Daily Papers

Accurate plant counting provides valuable information for agriculture such as crop yield prediction, plant density assessment, and phenotype quantification. Vision-based approaches are currently the mainstream solution. Prior art typically uses a detection or a regression model to count a specific plant. However, plants have biodiversity, and new cultivars are increasingly bred each year. It is almost impossible to exhaust and build all species-dependent counting models. Inspired by class-agnostic counting (CAC) in computer vision, we argue that it is time to rethink the problem formulation of plant counting, from what plants to count to how to count plants. In contrast to most daily objects with spatial and temporal invariance, plants are dynamic, changing with time and space. Their non-rigid structure often leads to worse performance than counting rigid instances like heads and cars such that current CAC and open-world detection models are suboptimal to count plants. In this work, we inherit the vein of the TasselNet plant counting model and introduce a new extension, TasselNetV4, shifting from species-specific counting to cross-species counting. TasselNetV4 marries the local counting idea of TasselNet with the extract-and-match paradigm in CAC. It builds upon a plain vision transformer and incorporates novel multi-branch box-aware local counters used to enhance cross-scale robustness. Two challenging datasets, PAC-105 and PAC-Somalia, are harvested. Extensive experiments against state-of-the-art CAC models show that TasselNetV4 achieves not only superior counting performance but also high efficiency.Our results indicate that TasselNetV4 emerges to be a vision foundation model for cross-scene, cross-scale, and cross-species plant counting.

Visually cataloging and quantifying the natural world requires pushing the boundaries of both detailed visual classification and counting at scale. Despite significant progress, particularly in crowd and traffic analysis, the fine-grained, taxonomy-aware plant counting remains underexplored in vision. In contrast to crowds, plants exhibit nonrigid morphologies and physical appearance variations across growth stages and environments. To fill this gap, we present TPC-268, the first plant counting benchmark incorporating plant taxonomy. Our dataset couples instance-level point annotations with Linnaean labels (kingdom -> species) and organ categories, enabling hierarchical reasoning and species-aware evaluation. The dataset features 10,000 images with 678,050 point annotations, includes 268 countable plant categories over 242 plant species in Plantae and Fungi, and spans observation scales from canopy-level remote sensing imagery to tissue-level microscopy. We follow the problem setting of class-agnostic counting (CAC), provide taxonomy-consistent, scale-aware data splits, and benchmark state-of-the-art regression- and detection-based CAC approaches. By capturing the biodiversity, hierarchical structure, and multi-scale nature of botanical and mycological taxa, TPC-268 provides a biologically grounded testbed to advance fine-grained class-agnostic counting. Dataset and code are available at https://github.com/tiny-smart/TPC-268.

Wildlife observation plays an important role in biodiversity conservation, necessitating robust methodologies for monitoring wildlife populations and interspecies interactions. Recent advances in computer vision have significantly contributed to automating fundamental wildlife observation tasks, such as animal detection and species identification. However, accurately identifying species from indirect evidence like footprints and feces remains relatively underexplored, despite its importance in contributing to wildlife monitoring. To bridge this gap, we introduce AnimalClue, the first large-scale dataset for species identification from images of indirect evidence. Our dataset consists of 159,605 bounding boxes encompassing five categories of indirect clues: footprints, feces, eggs, bones, and feathers. It covers 968 species, 200 families, and 65 orders. Each image is annotated with species-level labels, bounding boxes or segmentation masks, and fine-grained trait information, including activity patterns and habitat preferences. Unlike existing datasets primarily focused on direct visual features (e.g., animal appearances), AnimalClue presents unique challenges for classification, detection, and instance segmentation tasks due to the need for recognizing more detailed and subtle visual features. In our experiments, we extensively evaluate representative vision models and identify key challenges in animal identification from their traces. Our dataset and code are available at https://dahlian00.github.io/AnimalCluePage/

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Existing works on visual counting primarily focus on one specific category at a time, such as people, animals, and cells. In this paper, we are interested in counting everything, that is to count objects from any category given only a few annotated instances from that category. To this end, we pose counting as a few-shot regression task. To tackle this task, we present a novel method that takes a query image together with a few exemplar objects from the query image and predicts a density map for the presence of all objects of interest in the query image. We also present a novel adaptation strategy to adapt our network to any novel visual category at test time, using only a few exemplar objects from the novel category. We also introduce a dataset of 147 object categories containing over 6000 images that are suitable for the few-shot counting task. The images are annotated with two types of annotation, dots and bounding boxes, and they can be used for developing few-shot counting models. Experiments on this dataset shows that our method outperforms several state-of-the-art object detectors and few-shot counting approaches. Our code and dataset can be found at https://github.com/cvlab-stonybrook/LearningToCountEverything.

Animal vocalizations provide crucial insights for wildlife assessment, particularly in complex environments such as forests, aiding species identification and ecological monitoring. Recent advances in deep learning have enabled automatic species classification from their vocalizations. However, classifying species unseen during training remains challenging. To address this limitation, we introduce AnimalCLAP, a taxonomy-aware language-audio framework comprising a new dataset and model that incorporate hierarchical biological information. Specifically, our vocalization dataset consists of 4,225 hours of recordings covering 6,823 species, annotated with 22 ecological traits. The AnimalCLAP model is trained on this dataset to align audio and textual representations using taxonomic structures, improving the recognition of unseen species. We demonstrate that our proposed model effectively infers ecological and biological attributes of species directly from their vocalizations, achieving superior performance compared to CLAP. Our dataset, code, and models will be publicly available at https://dahlian00.github.io/AnimalCLAP_Page/.

Measuring biodiversity is crucial for understanding ecosystem health. While prior works have developed machine learning models for taxonomic classification of photographic images and DNA separately, in this work, we introduce a multimodal approach combining both, using CLIP-style contrastive learning to align images, barcode DNA, and text-based representations of taxonomic labels in a unified embedding space. This allows for accurate classification of both known and unknown insect species without task-specific fine-tuning, leveraging contrastive learning for the first time to fuse DNA and image data. Our method surpasses previous single-modality approaches in accuracy by over 8% on zero-shot learning tasks, showcasing its effectiveness in biodiversity studies.

Manual labeling of animal images remains a significant bottleneck in ecological research, limiting the scale and efficiency of biodiversity monitoring efforts. This study investigates whether state-of-the-art Vision Transformer (ViT) foundation models can reduce thousands of unlabeled animal images directly to species-level clusters. We present a comprehensive benchmarking framework evaluating five ViT models combined with five dimensionality reduction techniques and four clustering algorithms, two supervised and two unsupervised, across 60 species (30 mammals and 30 birds), with each test using a random subset of 200 validated images per species. We investigate when clustering succeeds at species-level, where it fails, and whether clustering within the species-level reveals ecologically meaningful patterns such as sex, age, or phenotypic variation. Our results demonstrate near-perfect species-level clustering (V-measure: 0.958) using DINOv3 embeddings with t-SNE and supervised hierarchical clustering methods. Unsupervised approaches achieve competitive performance (0.943) while requiring no prior species knowledge, rejecting only 1.14% of images as outliers requiring expert review. We further demonstrate robustness to realistic long-tailed distributions of species and show that intentional over-clustering can reliably extract intra-specific variation including age classes, sexual dimorphism, and pelage differences. We introduce an open-source benchmarking toolkit and provide recommendations for ecologists to select appropriate methods for sorting their specific taxonomic groups and data.

Automated video analysis is critical for wildlife conservation. A foundational task in this domain is multi-animal tracking (MAT), which underpins applications such as individual re-identification and behavior recognition. However, existing datasets are limited in scale, constrained to a few species, or lack sufficient temporal and geographical diversity - leaving no suitable benchmark for training general-purpose MAT models applicable across wild animal populations. To address this, we introduce SA-FARI, the largest open-source MAT dataset for wild animals. It comprises 11,609 camera trap videos collected over approximately 10 years (2014-2024) from 741 locations across 4 continents, spanning 99 species categories. Each video is exhaustively annotated culminating in ~46 hours of densely annotated footage containing 16,224 masklet identities and 942,702 individual bounding boxes, segmentation masks, and species labels. Alongside the task-specific annotations, we publish anonymized camera trap locations for each video. Finally, we present comprehensive benchmarks on SA-FARI using state-of-the-art vision-language models for detection and tracking, including SAM 3, evaluated with both species-specific and generic animal prompts. We also compare against vision-only methods developed specifically for wildlife analysis. SA-FARI is the first large-scale dataset to combine high species diversity, multi-region coverage, and high-quality spatio-temporal annotations, offering a new foundation for advancing generalizable multianimal tracking in the wild. The dataset is available at https://www.conservationxlabs.com/sa-fari{conservationxlabs.com/SA-FARI}.

The flexibility and accuracy of methods for automatically counting objects in images and videos are limited by the way the object can be specified. While existing methods allow users to describe the target object with text and visual examples, the visual examples must be manually annotated inside the image, and there is no way to specify what not to count. To address these gaps, we introduce novel capabilities that expand how the target object can be specified. Specifically, we extend the prompt to enable what not to count to be described with text and/or visual examples, introduce the concept of `pseudo-exemplars' that automate the annotation of visual examples at inference, and extend counting models to accept visual examples from both natural and synthetic external images. We also use our new counting model, CountGD++, as a vision expert agent for an LLM. Together, these contributions expand the prompt flexibility of multi-modal open-world counting and lead to significant improvements in accuracy, efficiency, and generalization across multiple datasets. Code is available at https://github.com/niki-amini-naieni/CountGDPlusPlus.

Class-agnostic counting methods enumerate objects of an arbitrary class, providing tremendous utility in many fields. Prior works have limited usefulness as they require either a set of examples of the type to be counted or that the query image contains only a single type of object. A significant factor in these shortcomings is the lack of a dataset to properly address counting in settings with more than one kind of object present. To address these issues, we propose the first Multi-class, Class-Agnostic Counting dataset (MCAC) and A Blind Counter (ABC123), a method that can count multiple types of objects simultaneously without using examples of type during training or inference. ABC123 introduces a new paradigm where instead of requiring exemplars to guide the enumeration, examples are found after the counting stage to help a user understand the generated outputs. We show that ABC123 outperforms contemporary methods on MCAC without needing human in-the-loop annotations. We also show that this performance transfers to FSC-147, the standard class-agnostic counting dataset. MCAC is available at MCAC.active.vision and ABC123 is available at ABC123.active.vision.

