closure of constraints means that a group of constraints, functionally individuated by their causal roles in self-maintenance, must persist despite continual material turnover of components and realizing structures. As argued elsewhere (Mossio et al. 2009), constraints subject to closure can be said to ground biological functions. Diachronic identity would therefore be a matter of conservation of function rather than of material structure. The trouble with this solution is that material turnover is not the only kind of constitutive change that organisms undergo. In organisms that develop, i.e. single-and multi-celled eukaryotes, the constraints involved in self-maintenance can themselves arise, transform, and disappear within a lifetime-even if they are defined in abstract functional terms. A dramatic example of developmental transformation is metamorphosis. Metamorphosis is a life history pattern characterized by successive life stages that differ markedly in their physiology, morphology, ecological niche, and reproductive capacity [START_REF] Bishop | What is metamorphosis?[END_REF]. Although the evolutionary origins of metamorphosis are not well understood, one of the hypothesized adaptive effects of metamorphosis as a life history strategy is to permit the same organism to possess dramatically different functional specializations at different stages of its life. In metamorphic life cycles, functions or constraints often fail to be conserved over entire lifetimes. Moreover, intra-lifetime functional variation is not restricted to functions that are unnecessary for metabolic self-maintenance, such as camouflage or reproduction. The adult forms of many butterflies, moths, and mayflies lack mouthparts for eating, yet mouthparts-mechanical constraints on the flow of food energy-are necessary for self-maintenance in the larval forms.

Of course, many functional constraints are conserved over the course of development, particularly those having to do with core metabolism. One might try to reconfigure the criterion of functional conservation in light of developmental change by claiming that only those functions that are necessary for self-maintenance throughout the entire lifetime need to be conserved. This amendment, however, is self-defeating. If we say that the boundaries of a lifetime are determined by closure of constraints, but exhibiting closure of constraints means conserving functions that are necessary throughout the entire lifetime, then we already have to know what the temporal boundaries are in order to apply our proposed necessary condition for temporal boundaries. This solution is therefore circular or uninformative. Moreover, it is objectionable for departing from the explanatory role of closure of constraints. The set of constraints that are conserved throughout a lifetime will often be a subset of the set of constraints that realize closure at different stages. This conserved subset is not identified in terms of its special role in explaining survival, but by the fact of being conserved. But the main reason for proposing closure of constraints as a necessary condition for organism identity in the first place was that it is necessary for explaining survival. A subset of constraints that does not realize closure at the specific stage when it exists is not the relevant set of constraints for explaining survival. For example, the set of constraints in the mayfly larva that includes those that realize closure minus the mouthparts is not the relevant explanans for the survival of the larva. The relevant explanans is the whole set of constraints that realizes closure at that stage. Subsets of constraints that happen to be conserved throughout a lifetime should not be construed as essential for tracking organism identity.

In order to continually exhibit closure of constraints, or to possess organizational continuity, an ontogenetic trajectory does not have to conserve anything in particular, neither structures nor functions. Nor do the different stages of life need to resemble each other. Being the same organized system over time, we argue, is based on a specific causal dependence relationship. If a system continually realizes closure of constraints, then at any given moment the organization of its parts is causally dependent on the effects of functional constraints that have operated at a previous moment. The organism at t 2 does not need to have the same set of constraints with the same inter-relationships as the organism at t 1 , but some of the constraints at t 2 must be causally dependent on those at t 1 . The particular set of constraints and their inter-relations-which we refer to as a regime of closure-can change over time as long as later regimes causally depend on earlier regimes. Hence, what must remain the same over time is closure construed as a general theoretical principle and not as a specific regime of closure (on this specific point see [START_REF] Mossio | Theoretical principles for biology: organisation[END_REF].

Note that organizational continuity implies spatiotemporal continuity, so by affirming the former as a necessary condition we include the latter. This implication stems from general physical relationships between causation, space, and time. In order for causal influence to propagate from x to y (without intermediaries) they cannot be separated by a temporal gap during which neither x nor y exists. Similarly, for the physical forces involved in biological interactions (primarily the electromagnetic force), interaction requires spatial proximity. This point might be taken to imply that organizational continuity also requires spatial proximity, but the implication is not obvious, and under-determined by current biological theories of organization. The causal influence implied by constraint relationships must propagate between the parts, under specific spatial and topological conditions that depend on how a given system realizes organizational closure, and on the level of organization being considered. For instance, while it seems to be generally accepted that unicellular organisms cannot realize closure unless their parts are contained within an unbroken spatial boundary, this requirement might be relaxed in the case of ecosystems, viewed as candidate higher-level organized systems, see Nunes-Neto et al., 2014). Nevertheless, it seems reasonable to conjecture that it will generally be difficult to implement the productive relations of dependence involved in closure of constraints in systems whose functional parts do not remain spatially close enough to be able to causally interact with each other.