Understanding animal species from multimodal data poses an emerging challenge at the intersection of computer vision and ecology. While recent biological models, such as BioCLIP, have demonstrated strong alignment between images and textual taxonomic information for species identification, the integration of the audio modality remains an open problem. We propose BioVITA, a novel visual-textual-acoustic alignment framework for biological applications. BioVITA involves (i) a training dataset, (ii) a representation model, and (iii) a retrieval benchmark. First, we construct a large-scale training dataset comprising 1.3 million audio clips and 2.3 million images, covering 14,133 species annotated with 34 ecological trait labels. Second, building upon BioCLIP2, we introduce a two-stage training framework to effectively align audio representations with visual and textual representations. Third, we develop a cross-modal retrieval benchmark that covers all possible directional retrieval across the three modalities (i.e., image-to-audio, audio-to-text, text-to-image, and their reverse directions), with three taxonomic levels: Family, Genus, and Species. Extensive experiments demonstrate that our model learns a unified representation space that captures species-level semantics beyond taxonomy, advancing multimodal biodiversity understanding. The project page is available at: https://dahlian00.github.io/BioVITA_Page/

Animal habitat surveys play a critical role in preserving the biodiversity of the land. One of the effective ways to gain insights into animal habitats involves identifying animal footprints, which offers valuable information about species distribution, abundance, and behavior. However, due to the scarcity of animal footprint images, there are no well-maintained public datasets, preventing recent advanced techniques in computer vision from being applied to animal tracking. In this paper, we introduce OpenAnimalTracks dataset, the first publicly available labeled dataset designed to facilitate the automated classification and detection of animal footprints. It contains various footprints from 18 wild animal species. Moreover, we build benchmarks for species classification and detection and show the potential of automated footprint identification with representative classifiers and detection models. We find SwinTransformer achieves a promising classification result, reaching 69.41% in terms of the averaged accuracy. Faster-RCNN achieves mAP of 0.295. We hope our dataset paves the way for automated animal tracking techniques, enhancing our ability to protect and manage biodiversity. Our dataset and code are available at https://github.com/dahlian00/OpenAnimalTracks.

Camera traps have transformed how ecologists study wildlife species distributions, activity patterns, and interspecific interactions. Although camera traps provide a cost-effective method for monitoring species, the time required for data processing can limit survey efficiency. Thus, the potential of Artificial Intelligence (AI), specifically Deep Learning (DL), to process camera-trap data has gained considerable attention. Using DL for these applications involves training algorithms, such as Convolutional Neural Networks (CNNs), to automatically detect objects and classify species. To overcome technical challenges associated with training CNNs, several research communities have recently developed platforms that incorporate DL in easy-to-use interfaces. We review key characteristics of four AI-powered platforms -- Wildlife Insights (WI), MegaDetector (MD), Machine Learning for Wildlife Image Classification (MLWIC2), and Conservation AI -- including data management tools and AI features. We also provide R code in an open-source GitBook, to demonstrate how users can evaluate model performance, and incorporate AI output in semi-automated workflows. We found that species classifications from WI and MLWIC2 generally had low recall values (animals that were present in the images often were not classified to the correct species). Yet, the precision of WI and MLWIC2 classifications for some species was high (i.e., when classifications were made, they were generally accurate). MD, which classifies images using broader categories (e.g., "blank" or "animal"), also performed well. Thus, we conclude that, although species classifiers were not accurate enough to automate image processing, DL could be used to improve efficiencies by accepting classifications with high confidence values for certain species or by filtering images containing blanks.

Marine visual understanding is essential for monitoring and protecting marine ecosystems, enabling automatic and scalable biological surveys. However, progress is hindered by limited training data and the lack of a systematic task formulation that aligns domain-specific marine challenges with well-defined computer vision tasks, thereby limiting effective model application. To address this gap, we present ORCA, a multi-modal benchmark for marine research comprising 14,647 images from 478 species, with 42,217 bounding box annotations and 22,321 expert-verified instance captions. The dataset provides fine-grained visual and textual annotations that capture morphology-oriented attributes across diverse marine species. To catalyze methodological advances, we evaluate 18 state-of-the-art models on three tasks: object detection (closed-set and open-vocabulary), instance captioning, and visual grounding. Results highlight key challenges, including species diversity, morphological overlap, and specialized domain demands, underscoring the difficulty of marine understanding. ORCA thus establishes a comprehensive benchmark to advance research in marine domain. Project Page: http://orca.hkustvgd.com/.

Monitoring critically endangered western lowland gorillas is currently hampered by the immense manual effort required to re-identify individuals from vast archives of camera trap footage. The primary obstacle to automating this process has been the lack of large-scale, "in-the-wild" video datasets suitable for training robust deep learning models. To address this gap, we introduce a comprehensive benchmark with three novel datasets: Gorilla-SPAC-Wild, the largest video dataset for wild primate re-identification to date; Gorilla-Berlin-Zoo, for assessing cross-domain re-identification generalization; and Gorilla-SPAC-MoT, for evaluating multi-object tracking in camera trap footage. Building on these datasets, we present GorillaWatch, an end-to-end pipeline integrating detection, tracking, and re-identification. To exploit temporal information, we introduce a multi-frame self-supervised pretraining strategy that leverages consistency in tracklets to learn domain-specific features without manual labels. To ensure scientific validity, a differentiable adaptation of AttnLRP verifies that our model relies on discriminative biometric traits rather than background correlations. Extensive benchmarking subsequently demonstrates that aggregating features from large-scale image backbones outperforms specialized video architectures. Finally, we address unsupervised population counting by integrating spatiotemporal constraints into standard clustering to mitigate over-segmentation. We publicly release all code and datasets to facilitate scalable, non-invasive monitoring of endangered species

Object counting has progressed from class-specific models, which count only known categories, to class-agnostic models that generalize to unseen categories. The next challenge is Referring Expression Counting (REC), where the goal is to count objects based on fine-grained attributes and contextual differences. Existing methods struggle with distinguishing visually similar objects that belong to the same category but correspond to different referring expressions. To address this, we propose C-REX, a novel contrastive learning framework, based on supervised contrastive learning, designed to enhance discriminative representation learning. Unlike prior works, C-REX operates entirely within the image space, avoiding the misalignment issues of image-text contrastive learning, thus providing a more stable contrastive signal. It also guarantees a significantly larger pool of negative samples, leading to improved robustness in the learned representations. Moreover, we showcase that our framework is versatile and generic enough to be applied to other similar tasks like class-agnostic counting. To support our approach, we analyze the key components of sota detection-based models and identify that detecting object centroids instead of bounding boxes is the key common factor behind their success in counting tasks. We use this insight to design a simple yet effective detection-based baseline to build upon. Our experiments show that C-REX achieves state-of-the-art results in REC, outperforming previous methods by more than 22\% in MAE and more than 10\% in RMSE, while also demonstrating strong performance in class-agnostic counting. Code is available at https://github.com/cvlab-stonybrook/c-rex.

Visual Species Recognition (VSR) is pivotal to biodiversity assessment and conservation, evolution research, and ecology and ecosystem management. Training a machine-learned model for VSR typically requires vast amounts of annotated images. Yet, species-level annotation demands domain expertise, making it realistic for domain experts to annotate only a few examples. These limited labeled data motivate training an ''expert'' model via few-shot learning (FSL). Meanwhile, advanced Large Multimodal Models (LMMs) have demonstrated prominent performance on general recognition tasks. It is straightforward to ask whether LMMs excel in the highly specialized VSR task and whether they outshine FSL expert models. Somewhat surprisingly, we find that LMMs struggle in this task, despite using various established prompting techniques. LMMs even significantly underperform FSL expert models, which are as simple as finetuning a pretrained visual encoder on the few-shot images. However, our in-depth analysis reveals that LMMs can effectively post-hoc correct the expert models' incorrect predictions. Briefly, given a test image, when prompted with the top predictions from an FSL expert model, LMMs can recover the ground-truth label. Building on this insight, we derive a simple method called Post-hoc Correction (POC), which prompts an LMM to re-rank the expert model's top predictions using enriched prompts that include softmax confidence scores and few-shot visual examples. Across five challenging VSR benchmarks, POC outperforms prior art of FSL by +6.4% in accuracy without extra training, validation, or manual intervention. Importantly, POC generalizes to different pretrained backbones and LMMs, serving as a plug-and-play module to significantly enhance existing FSL methods.

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

The goal of this paper is to improve the generality and accuracy of open-vocabulary object counting in images. To improve the generality, we repurpose an open-vocabulary detection foundation model (GroundingDINO) for the counting task, and also extend its capabilities by introducing modules to enable specifying the target object to count by visual exemplars. In turn, these new capabilities - being able to specify the target object by multi-modalites (text and exemplars) - lead to an improvement in counting accuracy. We make three contributions: First, we introduce the first open-world counting model, CountGD, where the prompt can be specified by a text description or visual exemplars or both; Second, we show that the performance of the model significantly improves the state of the art on multiple counting benchmarks - when using text only, CountGD is comparable to or outperforms all previous text-only works, and when using both text and visual exemplars, we outperform all previous models; Third, we carry out a preliminary study into different interactions between the text and visual exemplar prompts, including the cases where they reinforce each other and where one restricts the other. The code and an app to test the model are available at https://www.robots.ox.ac.uk/~vgg/research/countgd/.

Open-world object counting leverages the robust text-image alignment of pre-trained vision-language models (VLMs) to enable counting of arbitrary categories in images specified by textual queries. However, widely adopted naive fine-tuning strategies concentrate exclusively on text-image consistency for categories contained in training, which leads to limited generalizability for unseen categories. In this work, we propose a plug-and-play Semantic-Driven Visual Prompt Tuning framework (SDVPT) that transfers knowledge from the training set to unseen categories with minimal overhead in parameters and inference time. First, we introduce a two-stage visual prompt learning strategy composed of Category-Specific Prompt Initialization (CSPI) and Topology-Guided Prompt Refinement (TGPR). The CSPI generates category-specific visual prompts, and then TGPR distills latent structural patterns from the VLM's text encoder to refine these prompts. During inference, we dynamically synthesize the visual prompts for unseen categories based on the semantic correlation between unseen and training categories, facilitating robust text-image alignment for unseen categories. Extensive experiments integrating SDVPT with all available open-world object counting models demonstrate its effectiveness and adaptability across three widely used datasets: FSC-147, CARPK, and PUCPR+.

Monitoring animal behavior can facilitate conservation efforts by providing key insights into wildlife health, population status, and ecosystem function. Automatic recognition of animals and their behaviors is critical for capitalizing on the large unlabeled datasets generated by modern video devices and for accelerating monitoring efforts at scale. However, the development of automated recognition systems is currently hindered by a lack of appropriately labeled datasets. Existing video datasets 1) do not classify animals according to established biological taxonomies; 2) are too small to facilitate large-scale behavioral studies and are often limited to a single species; and 3) do not feature temporally localized annotations and therefore do not facilitate localization of targeted behaviors within longer video sequences. Thus, we propose MammalNet, a new large-scale animal behavior dataset with taxonomy-guided annotations of mammals and their common behaviors. MammalNet contains over 18K videos totaling 539 hours, which is ~10 times larger than the largest existing animal behavior dataset. It covers 17 orders, 69 families, and 173 mammal categories for animal categorization and captures 12 high-level animal behaviors that received focus in previous animal behavior studies. We establish three benchmarks on MammalNet: standard animal and behavior recognition, compositional low-shot animal and behavior recognition, and behavior detection. Our dataset and code have been made available at: https://mammal-net.github.io.