Organizational continuity: Between genidentity and substantialism

The idea of conceptualizing diachronic identity in terms of causal continuity, as opposed to material or functional conservation or resemblance, is not new. It was expressed in its modern form in Kurt Lewin's notion of genidentity, which has been promoted by some philosophers of biology as a criterion of diachronic identity for biological individuals [START_REF] Hull | A Matter of Individuality[END_REF][START_REF] Guay | To Be Continued: The Genidentity of Physical and Biological Processes[END_REF].

Organizational continuity is a specific type of causal continuity and is thus more restrictive than genidentity. One issue with unrestricted genidentity is that many items are related by causal dependence that we would not want to consider parts or stages of the same individual.

For example, organisms are causally continuous with their waste products as well as any artifacts they produce, but there seems to be no biologically interesting organism concept that includes these things as parts to be tracked through time. Organisms are also causally continuous with their parent(s) and the corpses they leave behind. [START_REF] Guay | To Be Continued: The Genidentity of Physical and Biological Processes[END_REF] propose that temporal boundaries can be drawn where there are relatively fast rates of change, particularly change in "internal organization," so that a single lifetime can comprise dramatic change as long as it is smooth and progressive. Although this rule would restrict genidentity in many cases, it is also likely to exclude metamorphic life cycles, as these can involve quite abrupt changes in internal organization. It also seems that our ability to measure rates of change is epistemically dependent on our ability to identify and track what it is that is changing, rather than the other way around. [START_REF] Hull | A Matter of Individuality[END_REF] writing on biological genidentity relies more narrowly on the idea that changes in "organization" mark the temporal boundaries of individuals, though he does not explicate the notion of organization in much detail. Our account of organizational continuity can be viewed as filling in the idea that biological identity is based on causal continuity (genidentity) and organization. An important difference between the accounts, however, is that [START_REF] Hull | A Matter of Individuality[END_REF] and [START_REF] Guay | To Be Continued: The Genidentity of Physical and Biological Processes[END_REF] use genidentity as a general model of persistence for all biological entities, including viruses, parts of organisms, and species. In fact, genidentity can be used as a criterion of identity for any kind of entity (e.g., molecules, stones, galaxies), which means that, as such, it does not restrictively apply to the biological domain. By contrast, organizational continuity applies only to systems realizing closure of constraints, which include, at most, unicellular and multicellular organisms, and possibly symbioses and ecosystems.

Let us now examine the connection between organizational continuity and substance ontology and sortals raised earlier. As [START_REF] Hull | A Matter of Individuality[END_REF] and [START_REF] Guay | To Be Continued: The Genidentity of Physical and Biological Processes[END_REF] point out, the theoretical decision to ground persistence on causal continuity rather than conservation or similarity runs counter to "substantialist" habits of thought, according to which being the same individual over time is a matter of retaining the same "substance," conceptualized either as matter or form (see [START_REF] Simondon | L'individu et sa genèse physico-biologique[END_REF]. The most sophisticated contemporary defenders of substance ontology, such as Wiggins (2001) and [START_REF] Lowe | More Kinds of Being: A Further Study of Individuation, Identity, and the Logic of Sortal Terms[END_REF], are careful to drop the requirement of material conservation. In Wiggins' framework, the identity of a substance is grounded in its form, dynamically conceptualized as an Aristotelian energeia or activity (Wiggins 2001, p. 80). Every natural entity possesses a principle of activity or functioning that at once determines its conditions of identity as well as its membership in a natural kind (Wiggins 2001, p. 72). As Wiggins writes:

A particular continuant x belongs to a natural kind, or is a natural thing, if and only if x has a principle of activity founded in lawlike dispositions and propensities that form the basis for extension-involving sortal identification(s) which will truly answer the question 'what is x?' (Wiggins 2001, p. 89) To be the same individual over time is thus to conserve the same principle of activity, which implies spatiotemporal continuity and falling under the same sortal.