Accurate individual identification is essential for monitoring rare amphibians, yet invasive marking is often unsuitable for critically endangered species. We evaluate state-of-the-art computer-vision methods for photographic re-identification of the Hula painted frog (Latonia nigriventer) using 1,233 ventral images from 191 individuals collected during 2013-2020 capture-recapture surveys. We compare deep local-feature matching in a zero-shot setting with deep global-feature embedding models. The local-feature pipeline achieves 98% top-1 closed-set identification accuracy, outperforming all global-feature models; fine-tuning improves the best global-feature model to 60% top-1 (91% top-10) but remains below local matching. To combine scalability with accuracy, we implement a two-stage workflow in which a fine-tuned global-feature model retrieves a short candidate list that is re-ranked by local-feature matching, reducing end-to-end runtime from 6.5-7.8 hours to ~38 minutes while maintaining ~96% top-1 closed-set accuracy on the labeled dataset. Separation of match scores between same- and different-individual pairs supports thresholding for open-set identification, enabling practical handling of novel individuals. We deploy this pipeline as a web application for routine field use, providing rapid, standardized, non-invasive identification to support conservation monitoring and capture-recapture analyses. Overall, in this species, zero-shot deep local-feature matching outperformed global-feature embedding and provides a strong default for photo-identification.

Birds are important indicators for monitoring both biodiversity and habitat health; they also play a crucial role in ecosystem management. Decline in bird populations can result in reduced eco-system services, including seed dispersal, pollination and pest control. Accurate and long-term monitoring of birds to identify species of concern while measuring the success of conservation interventions is essential for ecologists. However, monitoring is time consuming, costly and often difficult to manage over long durations and at meaningfully large spatial scales. Technology such as camera traps, acoustic monitors and drones provide methods for non-invasive monitoring. There are two main problems with using camera traps for monitoring: a) cameras generate many images, making it difficult to process and analyse the data in a timely manner; and b) the high proportion of false positives hinders the processing and analysis for reporting. In this paper, we outline an approach for overcoming these issues by utilising deep learning for real-time classi-fication of bird species and automated removal of false positives in camera trap data. Images are classified in real-time using a Faster-RCNN architecture. Images are transmitted over 3/4G cam-eras and processed using Graphical Processing Units (GPUs) to provide conservationists with key detection metrics therefore removing the requirement for manual observations. Our models achieved an average sensitivity of 88.79%, a specificity of 98.16% and accuracy of 96.71%. This demonstrates the effectiveness of using deep learning for automatic bird monitoring.

Insects comprise millions of species, many experiencing severe population declines under environmental and habitat changes. High-throughput approaches are crucial for accelerating our understanding of insect diversity, with DNA barcoding and high-resolution imaging showing strong potential for automatic taxonomic classification. However, most image-based approaches rely on individual specimen data, unlike the unsorted bulk samples collected in large-scale ecological surveys. We present the Mixed Arthropod Sample Segmentation and Identification (MassID45) dataset for training automatic classifiers of bulk insect samples. It uniquely combines molecular and imaging data at both the unsorted sample level and the full set of individual specimens. Human annotators, supported by an AI-assisted tool, performed two tasks on bulk images: creating segmentation masks around each individual arthropod and assigning taxonomic labels to over 17 000 specimens. Combining the taxonomic resolution of DNA barcodes with precise abundance estimates of bulk images holds great potential for rapid, large-scale characterization of insect communities. This dataset pushes the boundaries of tiny object detection and instance segmentation, fostering innovation in both ecological and machine learning research.

Biodiversity assessments are critically affected by the spatial scale at which species richness is measured. How species richness accumulates with sampling area depends on natural and anthropogenic processes whose effects can change depending on the spatial scale considered. These accumulation dynamics, described by the species-area relationship (SAR), are challenging to assess because most biodiversity surveys are restricted to sampling areas much smaller than the scales at which these processes operate. Here, we combine sampling theory and deep learning to predict local species richness within arbitrarily large sampling areas, enabling for the first time to estimate spatial differences in SARs. We demonstrate our approach by predicting vascular plant species richness across Europe and evaluate predictions against an independent dataset of plant community inventories. The resulting model, named deep SAR, delivers multi-scale species richness maps, improving coarse grain richness estimates by 32% compared to conventional methods, while delivering finer grain estimates. Additional to its predictive capabilities, we show how our deep SAR model can provide fundamental insights on the multi-scale effects of key biodiversity processes. The capacity of our approach to deliver comprehensive species richness estimates across the full spectrum of ecologically relevant scales is essential for robust biodiversity assessments and forecasts under global change.

Systematic under-counting effects are observed in data collected across many disciplines, e.g., epidemiology and ecology. Under-counted tensor completion (UC-TC) is well-motivated for many data analytics tasks, e.g., inferring the case numbers of infectious diseases at unobserved locations from under-counted case numbers in neighboring regions. However, existing methods for similar problems often lack supports in theory, making it hard to understand the underlying principles and conditions beyond empirical successes. In this work, a low-rank Poisson tensor model with an expressive unknown nonlinear side information extractor is proposed for under-counted multi-aspect data. A joint low-rank tensor completion and neural network learning algorithm is designed to recover the model. Moreover, the UC-TC formulation is supported by theoretical analysis showing that the fully counted entries of the tensor and each entry's under-counting probability can be provably recovered from partial observations -- under reasonable conditions. To our best knowledge, the result is the first to offer theoretical supports for under-counted multi-aspect data completion. Simulations and real-data experiments corroborate the theoretical claims.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Existing image classification datasets used in computer vision tend to have a uniform distribution of images across object categories. In contrast, the natural world is heavily imbalanced, as some species are more abundant and easier to photograph than others. To encourage further progress in challenging real world conditions we present the iNaturalist species classification and detection dataset, consisting of 859,000 images from over 5,000 different species of plants and animals. It features visually similar species, captured in a wide variety of situations, from all over the world. Images were collected with different camera types, have varying image quality, feature a large class imbalance, and have been verified by multiple citizen scientists. We discuss the collection of the dataset and present extensive baseline experiments using state-of-the-art computer vision classification and detection models. Results show that current non-ensemble based methods achieve only 67% top one classification accuracy, illustrating the difficulty of the dataset. Specifically, we observe poor results for classes with small numbers of training examples suggesting more attention is needed in low-shot learning.

The CLIP (Contrastive Language-Image Pretraining) model has exhibited outstanding performance in recognition problems, such as zero-shot image classification and object detection. However, its ability to count remains understudied due to the inherent challenges of transforming counting--a regression task--into a recognition task. In this paper, we investigate CLIP's potential in counting, focusing specifically on estimating crowd sizes. Existing classification-based crowd-counting methods have encountered issues, including inappropriate discretization strategies, which impede the application of CLIP and result in suboptimal performance. To address these challenges, we propose the Enhanced Blockwise Classification (EBC) framework. In contrast to previous methods, EBC relies on integer-valued bins that facilitate the learning of robust decision boundaries. Within our model-agnostic EBC framework, we introduce CLIP-EBC, the first fully CLIP-based crowd-counting model capable of generating density maps. Comprehensive evaluations across diverse crowd-counting datasets demonstrate the state-of-the-art performance of our methods. Particularly, EBC can improve existing models by up to 76.9%. Moreover, our CLIP-EBC model surpasses current crowd-counting methods, achieving mean absolute errors of 55.0 and 6.3 on ShanghaiTech part A and part B datasets, respectively. The code will be made publicly available.

Object counting is pivotal for understanding the composition of scenes. Previously, this task was dominated by class-specific methods, which have gradually evolved into more adaptable class-agnostic strategies. However, these strategies come with their own set of limitations, such as the need for manual exemplar input and multiple passes for multiple categories, resulting in significant inefficiencies. This paper introduces a new, more practical approach enabling simultaneous counting of multiple object categories using an open vocabulary framework. Our solution, OmniCount, stands out by using semantic and geometric insights from pre-trained models to count multiple categories of objects as specified by users, all without additional training. OmniCount distinguishes itself by generating precise object masks and leveraging point prompts via the Segment Anything Model for efficient counting. To evaluate OmniCount, we created the OmniCount-191 benchmark, a first-of-its-kind dataset with multi-label object counts, including points, bounding boxes, and VQA annotations. Our comprehensive evaluation in OmniCount-191, alongside other leading benchmarks, demonstrates OmniCount's exceptional performance, significantly outpacing existing solutions and heralding a new era in object counting technology.

Effective monitoring of wildlife is critical for assessing biodiversity and ecosystem health, as declines in key species often signal significant environmental changes. Birds, particularly ground-nesting species, serve as important ecological indicators due to their sensitivity to environmental pressures. Camera traps have become indispensable tools for monitoring nesting bird populations, enabling data collection across diverse habitats. However, the manual processing and analysis of such data are resource-intensive, often delaying the delivery of actionable conservation insights. This study presents an AI-driven approach for real-time species detection, focusing on the curlew (Numenius arquata), a ground-nesting bird experiencing significant population declines. A custom-trained YOLOv10 model was developed to detect and classify curlews and their chicks using 3/4G-enabled cameras linked to the Conservation AI platform. The system processes camera trap data in real-time, significantly enhancing monitoring efficiency. Across 11 nesting sites in Wales, the model achieved high performance, with a sensitivity of 90.56%, specificity of 100%, and F1-score of 95.05% for curlew detections, and a sensitivity of 92.35%, specificity of 100%, and F1-score of 96.03% for curlew chick detections. These results demonstrate the capability of AI-driven monitoring systems to deliver accurate, timely data for biodiversity assessments, facilitating early conservation interventions and advancing the use of technology in ecological research.

Large vision-language models (VLMs), such as CLIP, learn rich joint image-text representations, facilitating advances in numerous downstream tasks, including zero-shot classification and text-to-image generation. Nevertheless, existing VLMs exhibit a prominent well-documented limitation - they fail to encapsulate compositional concepts such as counting. We introduce a simple yet effective method to improve the quantitative understanding of VLMs, while maintaining their overall performance on common benchmarks. Specifically, we propose a new counting-contrastive loss used to finetune a pre-trained VLM in tandem with its original objective. Our counting loss is deployed over automatically-created counterfactual examples, each consisting of an image and a caption containing an incorrect object count. For example, an image depicting three dogs is paired with the caption "Six dogs playing in the yard". Our loss encourages discrimination between the correct caption and its counterfactual variant which serves as a hard negative example. To the best of our knowledge, this work is the first to extend CLIP's capabilities to object counting. Furthermore, we introduce "CountBench" - a new image-text counting benchmark for evaluating a model's understanding of object counting. We demonstrate a significant improvement over state-of-the-art baseline models on this task. Finally, we leverage our count-aware CLIP model for image retrieval and text-conditioned image generation, demonstrating that our model can produce specific counts of objects more reliably than existing ones.

We introduce T-Rex, an interactive object counting model designed to first detect and then count any objects. We formulate object counting as an open-set object detection task with the integration of visual prompts. Users can specify the objects of interest by marking points or boxes on a reference image, and T-Rex then detects all objects with a similar pattern. Guided by the visual feedback from T-Rex, users can also interactively refine the counting results by prompting on missing or falsely-detected objects. T-Rex has achieved state-of-the-art performance on several class-agnostic counting benchmarks. To further exploit its potential, we established a new counting benchmark encompassing diverse scenarios and challenges. Both quantitative and qualitative results show that T-Rex possesses exceptional zero-shot counting capabilities. We also present various practical application scenarios for T-Rex, illustrating its potential in the realm of visual prompting.

Animal visual perception is an important technique for automatically monitoring animal health, understanding animal behaviors, and assisting animal-related research. However, it is challenging to design a deep learning-based perception model that can freely adapt to different animals across various perception tasks, due to the varying poses of a large diversity of animals, lacking data on rare species, and the semantic inconsistency of different tasks. We introduce UniAP, a novel Universal Animal Perception model that leverages few-shot learning to enable cross-species perception among various visual tasks. Our proposed model takes support images and labels as prompt guidance for a query image. Images and labels are processed through a Transformer-based encoder and a lightweight label encoder, respectively. Then a matching module is designed for aggregating information between prompt guidance and the query image, followed by a multi-head label decoder to generate outputs for various tasks. By capitalizing on the shared visual characteristics among different animals and tasks, UniAP enables the transfer of knowledge from well-studied species to those with limited labeled data or even unseen species. We demonstrate the effectiveness of UniAP through comprehensive experiments in pose estimation, segmentation, and classification tasks on diverse animal species, showcasing its ability to generalize and adapt to new classes with minimal labeled examples.

Class-agnostic counting (CAC) aims to estimate the number of objects in images without being restricted to predefined categories. However, while current exemplar-based CAC methods offer flexibility at inference time, they still rely heavily on labeled data for training, which limits scalability and generalization to many downstream use cases. In this paper, we introduce CountingDINO, the first training-free exemplar-based CAC framework that exploits a fully unsupervised feature extractor. Specifically, our approach employs self-supervised vision-only backbones to extract object-aware features, and it eliminates the need for annotated data throughout the entire proposed pipeline. At inference time, we extract latent object prototypes via ROI-Align from DINO features and use them as convolutional kernels to generate similarity maps. These are then transformed into density maps through a simple yet effective normalization scheme. We evaluate our approach on the FSC-147 benchmark, where we consistently outperform a baseline based on an SOTA unsupervised object detector under the same label- and training-free setting. Additionally, we achieve competitive results -- and in some cases surpass -- training-free methods that rely on supervised backbones, non-training-free unsupervised methods, as well as several fully supervised SOTA approaches. This demonstrates that label- and training-free CAC can be both scalable and effective. Code: https://lorebianchi98.github.io/CountingDINO/.

We propose a novel framework for interactive class-agnostic object counting, where a human user can interactively provide feedback to improve the accuracy of a counter. Our framework consists of two main components: a user-friendly visualizer to gather feedback and an efficient mechanism to incorporate it. In each iteration, we produce a density map to show the current prediction result, and we segment it into non-overlapping regions with an easily verifiable number of objects. The user can provide feedback by selecting a region with obvious counting errors and specifying the range for the estimated number of objects within it. To improve the counting result, we develop a novel adaptation loss to force the visual counter to output the predicted count within the user-specified range. For effective and efficient adaptation, we propose a refinement module that can be used with any density-based visual counter, and only the parameters in the refinement module will be updated during adaptation. Our experiments on two challenging class-agnostic object counting benchmarks, FSCD-LVIS and FSC-147, show that our method can reduce the mean absolute error of multiple state-of-the-art visual counters by roughly 30% to 40% with minimal user input. Our project can be found at https://yifehuang97.github.io/ICACountProjectPage/.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Biologists all over the world use camera traps to monitor biodiversity and wildlife population density. The computer vision community has been making strides towards automating the species classification challenge in camera traps, but it has proven difficult to to apply models trained in one region to images collected in different geographic areas. In some cases, accuracy falls off catastrophically in new region, due to both changes in background and the presence of previously-unseen species. We propose a pipeline that takes advantage of a pre-trained general animal detector and a smaller set of labeled images to train a classification model that can efficiently achieve accurate results in a new region.

Camera traps are valuable tools in animal ecology for biodiversity monitoring and conservation. However, challenges like poor generalization to deployment at new unseen locations limit their practical application. Images are naturally associated with heterogeneous forms of context possibly in different modalities. In this work, we leverage the structured context associated with the camera trap images to improve out-of-distribution generalization for the task of species identification in camera traps. For example, a photo of a wild animal may be associated with information about where and when it was taken, as well as structured biology knowledge about the animal species. While typically overlooked by existing work, bringing back such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively integrating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that reformulates species classification as link prediction in a multimodal knowledge graph (KG). This framework seamlessly integrates various forms of multimodal context for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework successfully incorporates biological taxonomy for improved generalization and enhances sample efficiency for recognizing under-represented species.

Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of order q=1 by leveraging ideas from quantum statistical mechanics. Contrary to many diversity metrics in ecology, the Vendi Score accounts for similarity and does not require knowledge of the prevalence of the categories in the collection to be evaluated for diversity. However, the Vendi Score treats each item in a given collection with a level of sensitivity proportional to the item's prevalence. This is undesirable in settings where there is a significant imbalance in item prevalence. In this paper, we extend the other Hill numbers using similarity to provide flexibility in allocating sensitivity to rare or common items. This leads to a family of diversity metrics -- Vendi scores with different levels of sensitivity -- that can be used in a variety of applications. We study the properties of the scores in a synthetic controlled setting where the ground truth diversity is known. We then test their utility in improving molecular simulations via Vendi Sampling. Finally, we use the Vendi scores to better understand the behavior of image generative models in terms of memorization, duplication, diversity, and sample quality.

In this paper, we consider the problem of generalised visual object counting, with the goal of developing a computational model for counting the number of objects from arbitrary semantic categories, using arbitrary number of "exemplars", i.e. zero-shot or few-shot counting. To this end, we make the following four contributions: (1) We introduce a novel transformer-based architecture for generalised visual object counting, termed as Counting Transformer (CounTR), which explicitly capture the similarity between image patches or with given "exemplars" with the attention mechanism;(2) We adopt a two-stage training regime, that first pre-trains the model with self-supervised learning, and followed by supervised fine-tuning;(3) We propose a simple, scalable pipeline for synthesizing training images with a large number of instances or that from different semantic categories, explicitly forcing the model to make use of the given "exemplars";(4) We conduct thorough ablation studies on the large-scale counting benchmark, e.g. FSC-147, and demonstrate state-of-the-art performance on both zero and few-shot settings.

Biodiversity plays a crucial role in maintaining the balance of the ecosystem. However, poaching and unintentional human activities contribute to the decline in the population of many species. Hence, active monitoring is required to preserve these endangered species. Current human-led monitoring techniques are prone to errors and are labor-intensive. Therefore, we study the application of deep learning methods like Convolutional Neural Networks (CNNs) and transfer learning, which can aid in automating the process of monitoring endangered species. For this, we create our custom dataset utilizing trustworthy online databases like iNaturalist and ZooChat. To choose the best model for our use case, we compare the performance of different architectures like DenseNet, ResNet, VGGNet, and YOLOv8 on the custom wildlife dataset. Transfer learning reduces training time by freezing the pre-trained weights and replacing only the output layer with custom, fully connected layers designed for our dataset. Our results indicate that YOLOv8 performs better, achieving a training accuracy of 97.39 % and an F1 score of 96.50 %, surpassing other models. Our findings suggest that integrating YOLOv8 into conservation efforts could revolutionize wildlife monitoring with its high accuracy and efficiency, potentially transforming how endangered species are monitored and protected worldwide.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Currently available tools for the automated acoustic recognition of European insects in natural soundscapes are limited in scope. Large and ecologically heterogeneous acoustic datasets are currently needed for these algorithms to cross-contextually recognize the subtle and complex acoustic signatures produced by each species, thus making the availability of such datasets a key requisite for their development. Here we present ECOSoundSet (European Cicadidae and Orthoptera Sound dataSet), a dataset containing 10,653 recordings of 200 orthopteran and 24 cicada species (217 and 26 respective taxa when including subspecies) present in North, Central, and temperate Western Europe (Andorra, Belgium, Denmark, mainland France and Corsica, Germany, Ireland, Luxembourg, Monaco, Netherlands, United Kingdom, Switzerland), collected partly through targeted fieldwork in South France and Catalonia and partly through contributions from various European entomologists. The dataset is composed of a combination of coarsely labeled recordings, for which we can only infer the presence, at some point, of their target species (weak labeling), and finely annotated recordings, for which we know the specific time and frequency range of each insect sound present in the recording (strong labeling). We also provide a train/validation/test split of the strongly labeled recordings, with respective approximate proportions of 0.8, 0.1 and 0.1, in order to facilitate their incorporation in the training and evaluation of deep learning algorithms. This dataset could serve as a meaningful complement to recordings already available online for the training of deep learning algorithms for the acoustic classification of orthopterans and cicadas in North, Central, and temperate Western Europe.

Automated animal face identification plays a crucial role in the monitoring of behaviors, conducting of surveys, and finding of lost animals. Despite the advancements in human face identification, the lack of datasets and benchmarks in the animal domain has impeded progress. In this paper, we introduce the PetFace dataset, a comprehensive resource for animal face identification encompassing 257,484 unique individuals across 13 animal families and 319 breed categories, including both experimental and pet animals. This large-scale collection of individuals facilitates the investigation of unseen animal face verification, an area that has not been sufficiently explored in existing datasets due to the limited number of individuals. Moreover, PetFace also has fine-grained annotations such as sex, breed, color, and pattern. We provide multiple benchmarks including re-identification for seen individuals and verification for unseen individuals. The models trained on our dataset outperform those trained on prior datasets, even for detailed breed variations and unseen animal families. Our result also indicates that there is some room to improve the performance of integrated identification on multiple animal families. We hope the PetFace dataset will facilitate animal face identification and encourage the development of non-invasive animal automatic identification methods.