How does our proposal differ from Wiggins' activity-based substantialism? Initially it would seem that the principle of closure could be interpreted as a kind of principle of activity for organisms. However, problems arise from the supposition that a principle of activity is not only (1) necessarily conserved across a lifetime but is also (2) sufficient to determine the spatiotemporal extension or boundaries of an organism. These two roles pull the notion of a principle of activity in different directions, the first toward a coarser grain of individuation and the second toward a finer grain. There are often radically different modes of activity or functioning in different stages of metamorphosis, from physiological activity to morphological change to behavior. In such cases, in order to capture the activity that is common to all developmental stages, the activity will have to be defined as a quite general one, such as "self-maintaining," "living," or "developing." But it is hard to see how generic activities like these could be sufficiently "extension-involving" to determine the temporal boundaries of organisms, to distinguish parents and offspring, or even to distinguish between organisms belonging to different taxa. iv In contrast, the conservation of a principle of closure over the course of ontogenesis does not entail that each stage displays the same characteristic functioning or activity. The principle of closure is something more abstract; this is why we treat it as a necessary condition and not as providing "thick" sufficient conditions for individuation. Sometimes a principle of closure will correspond to a unitary regime of closure that picks out temporal boundaries without difficulty. This is relatively more likely to be the case in organisms that do not undergo massive functional changes during ontogenesis, e.g., non-eukaryotes and some eukaryotes, and in direct developers. But in our proposal the concept of a regime of closure is not attributed an individuating role as a condition of persistence.

These features of our account entail a significant departure from core principles of the substantialist model advanced by Wiggins and assumed by many others. Against substancebased sortalism, there are unlikely to be sortals for organisms that, by specifying a distinct principle of activity, determine the spatial and temporal extent of a life cycle at one stroke. Instead, theoretically useful sortals for organisms are more likely to resemble sortals for events, events being inherently temporally extended and typically time-heterogeneous. Event sortals do not single out events by specifying a property or activity that remains the same throughout the event, but rather a characteristic sequence or series of stages or temporal parts, each with their own distinctive qualities, activities, and in the present case, regimes of closure.

Ontologically, the key dynamic category that binds together stages into the same life cycle is not activities, but developments. Activities are homeomerous or "like-parted," in that what is happening in any sub-interval of the duration of an activity is itself the same kind of activity. Every sub-interval of the burning of a candle is also a burning. Developments are heteromerous or "non-like-parted" in the sense that what is present in any sub-interval of the development is not the same kind of development (on this distinction see [START_REF] Seibt | Beyond Endurance and Perdurance: Recurrent Dynamics[END_REF]. The larval stage of holometabolous development is not itself a metamorphosis. This implies that the sortals capable of determining boundaries for developments will be complex, specifying a normal or typical series of stages as well as a relation that makes them stages of the same process (see DiFrisco 2017, 2018a). In fact, this is what we see when biology texts introduce life cycles so that they can be identified by field workers [START_REF] Gilbert | Developmental Biology[END_REF]: not a conserved property or activity, but a normal sequence of stages of a specific sort of causal process.

The idea of organizational continuity is therefore more germane to a process model than a substance model of organism identity. To put this idea to use, however, we need more than just a necessary condition for organism persistence. The next section examines sufficient conditions and introduces distinctions between developmental and reproductive processes.

Development versus reproduction

One of the primary ways in which reflection on organism identity matters is in connection with the biologically important distinction between development and reproduction. The distinction is particularly difficult in complex life cycles of non-vertebrate multicellular entities such as plants, fungi, colonies of various kinds, and various invertebrates, where we see processes like metamorphosis, metagenesis, apomixis, symbiosis, fission, and fusion (see Fusco and Minelli in press, chs. 1-2, for many examples of borderline cases).

As we saw earlier, amid this tangle of generative biological processes, principled attempts to distinguish between development and reproduction face a general dilemma. On the one hand, if criteria of diachronic identity are too strict, they will not be able to include dramatic transformations such as metamorphosis within the same lifetime. On the other hand, if they are too permissive, they will often be unable to close the temporal boundaries of a lifetime, and reproductive events will be tracked as developments of one and the same organism. Organizational continuity is a quite permissive criterion of identity, given that it does not require conservation or resemblance. Accordingly, it can be expected to face difficulties marking reproductive events-or more precisely, fission and fusion.