Class-agnostic object counting aims to count all objects in an image with respect to example boxes or class names, a.k.a few-shot and zero-shot counting. In this paper, we propose a generalized framework for both few-shot and zero-shot object counting based on detection. Our framework combines the superior advantages of two foundation models without compromising their zero-shot capability: (i) SAM to segment all possible objects as mask proposals, and (ii) CLIP to classify proposals to obtain accurate object counts. However, this strategy meets the obstacles of efficiency overhead and the small crowded objects that cannot be localized and distinguished. To address these issues, our framework, termed PseCo, follows three steps: point, segment, and count. Specifically, we first propose a class-agnostic object localization to provide accurate but least point prompts for SAM, which consequently not only reduces computation costs but also avoids missing small objects. Furthermore, we propose a generalized object classification that leverages CLIP image/text embeddings as the classifier, following a hierarchical knowledge distillation to obtain discriminative classifications among hierarchical mask proposals. Extensive experimental results on FSC-147, COCO, and LVIS demonstrate that PseCo achieves state-of-the-art performance in both few-shot/zero-shot object counting/detection. Code: https://github.com/Hzzone/PseCo

We present the PanAf20K dataset, the largest and most diverse open-access annotated video dataset of great apes in their natural environment. It comprises more than 7 million frames across ~20,000 camera trap videos of chimpanzees and gorillas collected at 18 field sites in tropical Africa as part of the Pan African Programme: The Cultured Chimpanzee. The footage is accompanied by a rich set of annotations and benchmarks making it suitable for training and testing a variety of challenging and ecologically important computer vision tasks including ape detection and behaviour recognition. Furthering AI analysis of camera trap information is critical given the International Union for Conservation of Nature now lists all species in the great ape family as either Endangered or Critically Endangered. We hope the dataset can form a solid basis for engagement of the AI community to improve performance, efficiency, and result interpretation in order to support assessments of great ape presence, abundance, distribution, and behaviour and thereby aid conservation efforts.

Bioacoustics, the study of sounds produced by living organisms, plays a vital role in conservation, biodiversity monitoring, and behavioral studies. Many tasks in this field, such as species, individual, and behavior classification and detection, are well-suited to machine learning. However, they often suffer from limited annotated data, highlighting the need for a general-purpose bioacoustic encoder capable of extracting useful representations for diverse downstream tasks. Such encoders have been proposed before, but are often limited in scope due to a focus on a narrow range of species (typically birds), and a reliance on a single model architecture or training paradigm. Moreover, they are usually evaluated on a small set of tasks and datasets. In this work, we present a large-scale empirical study that covers aspects of bioacoustics that are relevant to research but have previously been scarcely considered: training data diversity and scale, model architectures and training recipes, and the breadth of evaluation tasks and datasets. We obtain encoders that are state-of-the-art on the existing and proposed benchmarks. We also identify what matters for training these encoders, such that this work can be extended when more data are available or better architectures are proposed. Specifically, across 26 datasets with tasks including species classification, detection, individual ID, and vocal repertoire discovery, we find self-supervised pre-training followed by supervised post-training on a mixed bioacoustics + general-audio corpus yields the strongest in- and out-of-distribution performance. We show the importance of data diversity in both stages. To support ongoing research and application, we will release the model checkpoints.

A comprehensive understanding of animal behavior ecology depends on scalable approaches to quantify and interpret complex, multidimensional behavioral patterns. Traditional field observations are often limited in scope, time-consuming, and labor-intensive, hindering the assessment of behavioral responses across landscapes. To address this, we present kabr-tools (Kenyan Animal Behavior Recognition Tools), an open-source package for automated multi-species behavioral monitoring. This framework integrates drone-based video with machine learning systems to extract behavioral, social, and spatial metrics from wildlife footage. Our pipeline leverages object detection, tracking, and behavioral classification systems to generate key metrics, including time budgets, behavioral transitions, social interactions, habitat associations, and group composition dynamics. Compared to ground-based methods, drone-based observations significantly improved behavioral granularity, reducing visibility loss by 15% and capturing more transitions with higher accuracy and continuity. We validate kabr-tools through three case studies, analyzing 969 behavioral sequences, surpassing the capacity of traditional methods for data capture and annotation. We found that, like Plains zebras, vigilance in Grevy's zebras decreases with herd size, but, unlike Plains zebras, habitat has a negligible impact. Plains and Grevy's zebras exhibit strong behavioral inertia, with rare transitions to alert behaviors and observed spatial segregation between Grevy's zebras, Plains zebras, and giraffes in mixed-species herds. By enabling automated behavioral monitoring at scale, kabr-tools offers a powerful tool for ecosystem-wide studies, advancing conservation, biodiversity research, and ecological monitoring.

We present TaxaBind, a unified embedding space for characterizing any species of interest. TaxaBind is a multimodal embedding space across six modalities: ground-level images of species, geographic location, satellite image, text, audio, and environmental features, useful for solving ecological problems. To learn this joint embedding space, we leverage ground-level images of species as a binding modality. We propose multimodal patching, a technique for effectively distilling the knowledge from various modalities into the binding modality. We construct two large datasets for pretraining: iSatNat with species images and satellite images, and iSoundNat with species images and audio. Additionally, we introduce TaxaBench-8k, a diverse multimodal dataset with six paired modalities for evaluating deep learning models on ecological tasks. Experiments with TaxaBind demonstrate its strong zero-shot and emergent capabilities on a range of tasks including species classification, cross-model retrieval, and audio classification. The datasets and models are made available at https://github.com/mvrl/TaxaBind.

Ecological imbalance owing to rapid urbanization and deforestation has adversely affected the population of several wild animals. This loss of habitat has skewed the population of several non-human primate species like chimpanzees and macaques and has constrained them to co-exist in close proximity of human settlements, often leading to human-wildlife conflicts while competing for resources. For effective wildlife conservation and conflict management, regular monitoring of population and of conflicted regions is necessary. However, existing approaches like field visits for data collection and manual analysis by experts is resource intensive, tedious and time consuming, thus necessitating an automated, non-invasive, more efficient alternative like image based facial recognition. The challenge in individual identification arises due to unrelated factors like pose, lighting variations and occlusions due to the uncontrolled environments, that is further exacerbated by limited training data. Inspired by human perception, we propose to learn representations that are robust to such nuisance factors and capture the notion of similarity over the individual identity sub-manifolds. The proposed approach, Primate Face Identification (PFID), achieves this by training the network to distinguish between positive and negative pairs of images. The PFID loss augments the standard cross entropy loss with a pairwise loss to learn more discriminative and generalizable features, thus making it appropriate for other related identification tasks like open-set, closed set and verification. We report state-of-the-art accuracy on facial recognition of two primate species, rhesus macaques and chimpanzees under the four protocols of classification, verification, closed-set identification and open-set recognition.

In the era of foundation models, achieving a unified understanding of different dynamic objects through a single network has the potential to empower stronger spatial intelligence. Moreover, accurate estimation of animal pose and shape across diverse species is essential for quantitative analysis in biological research. However, this topic remains underexplored due to the limited network capacity of previous methods and the scarcity of comprehensive multi-species datasets. To address these limitations, we introduce AniMer+, an extended version of our scalable AniMer framework. In this paper, we focus on a unified approach for reconstructing mammals (mammalia) and birds (aves). A key innovation of AniMer+ is its high-capacity, family-aware Vision Transformer (ViT) incorporating a Mixture-of-Experts (MoE) design. Its architecture partitions network layers into taxa-specific components (for mammalia and aves) and taxa-shared components, enabling efficient learning of both distinct and common anatomical features within a single model. To overcome the critical shortage of 3D training data, especially for birds, we introduce a diffusion-based conditional image generation pipeline. This pipeline produces two large-scale synthetic datasets: CtrlAni3D for quadrupeds and CtrlAVES3D for birds. To note, CtrlAVES3D is the first large-scale, 3D-annotated dataset for birds, which is crucial for resolving single-view depth ambiguities. Trained on an aggregated collection of 41.3k mammalian and 12.4k avian images (combining real and synthetic data), our method demonstrates superior performance over existing approaches across a wide range of benchmarks, including the challenging out-of-domain Animal Kingdom dataset. Ablation studies confirm the effectiveness of both our novel network architecture and the generated synthetic datasets in enhancing real-world application performance.

Having accurate, detailed, and up-to-date information about the location and behavior of animals in the wild would revolutionize our ability to study and conserve ecosystems. We investigate the ability to automatically, accurately, and inexpensively collect such data, which could transform many fields of biology, ecology, and zoology into "big data" sciences. Motion sensor "camera traps" enable collecting wildlife pictures inexpensively, unobtrusively, and frequently. However, extracting information from these pictures remains an expensive, time-consuming, manual task. We demonstrate that such information can be automatically extracted by deep learning, a cutting-edge type of artificial intelligence. We train deep convolutional neural networks to identify, count, and describe the behaviors of 48 species in the 3.2-million-image Snapshot Serengeti dataset. Our deep neural networks automatically identify animals with over 93.8% accuracy, and we expect that number to improve rapidly in years to come. More importantly, if our system classifies only images it is confident about, our system can automate animal identification for 99.3% of the data while still performing at the same 96.6% accuracy as that of crowdsourced teams of human volunteers, saving more than 8.4 years (at 40 hours per week) of human labeling effort (i.e. over 17,000 hours) on this 3.2-million-image dataset. Those efficiency gains immediately highlight the importance of using deep neural networks to automate data extraction from camera-trap images. Our results suggest that this technology could enable the inexpensive, unobtrusive, high-volume, and even real-time collection of a wealth of information about vast numbers of animals in the wild.

Object counting methods typically rely on manually annotated datasets. The cost of creating such datasets has restricted the versatility of these networks to count objects from specific classes (such as humans or penguins), and counting objects from diverse categories remains a challenge. The availability of robust text-to-image latent diffusion models (LDMs) raises the question of whether these models can be utilized to generate counting datasets. However, LDMs struggle to create images with an exact number of objects based solely on text prompts but they can be used to offer a dependable sorting signal by adding and removing objects within an image. Leveraging this data, we initially introduce an unsupervised sorting methodology to learn object-related features that are subsequently refined and anchored for counting purposes using counting data generated by LDMs. Further, we present a density classifier-guided method for dividing an image into patches containing objects that can be reliably counted. Consequently, we can generate counting data for any type of object and count them in an unsupervised manner. Our approach outperforms other unsupervised and few-shot alternatives and is not restricted to specific object classes for which counting data is available. Code to be released upon acceptance.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

Real-time wildlife detection in drone imagery is critical for numerous applications, including animal ecology, conservation, and biodiversity monitoring. Low-altitude drone missions are effective for collecting fine-grained animal movement and behavior data, particularly if missions are automated for increased speed and consistency. However, little work exists on evaluating computer vision models on low-altitude aerial imagery and generalizability across different species and settings. To fill this gap, we present a novel multi-environment, multi-species, low-altitude aerial footage (MMLA) dataset. MMLA consists of drone footage collected across three diverse environments: Ol Pejeta Conservancy and Mpala Research Centre in Kenya, and The Wilds Conservation Center in Ohio, which includes five species: Plains zebras, Grevy's zebras, giraffes, onagers, and African Painted Dogs. We comprehensively evaluate three YOLO models (YOLOv5m, YOLOv8m, and YOLOv11m) for detecting animals. Results demonstrate significant performance disparities across locations and species-specific detection variations. Our work highlights the importance of evaluating detection algorithms across different environments for robust wildlife monitoring applications using drones.