To a first approximation, one might hold that organizational continuity provides both necessary and sufficient criteria for diachronic identity. The idea would be that any temporal interval where continuity is broken marks a temporal boundary of an organism's life, either due to death or birth, which appear to be straightforward from an organizational perspective. An organism dies when it loses the property of closure of constraints, as this is responsible for its capacity to maintain itself far from equilibrium, and is born when a closed regime appears. Any corpse or parts that remain after death, as well as any preceding material constituents will be spatiotemporally continuous but not organizationally continuous with the organism. v To see why this solution generally does not work, recall that organizational continuity between two successive stages is present as long as both stages instantiate the principle of closure of constraints, the stages are spatiotemporally continuous with one another, and the later stage is causally dependent on constraints acting in the previous stage. The problem is that these conditions are satisfied not only between stages of metamorphosis, but also when the earlier stage is a parent and the later stage is an offspring. Parents and offspring are organized systems, they are spatiotemporally continuous with one another, and the offspring is dependent on constraints exerted by the parent, at least in the sense that the very generation of the former depends on constraints exerted by the latter. Hence, parents and offspring are organizationally continuous with one another. vi If organizational continuity were not only necessary but also always sufficient for diachronic identity, then parents and offspring would count as continuations of the same organism. This has the unwelcome consequence that whenever a parent continues to exist after reproducing, we would have a spatially scattered system comprising both parents and offspring as parts. This system lacks the right causal connections between parts to count as an individual organism in its own right, so we have to choose which system to track as a continuation of the pre-reproductive parental stages. Each tracking path satisfies organizational continuity equally well, however. A similar problem follows from treating fusion solely in terms of organizational continuity (see Fig. 1). Two fusing systems may each individually be organizationally continuous with the fused system, but they cannot both be the same as the fused system, because before fusion they do not together comprise an individual organism.

Fig. 2. Fission (left) and fusion (right).

To address this problem, we can modify our criterion by proposing that organizational continuity is sufficient for diachronic identity unless there is a change in the local number of organized systems that are organizationally continuous with one another, either via an event of multiplication (fission) or reduction (fusion). When a spatial separation of this sort appears or disappears, then we have a temporal boundary and a change of identity. vii The issue of spatial separation raises complex problems that go beyond the scope of this chapter, as it would in some sense require a full-blown organizational account of biological individuality. Nonetheless we can say the following. In general, spatial separation occurs when the involved systems do not realize a global closure with mutual dependence. In borderline cases where it is unclear whether there is one organized system or two, the critical consideration is whether the putatively distinct systems are functionally interdependent in virtue of constraint relationships. If organized systems share functional constraints, then the repair and replacement of the constraints depends ultimately on the action of other constraints in each system. In this case, they are not actually separately closed, and the wider system that includes them both is the one that realizes closure of constraints. By contrast, mere causal dependence without constraint relationships does not make the involved systems parts of the same organized whole.

We can clarify and sharpen this characterization of temporal boundaries by seeing how it deals with examples of fission, fusion, and life cycles that combine both.

Fission

In general, fission occurs when two or more spatially separated organized systems result from a preceding single one, with which they are all organizationally continuous. Fission allows drawing a temporal boundary in a straightforward way: the preceding system ceases to exist and two new individuals appear. However, this interpretation is not the only possible one, and we need some way of determining whether one of the systems which result from a fission event is a continuation of the life of the preceding system, i.e., whether a parent persists after reproduction.

To tackle this issue, we propose that parent and offspring can be discriminated by the presence of transitory asymmetrical dependence relationships. In reproduction, the materials that will constitute the offspring begin as parts of the parent(s). This is expressed in [START_REF] Griesemer | Development, Culture, and the Units of Inheritance[END_REF] condition of "material overlap." Eventually what begins as a part of the parent breaks the symmetry of dependence: it depends on the parent but the parent does not depend on it. When there is a transitory relation of asymmetric causal dependence during the process of multiplication of organized systems, the dependent system can be identified as the offspring, whereas the non-dependent organized system is the parent. If an asymmetry is not present but there is still multiplication of organized systems-e.g., in binary fission-then neither of the resultant systems is a continuation of the parent and both are offspring (new individuals). In most organisms the asymmetrical parental dependence is quite short-lived on the scale of the organism's lifetime, and tends to cease either when there is a physical separation between bodies or the formation of a metabolic boundary such as an egg. Note the loose connection to spatial contiguity implicit in this characterization of multiplication. In order for causal influence to propagate from parent to offspring, they must be at least partially contiguous. But they can remain contiguous without the parent continuing to exert constraints on the constitutive self-maintaining processes of the offspring, such as when eggs are carried around by the parent, or when plants like Aspen trees are connected by underground runners.

The simplest and most ancestral form of reproduction of organized systems is cell division. viii When cell division is "symmetric" in the sense that cell biologists use the termi.e. the resultant two cells have roughly the same kinds of components and the same size-it is thought that the parent cell ceases to exist upon division and gives rise to two offspring. Cell division can also be "asymmetric" in the sense that the parental components are unevenly distributed to the daughter cells, which are often different in size. When asymmetric division occurs in the cells of multicellular organisms, such as in stem cells, typically the parent cell is again treated as ceasing to exist upon division. But when it occurs in unicellular organisms, such as budding in yeast, it is more common to treat one of the resulting cells as a continuation of the parent. ix In budding yeast (Saccharomycetales), the parent cell can be distinguished by several features-for example, it is usually larger, bears scars on the membrane where the bud formed, and retains the aging factors such as carbonylated proteins and DNA circles [START_REF] Mortimer | Life span of individual yeast cells[END_REF][START_REF] Shcheprova | A mechanism for asymmetric segregation of age during yeast budding[END_REF]. During the generation of a bud, the parent cell dedicates biosynthesis to the bud, whereas the bud dedicates biosynthesis to its own growth (Shcheprova et al. 2008, p. 728). Arguably this is a form of asymmetrical dependence in our (functional) sense, which marks budding as a reproductive process with an identifiable parent that survives it. x It is quite likely, however, that there are similar asymmetrical dependencies that can be found in asymmetrical cell division within multicellular organisms, and so additional factors must be invoked to explain their different biological treatment. The most obvious difference is that although somatic cells and free-living cells are both organized systems, only the latter are able to develop and reproduce without being normally subordinated to the reproduction of a higher-level entity. Yeast can have complex life cycles with alternating asexual and sexual reproduction. Unlike somatic cells, they produce not only diploid daughter cells but also haploid "gametes" which fuse with gametes from another yeast to form another genetically unique diploid yeast cell. This process is distinguished from gametogenesis and syngamy in multicellular organisms because the fusion yields a yeast cell that is itself able to reproduce asexually and sexually, without intermediary stages of cell division and differentiation.

Attention to these differences illuminates why it is productive to view the yeast cell, but not a somatic cell, as an organism with a life history that persists through multiple reproductive events. Drawing the temporal boundaries in this way yields a developmental unit that is an informative base for generalization and comparison with other developmental units. For example, yeast cells undergo aging and experience trade-offs between growth rate and reproductive rate due to antagonistic pleiotropy, like many developing organisms [START_REF] Christie | Life history variation is maintained by fitness tradeoffs and negative frequency-dependent selection[END_REF]). If we stipulated that, like in somatic cells, the parent cell ceased to exist after each budding event, then the life cycle of yeast would become less comparable to these other life cycles in terms of aging and life history strategy, as well as in terms of ecological and evolutionary dynamics of alternating asexual and sexual reproduction. A similar pattern of reasoning could be applied to multicellular life cycles that include stages of asexual reproduction, such as fission by fragmentation in sea sponges, budding in hydrozoa, and cyclical parthenogenesis more generally. The result of this reflection is that in some contexts, the presence of asymmetric dependence between organisms is not sufficient to assign the identities of parent and offspring. We also need to take into account how drawing the temporal boundaries in one way rather than another can provide a more informative and inferentially rich classification scheme for that individual, giving access to generalizations and enabling the application of explanatory models of its developmental processes.

Fusion

Having looked at temporal boundaries in a few salient cases of fission, now we can turn to cases of fusion (cf. Hull 1978;[START_REF] Guay | To Be Continued: The Genidentity of Physical and Biological Processes[END_REF]. In contrast to fission, fusion occurs when organizationally continuous systems merge in space in such a way that the persistence of one or both systems is affected. xi An individual x and an individual y merge to form an individual z (see Fig. 1). Fusion is not reproduction, but one kind of fusion-syngamy, or fusion of gametes-is part of the process of sexual reproduction, and all kinds of fusion pose issues of temporal boundaries. The question with fission was whether one of the two individuals that are produced is a continuation of the earlier individual (the parent), and with fusion it is the same except reversed in time. In fusion, one of two outcomes can occur:

(1) x is the same individual as z and y becomes a part of z during fusion, or y is the same individual as z and x becomes a part of z during fusion; or (2) neither x nor y are the same individual as z, and x and y cease to exist upon fusion.

The first case corresponds to parental persistence after fission, and the second corresponds to parental cessation upon fission.

An outcome of spatial merging that is not fusion would be:

(3) neither x nor y are the same individual as z, and x and y persist through merging.