Scale variation is a deep-rooted problem in object counting, which has not been effectively addressed by existing scale-aware algorithms. An important factor is that they typically involve cooperative learning across multi-resolutions, which could be suboptimal for learning the most discriminative features from each scale. In this paper, we propose a novel method termed STEERER (SelecTivE inhERitance lEaRning) that addresses the issue of scale variations in object counting. STEERER selects the most suitable scale for patch objects to boost feature extraction and only inherits discriminative features from lower to higher resolution progressively. The main insights of STEERER are a dedicated Feature Selection and Inheritance Adaptor (FSIA), which selectively forwards scale-customized features at each scale, and a Masked Selection and Inheritance Loss (MSIL) that helps to achieve high-quality density maps across all scales. Our experimental results on nine datasets with counting and localization tasks demonstrate the unprecedented scale generalization ability of STEERER. Code is available at https://github.com/taohan10200/STEERER.

We address a persistent challenge in text-to-image models: accurately generating a specified number of objects. Current models, which learn from image-text pairs, inherently struggle with counting, as training data cannot depict every possible number of objects for any given object. To solve this, we propose optimizing the generated image based on a counting loss derived from a counting model that aggregates an object\'s potential. Employing an out-of-the-box counting model is challenging for two reasons: first, the model requires a scaling hyperparameter for the potential aggregation that varies depending on the viewpoint of the objects, and second, classifier guidance techniques require modified models that operate on noisy intermediate diffusion steps. To address these challenges, we propose an iterated online training mode that improves the accuracy of inferred images while altering the text conditioning embedding and dynamically adjusting hyperparameters. Our method offers three key advantages: (i) it can consider non-derivable counting techniques based on detection models, (ii) it is a zero-shot plug-and-play solution facilitating rapid changes to the counting techniques and image generation methods, and (iii) the optimized counting token can be reused to generate accurate images without additional optimization. We evaluate the generation of various objects and show significant improvements in accuracy. The project page is available at https://ozzafar.github.io/count_token.

Computer vision analysis of camera trap video footage is essential for wildlife conservation, as captured behaviours offer some of the earliest indicators of changes in population health. Recently, several high-impact animal behaviour datasets and methods have been introduced to encourage their use; however, the role of behaviour-correlated background information and its significant effect on out-of-distribution generalisation remain unexplored. In response, we present the PanAf-FGBG dataset, featuring 20 hours of wild chimpanzee behaviours, recorded at over 350 individual camera locations. Uniquely, it pairs every video with a chimpanzee (referred to as a foreground video) with a corresponding background video (with no chimpanzee) from the same camera location. We present two views of the dataset: one with overlapping camera locations and one with disjoint locations. This setup enables, for the first time, direct evaluation of in-distribution and out-of-distribution conditions, and for the impact of backgrounds on behaviour recognition models to be quantified. All clips come with rich behavioural annotations and metadata including unique camera IDs and detailed textual scene descriptions. Additionally, we establish several baselines and present a highly effective latent-space normalisation technique that boosts out-of-distribution performance by +5.42% mAP for convolutional and +3.75% mAP for transformer-based models. Finally, we provide an in-depth analysis on the role of backgrounds in out-of-distribution behaviour recognition, including the so far unexplored impact of background durations (i.e., the count of background frames within foreground videos).

This paper presents the first large-scale multi-species dataset of acoustic recordings of mosquitoes tracked continuously in free flight. We present 20 hours of audio recordings that we have expertly labelled and tagged precisely in time. Significantly, 18 hours of recordings contain annotations from 36 different species. Mosquitoes are well-known carriers of diseases such as malaria, dengue and yellow fever. Collecting this dataset is motivated by the need to assist applications which utilise mosquito acoustics to conduct surveys to help predict outbreaks and inform intervention policy. The task of detecting mosquitoes from the sound of their wingbeats is challenging due to the difficulty in collecting recordings from realistic scenarios. To address this, as part of the HumBug project, we conducted global experiments to record mosquitoes ranging from those bred in culture cages to mosquitoes captured in the wild. Consequently, the audio recordings vary in signal-to-noise ratio and contain a broad range of indoor and outdoor background environments from Tanzania, Thailand, Kenya, the USA and the UK. In this paper we describe in detail how we collected, labelled and curated the data. The data is provided from a PostgreSQL database, which contains important metadata such as the capture method, age, feeding status and gender of the mosquitoes. Additionally, we provide code to extract features and train Bayesian convolutional neural networks for two key tasks: the identification of mosquitoes from their corresponding background environments, and the classification of detected mosquitoes into species. Our extensive dataset is both challenging to machine learning researchers focusing on acoustic identification, and critical to entomologists, geo-spatial modellers and other domain experts to understand mosquito behaviour, model their distribution, and manage the threat they pose to humans.

Most counting questions in visual question answering (VQA) datasets are simple and require no more than object detection. Here, we study algorithms for complex counting questions that involve relationships between objects, attribute identification, reasoning, and more. To do this, we created TallyQA, the world's largest dataset for open-ended counting. We propose a new algorithm for counting that uses relation networks with region proposals. Our method lets relation networks be efficiently used with high-resolution imagery. It yields state-of-the-art results compared to baseline and recent systems on both TallyQA and the HowMany-QA benchmark.

We propose a novel end-to-end curriculum learning approach for sparsely labelled animal datasets leveraging large volumes of unlabelled data to improve supervised species detectors. We exemplify the method in detail on the task of finding great apes in camera trap footage taken in challenging real-world jungle environments. In contrast to previous semi-supervised methods, our approach adjusts learning parameters dynamically over time and gradually improves detection quality by steering training towards virtuous self-reinforcement. To achieve this, we propose integrating pseudo-labelling with curriculum learning policies and show how learning collapse can be avoided. We discuss theoretical arguments, ablations, and significant performance improvements against various state-of-the-art systems when evaluating on the Extended PanAfrican Dataset holding approx. 1.8M frames. We also demonstrate our method can outperform supervised baselines with significant margins on sparse label versions of other animal datasets such as Bees and Snapshot Serengeti. We note that performance advantages are strongest for smaller labelled ratios common in ecological applications. Finally, we show that our approach achieves competitive benchmarks for generic object detection in MS-COCO and PASCAL-VOC indicating wider applicability of the dynamic learning concepts introduced. We publish all relevant source code, network weights, and data access details for full reproducibility. The code is available at https://github.com/youshyee/DCL-Detection.

We present the Caltech Fish Counting Dataset (CFC), a large-scale dataset for detecting, tracking, and counting fish in sonar videos. We identify sonar videos as a rich source of data for advancing low signal-to-noise computer vision applications and tackling domain generalization in multiple-object tracking (MOT) and counting. In comparison to existing MOT and counting datasets, which are largely restricted to videos of people and vehicles in cities, CFC is sourced from a natural-world domain where targets are not easily resolvable and appearance features cannot be easily leveraged for target re-identification. With over half a million annotations in over 1,500 videos sourced from seven different sonar cameras, CFC allows researchers to train MOT and counting algorithms and evaluate generalization performance at unseen test locations. We perform extensive baseline experiments and identify key challenges and opportunities for advancing the state of the art in generalization in MOT and counting.

Estimating the geographical range of a species from sparse observations is a challenging and important geospatial prediction problem. Given a set of locations where a species has been observed, the goal is to build a model to predict whether the species is present or absent at any location. This problem has a long history in ecology, but traditional methods struggle to take advantage of emerging large-scale crowdsourced datasets which can include tens of millions of records for hundreds of thousands of species. In this work, we use Spatial Implicit Neural Representations (SINRs) to jointly estimate the geographical range of 47k species simultaneously. We find that our approach scales gracefully, making increasingly better predictions as we increase the number of species and the amount of data per species when training. To make this problem accessible to machine learning researchers, we provide four new benchmarks that measure different aspects of species range estimation and spatial representation learning. Using these benchmarks, we demonstrate that noisy and biased crowdsourced data can be combined with implicit neural representations to approximate expert-developed range maps for many species.

Large vision-language models (VLMs) are shown to learn rich joint image-text representations enabling high performances in relevant downstream tasks. However, they fail to showcase their quantitative understanding of objects, and they lack good counting-aware representation. This paper conducts a reproducibility study of 'Teaching CLIP to Count to Ten' (Paiss et al., 2023), which presents a method to finetune a CLIP model (Radford et al., 2021) to improve zero-shot counting accuracy in an image while maintaining the performance for zero-shot classification by introducing a counting-contrastive loss term. We improve the model's performance on a smaller subset of their training data with lower computational resources. We verify these claims by reproducing their study with our own code. The implementation can be found at https://github.com/SforAiDl/CountCLIP.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

The development and evaluation of Large Language Models (LLMs) have largely focused on individual capabilities. However, this overlooks the intersection of multiple abilities across different types of expertise that are often required for real-world tasks, which we term cross capabilities. To systematically explore this concept, we first define seven core individual capabilities and then pair them to form seven common cross capabilities, each supported by a manually constructed taxonomy. Building on these definitions, we introduce CrossEval, a benchmark comprising 1,400 human-annotated prompts, with 100 prompts for each individual and cross capability. To ensure reliable evaluation, we involve expert annotators to assess 4,200 model responses, gathering 8,400 human ratings with detailed explanations to serve as reference examples. Our findings reveal that, in both static evaluations and attempts to enhance specific abilities, current LLMs consistently exhibit the "Law of the Weakest Link," where cross-capability performance is significantly constrained by the weakest component. Specifically, across 58 cross-capability scores from 17 models, 38 scores are lower than all individual capabilities, while 20 fall between strong and weak, but closer to the weaker ability. These results highlight the under-performance of LLMs in cross-capability tasks, making the identification and improvement of the weakest capabilities a critical priority for future research to optimize performance in complex, multi-dimensional scenarios.

Zero-shot object counting (ZOC) aims to enumerate objects in images using only the names of object classes during testing, without the need for manual annotations. However, a critical challenge in current ZOC methods lies in their inability to identify high-quality exemplars effectively. This deficiency hampers scalability across diverse classes and undermines the development of strong visual associations between the identified classes and image content. To this end, we propose the Visual Association-based Zero-shot Object Counting (VA-Count) framework. VA-Count consists of an Exemplar Enhancement Module (EEM) and a Noise Suppression Module (NSM) that synergistically refine the process of class exemplar identification while minimizing the consequences of incorrect object identification. The EEM utilizes advanced vision-language pretaining models to discover potential exemplars, ensuring the framework's adaptability to various classes. Meanwhile, the NSM employs contrastive learning to differentiate between optimal and suboptimal exemplar pairs, reducing the negative effects of erroneous exemplars. VA-Count demonstrates its effectiveness and scalability in zero-shot contexts with superior performance on two object counting datasets.