Because this does not involve a disruption of the identities of the fusing entities, we will call this "integration" of x and y.

Continuing the parallelism with fission, what happens to biological individuals when they fuse is determined most basically by whether there is an asymmetrical dependence relation between the fusing systems once they have come together in space. When there is, we have outcome (1): the dependent system becomes part of the non-dependent system, and the nondependent system persists through fusion. In Ceratioid anglerfish, for example, when a male finds a female he will bite into her skin and fuse their circulatory systems indefinitely. Males parasitize the metabolism of the females, which are much larger, in exchange for providing a constant source of sperm. Because the male becomes dependent on the self-maintaining processes of the female once they have merged, whereas the female is not similarly dependent on the male, we have an asymmetrical dependence relationship and thus (1). The female persists through fusion and the male becomes a part of her while (presumably) losing its individual closure of constraints. In fact, this assessment agrees with the naïve judgment of early investigators, who mistook the fused males as "lumps" on the female's body and searched in vain to find male exemplars of the group. An example of fusion in which neither fusing partner persists through fusion (2)-instead becoming parts of a new organized system-would be syngamy, or fusion of gametes (Hull 1978, p. 346). In syngamy, each of x, y, and z is an organized system, and the gametes x and y do not maintain their respective closure once fusion occurs because their functional components get mixed together. This is what distinguishes syngamy from obligate fusion of anglerfish as a case of outcome (1). During fusion, male gametes do not retain sufficient cohesion as cells or even as unified parts of the female gamete to stand in a stable asymmetric dependence relationship xii . The female gamete is, moreover, dependent on the ingression of the male gamete to initiate an individual process of development, giving an additional reason to consider them parts of a single individual. xiii What distinguishes between outcomes (2) and ( 3) is whether x and y cease to be organized systems in their own right during merging. When x and y retain their closure of constraints, then (3) they persist through the merger. Outcome (2) implies that the fused individual (z) is an organized system. But outcome (3) is consistent with the possibility that the merged individual (z) is an organized system (which might actually be taken as a necessary requirement for being an individual from the organizational perspective), or that it is not.

"Integration" can be characterized as a biological relationship in which spatially contiguous partners influence each other's functioning in a way that benefits either some partners (asymmetrical dependence, as in parasitism or commensalism) or all partners (symmetrical dependence, as in mutualism). When the dependence is symmetrical, integration generates a new encompassing organized system that realizes closure. An example of (3) that creates a new organized system would be slime molds. Slime molds are groups of free-living amoebae that facultatively aggregate and disaggregate depending on the presence of food. The aggregated amoebas each contribute to the self-maintenance of the whole and even undergo temporary differentiation and functional specialization.

Sexual Reproduction

With the preceding characterizations of fission, fusion and integration in hand, we can now briefly consider life cycles that involve both. Sexual reproduction of multicellular organisms involves a complex succession of events: fission of gametes from parents or parental cells is followed by fusion of gametes (syngamy) which, in many organisms, is shortly followed by integration of the zygote with the mother.

Applying our criteria yields two interpretations of this sort of sexual reproduction (Fig. 3). Under the first (A), the zygote is part of the mother due to its continuing asymmetrical dependence. The production of a new individual only definitively occurs when this dependence is broken due to the fission of mother and offspring, for example at birth.

A second interpretation (B) would count the zygote as a distinct individual from the mother on the grounds that its appearance constitutes the start of a developmental process. The asymmetrical dependence is an intermediate phase in the development of functional and spatial separation of the same entity, which allows tracking the zygote as the same individual as the offspring at birth. Under this interpretation, gametes form a new individual by syngamy, this zygote persists through its integration with the mother, and is the same individual as the eventual infant. The temporary asymmetric dependence of metabolism between parents and offspring should not preclude our ascribing distinct individuality to the offspring in all contexts and for all purposes of inquiry. In line with interpretation (A), the idea that the developing embryo is part of the mother (in placental mammals) has been promoted in recent discussion of the "metaphysics of pregnancy" (Kingma forthcoming). However, from an evolutionary perspective, a zygote is already a new evolutionary individual due to its genetic uniqueness and homogeneity [START_REF] Clarke | The Multiple Realizability of Biological Individuals[END_REF]. This new individual plausibly persists through its integration with the mother during implantation in the uterine wall, though it is not yet a physically separate organized system throughout its existence. The distinction between mother and offspring is even more evident from a developmental perspective. The embryo is undergoing completely different ontogenetic processes and stages than those of the mother. For purposes of applying models of human development, then, it is more productive to think of the mother and embryo as distinct individuals. In the terminology of DiFrisco (2018b), mother and embryo are parts of the same physiological and ecological individual, but they are distinct evolutionary and developmental individuals. Which classification scheme we choose in different classes of cases should be determined by our theoretical framework and its investigative and explanatory aims.