Insects represent half of all global biodiversity, yet many of the world's insects are disappearing, with severe implications for ecosystems and agriculture. Despite this crisis, data on insect diversity and abundance remain woefully inadequate, due to the scarcity of human experts and the lack of scalable tools for monitoring. Ecologists have started to adopt camera traps to record and study insects, and have proposed computer vision algorithms as an answer for scalable data processing. However, insect monitoring in the wild poses unique challenges that have not yet been addressed within computer vision, including the combination of long-tailed data, extremely similar classes, and significant distribution shifts. We provide the first large-scale machine learning benchmarks for fine-grained insect recognition, designed to match real-world tasks faced by ecologists. Our contributions include a curated dataset of images from citizen science platforms and museums, and an expert-annotated dataset drawn from automated camera traps across multiple continents, designed to test out-of-distribution generalization under field conditions. We train and evaluate a variety of baseline algorithms and introduce a combination of data augmentation techniques that enhance generalization across geographies and hardware setups. Code and datasets are made publicly available.

Understanding biodiversity is a global challenge, in which DNA barcodes - short snippets of DNA that cluster by species - play a pivotal role. In particular, invertebrates, a highly diverse and under-explored group, pose unique taxonomic complexities. We explore machine learning approaches, comparing supervised CNNs, fine-tuned foundation models, and a DNA barcode-specific masking strategy across datasets of varying complexity. While simpler datasets and tasks favor supervised CNNs or fine-tuned transformers, challenging species-level identification demands a paradigm shift towards self-supervised pretraining. We propose BarcodeBERT, the first self-supervised method for general biodiversity analysis, leveraging a 1.5 M invertebrate DNA barcode reference library. This work highlights how dataset specifics and coverage impact model selection, and underscores the role of self-supervised pretraining in achieving high-accuracy DNA barcode-based identification at the species and genus level. Indeed, without the fine-tuning step, BarcodeBERT pretrained on a large DNA barcode dataset outperforms DNABERT and DNABERT-2 on multiple downstream classification tasks. The code repository is available at https://github.com/Kari-Genomics-Lab/BarcodeBERT

Large language models (LLMs) are increasingly essential in processing natural languages, yet their application is frequently compromised by biases and inaccuracies originating in their training data. In this study, we introduce Cross-Care, the first benchmark framework dedicated to assessing biases and real world knowledge in LLMs, specifically focusing on the representation of disease prevalence across diverse demographic groups. We systematically evaluate how demographic biases embedded in pre-training corpora like ThePile influence the outputs of LLMs. We expose and quantify discrepancies by juxtaposing these biases against actual disease prevalences in various U.S. demographic groups. Our results highlight substantial misalignment between LLM representation of disease prevalence and real disease prevalence rates across demographic subgroups, indicating a pronounced risk of bias propagation and a lack of real-world grounding for medical applications of LLMs. Furthermore, we observe that various alignment methods minimally resolve inconsistencies in the models' representation of disease prevalence across different languages. For further exploration and analysis, we make all data and a data visualization tool available at: www.crosscare.net.

The dynamic imbalance of the fore-background is a major challenge in video object counting, which is usually caused by the sparsity of target objects. This remains understudied in existing works and often leads to severe under-/over-prediction errors. To tackle this issue in video object counting, we propose a density-embedded Efficient Masked Autoencoder Counting (E-MAC) framework in this paper. To empower the model's representation ability on density regression, we develop a new Density-Embedded Masked mOdeling (DEMO) method, which first takes the density map as an auxiliary modality to perform multimodal self-representation learning for image and density map. Although DEMO contributes to effective cross-modal regression guidance, it also brings in redundant background information, making it difficult to focus on the foreground regions. To handle this dilemma, we propose an efficient spatial adaptive masking derived from density maps to boost efficiency. Meanwhile, we employ an optical flow-based temporal collaborative fusion strategy to effectively capture the dynamic variations across frames, aligning features to derive multi-frame density residuals. The counting accuracy of the current frame is boosted by harnessing the information from adjacent frames. In addition, considering that most existing datasets are limited to human-centric scenarios, we first propose a large video bird counting dataset, DroneBird, in natural scenarios for migratory bird protection. Extensive experiments on three crowd datasets and our DroneBird validate our superiority against the counterparts. The code and dataset are available.

We propose a metadata-aware self-supervised learning~(SSL)~framework useful for fine-grained classification and ecological mapping of bird species around the world. Our framework unifies two SSL strategies: Contrastive Learning~(CL) and Masked Image Modeling~(MIM), while also enriching the embedding space with metadata available with ground-level imagery of birds. We separately train uni-modal and cross-modal ViT on a novel cross-view global bird species dataset containing ground-level imagery, metadata (location, time), and corresponding satellite imagery. We demonstrate that our models learn fine-grained and geographically conditioned features of birds, by evaluating on two downstream tasks: fine-grained visual classification~(FGVC) and cross-modal retrieval. Pre-trained models learned using our framework achieve SotA performance on FGVC of iNAT-2021 birds and in transfer learning settings for CUB-200-2011 and NABirds datasets. Moreover, the impressive cross-modal retrieval performance of our model enables the creation of species distribution maps across any geographic region. The dataset and source code will be released at https://github.com/mvrl/BirdSAT}.

Accurate maize seedling detection is crucial for precision agriculture, yet curated datasets remain scarce. We introduce MSDD, a high-quality aerial image dataset for maize seedling stand counting, with applications in early-season crop monitoring, yield prediction, and in-field management. Stand counting determines how many plants germinated, guiding timely decisions such as replanting or adjusting inputs. Traditional methods are labor-intensive and error-prone, while computer vision enables efficient, accurate detection. MSDD contains three classes-single, double, and triple plants-capturing diverse growth stages, planting setups, soil types, lighting conditions, camera angles, and densities, ensuring robustness for real-world use. Benchmarking shows detection is most reliable during V4-V6 stages and under nadir views. Among tested models, YOLO11 is fastest, while YOLOv9 yields the highest accuracy for single plants. Single plant detection achieves precision up to 0.984 and recall up to 0.873, but detecting doubles and triples remains difficult due to rarity and irregular appearance, often from planting errors. Class imbalance further reduces accuracy in multi-plant detection. Despite these challenges, YOLO11 maintains efficient inference at 35 ms per image, with an additional 120 ms for saving outputs. MSDD establishes a strong foundation for developing models that enhance stand counting, optimize resource allocation, and support real-time decision-making. This dataset marks a step toward automating agricultural monitoring and advancing precision agriculture.

ImageNet-1k is a dataset often used for benchmarking machine learning (ML) models and evaluating tasks such as image recognition and object detection. Wild animals make up 27% of ImageNet-1k but, unlike classes representing people and objects, these data have not been closely scrutinized. In the current paper, we analyze the 13,450 images from 269 classes that represent wild animals in the ImageNet-1k validation set, with the participation of expert ecologists. We find that many of the classes are ill-defined or overlapping, and that 12% of the images are incorrectly labeled, with some classes having >90% of images incorrect. We also find that both the wildlife-related labels and images included in ImageNet-1k present significant geographical and cultural biases, as well as ambiguities such as artificial animals, multiple species in the same image, or the presence of humans. Our findings highlight serious issues with the extensive use of this dataset for evaluating ML systems, the use of such algorithms in wildlife-related tasks, and more broadly the ways in which ML datasets are commonly created and curated.

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) that are traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time-series of climatic variables, and satellite time-series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Cats and humans differ in ocular anatomy. Most notably, Felis Catus (domestic cats) have vertically elongated pupils linked to ambush predation; yet, how such specializations manifest in downstream visual representations remains incompletely understood. We present a unified, frozen-encoder benchmark that quantifies feline-human cross-species representational alignment in the wild, across convolutional networks, supervised Vision Transformers, windowed transformers, and self-supervised ViTs (DINO), using layer-wise Centered Kernel Alignment (linear and RBF) and Representational Similarity Analysis, with additional distributional and stability tests reported in the paper. Across models, DINO ViT-B/16 attains the most substantial alignment (mean CKA-RBF approx0.814, mean CKA-linear approx0.745, mean RSA approx0.698), peaking at early blocks, indicating that token-level self-supervision induces early-stage features that bridge species-specific statistics. Supervised ViTs are competitive on CKA yet show weaker geometric correspondence than DINO (e.g., ViT-B/16 RSA approx0.53 at block8; ViT-L/16 approx0.47 at block14), revealing depth-dependent divergences between similarity and representational geometry. CNNs remain strong baselines but below plain ViTs on alignment, and windowed transformers underperform plain ViTs, implicating architectural inductive biases in cross-species alignment. Results indicate that self-supervision coupled with ViT inductive biases yields representational geometries that more closely align feline and human visual systems than widely used CNNs and windowed Transformers, providing testable neuroscientific hypotheses about where and how cross-species visual computations converge. We release our code and dataset for reference and reproducibility.

We propose the use of dilated filters to construct an aggregation module in a multicolumn convolutional neural network for perspective-free counting. Counting is a common problem in computer vision (e.g. traffic on the street or pedestrians in a crowd). Modern approaches to the counting problem involve the production of a density map via regression whose integral is equal to the number of objects in the image. However, objects in the image can occur at different scales (e.g. due to perspective effects) which can make it difficult for a learning agent to learn the proper density map. While the use of multiple columns to extract multiscale information from images has been shown before, our approach aggregates the multiscale information gathered by the multicolumn convolutional neural network to improve performance. Our experiments show that our proposed network outperforms the state-of-the-art on many benchmark datasets, and also that using our aggregation module in combination with a higher number of columns is beneficial for multiscale counting.

Natural language processing (NLP) practitioners are leveraging large language models (LLM) to create structured datasets from semi-structured and unstructured data sources such as patents, papers, and theses, without having domain-specific knowledge. At the same time, ecological experts are searching for a variety of means to preserve biodiversity. To contribute to these efforts, we focused on endangered species and through in-context learning, we distilled knowledge from GPT-4. In effect, we created datasets for both named entity recognition (NER) and relation extraction (RE) via a two-stage process: 1) we generated synthetic data from GPT-4 of four classes of endangered species, 2) humans verified the factual accuracy of the synthetic data, resulting in gold data. Eventually, our novel dataset contains a total of 3.6K sentences, evenly divided between 1.8K NER and 1.8K RE sentences. The constructed dataset was then used to fine-tune both general BERT and domain-specific BERT variants, completing the knowledge distillation process from GPT-4 to BERT, because GPT-4 is resource intensive. Experiments show that our knowledge transfer approach is effective at creating a NER model suitable for detecting endangered species from texts.