Conclusions

In this chapter, we have seen how diachronic identity for organisms can be plausibly grounded in a special kind of causal continuity. In order to capture sameness over time despite radical developmental changes such as metamorphoses, continuity should not be based on conservation of matter, function, form, or activity, but rather on a causal dependence relation called organizational continuity. For two stages of a developmental process to be organizationally continuous with one another, they must be spatiotemporally continuous, must realize closure of constraints (by whatever particular regime of closure), and the later stage must be dependent on constraints exerted in the earlier state. This permissive conception of organism identity entailed a departure from the substantialist model of persistence due to Wiggins (2001) and others, while also enriching and specifying existing accounts of genidentity due to [START_REF] Hull | A Matter of Individuality[END_REF], [START_REF] Guay | To Be Continued: The Genidentity of Physical and Biological Processes[END_REF].

Organizational continuity is consistent with dramatic developmental change, but it does not differentiate development and reproduction. This is because parent and offspring are organizationally continuous with one another just as the successive stages of parental development are. To distinguish parent and offspring, then, it is necessary to adopt working notions of fission and fusion. We argued that the reproduction of organized systems entails their spatial multiplication, and that the presence of a temporary asymmetrical dependence relationship between systems largely determines whether one of them is a continuation of the life of the parent. With fusion, similarly, the outcome is determined by the presence of asymmetrical dependence as well as by whether the fusing systems retain their separate closures.

With this account in hand, we can now assess it in light of the problems of individuality introduced at the start. On the problem of distinguishing development and reproduction, our account weaves between overly permissive and overly restrictive criteria of diachronic identity while making sense of a wide range of generative phenomena in biology. This provides a productive starting point for thinking about organism identity, but we also saw how, with the examples of reproduction in yeast and placental mammals, alternative temporal boundaries can be promoted from within different perspectives that bring different modeling and generalization strategies. Further work will be needed to sort through this variation in a more fine-grained way, to determine exactly which empirical situations demand which kinds of temporal boundaries.

Other theoretical aims foregrounded by existing accounts of biological individuality can, in most cases, be fruitfully embedded within an organizational account of organism identity. Part of the reason these other criteria can be superimposed on an organizational account is that the latter starts from the biologically basic process of self-maintenance rather than more complex developmental, ecological, or evolutionary processes. There is a clear sense in which, in order to be able to participate in those dynamic processes, a physical system must first be able to maintain itself far from equilibrium with its environment. In many cases, criteria focused on these other processes will individuate subsets and supersets of organized systems across time, and may also single out different temporal segments of biological process, but closure nonetheless explains what keeps it all going physically. An open task for future work will be to account for how these elements ultimately hang together.

The picture of organism identity outlined here has an interesting implication for classificatory practice in biology. Substantialist views lend themselves to a "phenetic" approach in which the identity of organisms and classes of organisms is determined by qualitative similarity, resemblance, or sameness of properties or activities. This type of approach has historically been associated with classification errors in which stages of the same polymorphic life cycle are assigned to different taxa because of their dissimilarity [START_REF] Hull | A Matter of Individuality[END_REF][START_REF] Nyhart | Alternation of Generations and Individuality[END_REF]. The propensity to make this error can be corrected by shifting from a similarity-based view to a causal continuity-based view of organism identity. Instead of looking for similarity between different stages of development, one looks for the right sort of causal connections between stages of the same four-dimensional developmental process.

organism does not count as fusion, because the eating organism consumes the eaten organism and no functional integration occurs. The theoretical distinction between constraints and processes outlined above is at work here.

xiii Isogamy, an ancestral state of sexual reproduction in which there is no male-female differentiated gametes, fits the interpretation of syngamy as (2) even more naturally. Other examples of fusions (2) would occur during the split-embryo development of certain freshwater fish (Cynolebias) (Minelli 2011, p. 11) and the formation of a syncytium.

Fig. 1 .

 1 Fig. 1. Material and functional change during metamorphosis in Drosophila. Many adult body parts are formed out of the set-aside cells in corresponding imaginal discs in the larva. Image reprinted from Current Biology, 20(10), Silvia Aldaz and Luis M. Escudero, "Imaginal Discs" PR429-R431, Copyright (2010), with permission from Elsevier. https://www.sciencedirect.com/journal/current-biology

Fig. 3 .

 3 Fig. 3. Differing interpretations of temporal boundaries and parthood in sexual reproduction in placental mammals. Gray segments denote parts of the female parent (f), and circles mark fission or fusion events. Time intervals are not to scale.

Acknowledgements:

The authors thank John Dupré, Anne Sophie Meincke, Alessandro Minelli and Alvaro Moreno for insightful comments. J. D. thanks the Research Fund -Flanders (FWO) and the Konrad Lorenz Institute for Evolution and Cognition Research for financial support.

 Wiggins, D. (2001)Sameness and Substance Renewed, Cambridge: Cambridge University Press.

Wiggins, D. ( 2016) Continuants: Their Activity, their Being, and their Identity, Oxford: Oxford University Press.

Yashiro K, Shiratori H, Hamada H (2007). "Haemodynamics determined by a genetic programme govern asymmetric development of the aortic arch." Nature 450: 285-288

i The fact that so many authors have expressed the shared intuition that spatiotemporal continuity is necessary for object identity is plausibly a reflection of deep-seated psychological mechanisms that allow us to perceive objects as persistent, an insight explored by [START_REF] Scholl | Object persistence in philosophy and psychology[END_REF]. Thanks for Riana J. Betzler for pointing us to this work.

ii During morphogenesis, however, the structure of the vascular system is influenced by the dynamics of blood flow (hemodynamics), as Alessandro Minelli points out (personal communication). See Yashiro et al ( 2007) and [START_REF] Kowalski | Critical Transitions in Early Embryonic Aortic Arch Patterning and Hemodynamics[END_REF].

iii Note that closure of constraints is importantly different from causal closure, a notion that is often invoked in discussions of physicalism or materialism. For more on the connection between physicalism and organization see [START_REF] Mossio | Emergence, closure and inter-level causation in biological systems[END_REF] and DiFrisco (2017).

iv Curiously, Wiggins maintains that "live things exemplify most perfectly and completely a category of substance that is extension-involving, imports the idea of characteristic activity, and is unproblematic for individuation" (2001, p. 90). This may be true if the task is one of distinguishing organisms from artifacts and other non-living things, but problems of individuality in contemporary biology are more demanding.

v In practice, it may be that we cannot specify an exact moment of death or birth, but only a temporal interval during which they have occurred. However, the ability to pinpoint an exact time of death does not seem to matter much from a biological perspective.

vi Recently, one of us has argued that organizational continuity among generations is actually a fundamental requirement for biological heredity, understood from an organizational perspective [START_REF] Mossio | Conserving functions across generations: heredity in light of biological organization[END_REF].

vii Note that we are not attempting to define reproduction directly, but to identify temporal boundaries of lifetimes. One such temporal boundary occurs with the spatial multiplication of organisms, which is not quite the same as reproduction. To distinguish reproduction from mere production of a new organized system, it may be necessary that the offspring resemble the parent or belong to the same kind (Godfrey-Smith 2009, p. 78).

Certainly some form of parent-offspring resemblance, probabilistic dependence, or covariance is necessary in order for reproduction to lead to evolution by natural selection, as [START_REF] Lewontin | The Units of Selection[END_REF] pointed out. That being understood, we sometimes still use the term "reproduction" for its familiarity.

viii Many authors think of replication as the most fundamental form of reproduction, the paradigm case being replication of nucleic acids. Our characterization is not intended to cover reproduction or replication in nonorganized systems such as nucleic acids, genes, or viruses.

ix Some yeasts, namely "fission yeasts" (Schizosaccharomycetes), reproduce asexually with symmetric cell divisions, so what follows does not apply to them.

x Recent evidence suggests that some paradigmatic cases of symmetrical cell fission (e.g., E. coli) may actually involve asymmetries in the retention of ageing components (see [START_REF] Nyström | A Bacterial Kind of Aging[END_REF]. Thanks to John Dupré for pointing this out.

xi Another phenomenon sometimes included under the heading of fusion is conjugation, a merger between cells in which genetic material is exchanged. Conjugation is a form of sexuality without reproduction (see Fusco and Minelli in press). Since conjugagtion does not affect the persistence of organized systems, we do not include it as a case of fusion.

xii It should be noted that, in this framework, fusion is understood as a functional issue, and refers to the merging of constraints between two individuals. For this reason, the situation in which an organism eats another