We consider the problem of detecting, isolating and classifying elephant calls in continuously recorded audio. Such automatic call characterisation can assist conservation efforts and inform environmental management strategies. In contrast to previous work in which call detection was performed at a segment level, we perform call detection at a frame level which implicitly also allows call endpointing, the isolation of a call in a longer recording. For experimentation, we employ two annotated datasets, one containing Asian and the other African elephant vocalisations. We evaluate several shallow and deep classifier models, and show that the current best performance can be improved by using an audio spectrogram transformer (AST), a neural architecture which has not been used for this purpose before, and which we have configured in a novel sequence-to-sequence manner. We also show that using transfer learning by pre-training leads to further improvements both in terms of computational complexity and performance. Finally, we consider sub-call classification using an accepted taxonomy of call types, a task which has not previously been considered. We show that also in this case the transformer architectures provide the best performance. Our best classifiers achieve an average precision (AP) of 0.962 for framewise binary call classification, and an area under the receiver operating characteristic (AUC) of 0.957 and 0.979 for call classification with 5 classes and sub-call classification with 7 classes respectively. All of these represent either new benchmarks (sub-call classifications) or improvements on previously best systems. We conclude that a fully-automated elephant call detection and subcall classification system is within reach. Such a system would provide valuable information on the behaviour and state of elephant herds for the purposes of conservation and management.

The alarming decline in global biodiversity, driven by various factors, underscores the urgent need for large-scale wildlife monitoring. In response, scientists have turned to automated deep learning methods for data processing in wildlife monitoring. However, applying these advanced methods in real-world scenarios is challenging due to their complexity and the need for specialized knowledge, primarily because of technical challenges and interdisciplinary barriers. To address these challenges, we introduce Pytorch-Wildlife, an open-source deep learning platform built on PyTorch. It is designed for creating, modifying, and sharing powerful AI models. This platform emphasizes usability and accessibility, making it accessible to individuals with limited or no technical background. It also offers a modular codebase to simplify feature expansion and further development. Pytorch-Wildlife offers an intuitive, user-friendly interface, accessible through local installation or Hugging Face, for animal detection and classification in images and videos. As two real-world applications, Pytorch-Wildlife has been utilized to train animal classification models for species recognition in the Amazon Rainforest and for invasive opossum recognition in the Galapagos Islands. The Opossum model achieves 98% accuracy, and the Amazon model has 92% recognition accuracy for 36 animals in 90% of the data. As Pytorch-Wildlife evolves, we aim to integrate more conservation tasks, addressing various environmental challenges. Pytorch-Wildlife is available at https://github.com/microsoft/CameraTraps.

Passive acoustic monitoring (PAM) is crucial for bioacoustic research, enabling non-invasive species tracking and biodiversity monitoring. Citizen science platforms like Xeno-Canto provide large annotated datasets from focal recordings, where the target species is intentionally recorded. However, PAM requires monitoring in passive soundscapes, creating a domain shift between focal and passive recordings, which challenges deep learning models trained on focal recordings. To address this, we leverage supervised contrastive learning to improve domain generalization in bird sound classification, enforcing domain invariance across same-class examples from different domains. We also propose ProtoCLR (Prototypical Contrastive Learning of Representations), which reduces the computational complexity of the SupCon loss by comparing examples to class prototypes instead of pairwise comparisons. Additionally, we present a new few-shot classification evaluation based on BIRB, a large-scale bird sound benchmark to evaluate bioacoustic pre-trained models.

We propose YOLO-Count, a differentiable open-vocabulary object counting model that tackles both general counting challenges and enables precise quantity control for text-to-image (T2I) generation. A core contribution is the 'cardinality' map, a novel regression target that accounts for variations in object size and spatial distribution. Leveraging representation alignment and a hybrid strong-weak supervision scheme, YOLO-Count bridges the gap between open-vocabulary counting and T2I generation control. Its fully differentiable architecture facilitates gradient-based optimization, enabling accurate object count estimation and fine-grained guidance for generative models. Extensive experiments demonstrate that YOLO-Count achieves state-of-the-art counting accuracy while providing robust and effective quantity control for T2I systems.

We focus on the problem of species distribution modeling using global-scale presence-only data. Most previous studies have mapped the range of a given species using geographical and environmental features alone. To capture a stronger implicit relationship between species, we encode the taxonomic hierarchy of species using a large language model. This enables range mapping for any taxonomic rank and unseen species without additional supervision. Further, we propose a novel proximity-aware evaluation metric that enables evaluating species distribution models using any pixel-level representation of ground-truth species range map. The proposed metric penalizes the predictions of a model based on its proximity to the ground truth. We describe the effectiveness of our model by systematically evaluating on the task of species range prediction, zero-shot prediction and geo-feature regression against the state-of-the-art. Results show our model outperforms the strong baselines when trained with a variety of multi-label learning losses.

This paper introduces the first public large-scale, long-span dataset with sea turtle photographs captured in the wild -- SeaTurtleID2022 (https://www.kaggle.com/datasets/wildlifedatasets/seaturtleid2022). The dataset contains 8729 photographs of 438 unique individuals collected within 13 years, making it the longest-spanned dataset for animal re-identification. All photographs include various annotations, e.g., identity, encounter timestamp, and body parts segmentation masks. Instead of standard "random" splits, the dataset allows for two realistic and ecologically motivated splits: (i) a time-aware closed-set with training, validation, and test data from different days/years, and (ii) a time-aware open-set with new unknown individuals in test and validation sets. We show that time-aware splits are essential for benchmarking re-identification methods, as random splits lead to performance overestimation. Furthermore, a baseline instance segmentation and re-identification performance over various body parts is provided. Finally, an end-to-end system for sea turtle re-identification is proposed and evaluated. The proposed system based on Hybrid Task Cascade for head instance segmentation and ArcFace-trained feature-extractor achieved an accuracy of 86.8%.

Multimodal Large Language Models (MLLMs) demonstrate remarkable fluency in understanding visual scenes, yet they exhibit a critical lack in a fundamental cognitive skill: object counting. This blind spot severely limits their reliability in real-world applications. To date, this capability has been largely unevaluated in complex scenarios, as existing benchmarks either feature sparse object densities or are confined to specific visual domains, failing to test models under realistic conditions. Addressing this gap, we introduce CountQA, a challenging new benchmark designed to probe this deficiency. Comprising over 1,500 question-answer pairs, CountQA features real-world images with high object density, clutter, and occlusion. We investigate this weakness by evaluating 15 prominent MLLMs on the CountQA benchmark and reveal that the top-performing model achieves a mere 42.9% accuracy, with performance declining as object counts rise. By providing a dedicated benchmark to diagnose and rectify this core weakness, CountQA paves the way for a new generation of MLLMs that are not only descriptively fluent but also numerically grounded and spatially aware. We will open-source the dataset and code upon paper acceptance to foster further research.

Although advances in deep learning and aerial surveillance technology are improving wildlife conservation efforts, complex and erratic environmental conditions still pose a problem, requiring innovative solutions for cost-effective small animal detection. This work introduces DEAL-YOLO, a novel approach that improves small object detection in Unmanned Aerial Vehicle (UAV) images by using multi-objective loss functions like Wise IoU (WIoU) and Normalized Wasserstein Distance (NWD), which prioritize pixels near the centre of the bounding box, ensuring smoother localization and reducing abrupt deviations. Additionally, the model is optimized through efficient feature extraction with Linear Deformable (LD) convolutions, enhancing accuracy while maintaining computational efficiency. The Scaled Sequence Feature Fusion (SSFF) module enhances object detection by effectively capturing inter-scale relationships, improving feature representation, and boosting metrics through optimized multiscale fusion. Comparison with baseline models reveals high efficacy with up to 69.5\% fewer parameters compared to vanilla Yolov8-N, highlighting the robustness of the proposed modifications. Through this approach, our paper aims to facilitate the detection of endangered species, animal population analysis, habitat monitoring, biodiversity research, and various other applications that enrich wildlife conservation efforts. DEAL-YOLO employs a two-stage inference paradigm for object detection, refining selected regions to improve localization and confidence. This approach enhances performance, especially for small instances with low objectness scores.

Despite the ecological significance of invertebrates, global trait databases remain heavily biased toward vertebrates and plants, limiting comprehensive ecological analyses of high-diversity groups like ground beetles. Ground beetles (Coleoptera: Carabidae) serve as critical bioindicators of ecosystem health, providing valuable insights into biodiversity shifts driven by environmental changes. While the National Ecological Observatory Network (NEON) maintains an extensive collection of carabid specimens from across the United States, these primarily exist as physical collections, restricting widespread research access and large-scale analysis. To address these gaps, we present a multimodal dataset digitizing over 13,200 NEON carabids from 30 sites spanning the continental US and Hawaii through high-resolution imaging, enabling broader access and computational analysis. The dataset includes digitally measured elytra length and width of each specimen, establishing a foundation for automated trait extraction using AI. Validated against manual measurements, our digital trait extraction achieves sub-millimeter precision, ensuring reliability for ecological and computational studies. By addressing invertebrate under-representation in trait databases, this work supports AI-driven tools for automated species identification and trait-based research, fostering advancements in biodiversity monitoring and conservation.

Vision--language models (VLMs) have achieved impressive performance on complex multimodal reasoning tasks, yet they still fail on simple grounding skills such as object counting. Existing evaluations mostly assess only final outputs, offering limited insight into where these failures arise inside the model. In this work, we present an empirical study of VLM counting behavior through both behavioral and mechanistic analysis. We introduce COUNTINGTRICKS, a controlled evaluation suite of simple shape-based counting cases designed to expose vulnerabilities under different patchification layouts and adversarial prompting conditions. Using attention analysis and component-wise probing, we show that count-relevant visual evidence is strongest in the modality projection stage but degrades substantially in later language layers, where models become more susceptible to text priors. Motivated by this finding, we further evaluate Modality Attention Share (MAS), a lightweight intervention that encourages a minimum budget of visual attention during answer generation. Our results suggest that counting failures in VLMs stem not only from visual perception limits, but also from the underuse of visual evidence during language-stage reasoning. Code and dataset will be released at https://github.com/leduy99/-CVPRW26-Modality-Attention-Share.

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

Large language models (LLMs) prompted with text and audio represent the state of the art in various auditory tasks, including speech, music, and general audio, showing emergent abilities on unseen tasks. However, these capabilities have yet to be fully demonstrated in bioacoustics tasks, such as detecting animal vocalizations in large recordings, classifying rare and endangered species, and labeling context and behavior - tasks that are crucial for conservation, biodiversity monitoring, and the study of animal behavior. In this work, we present NatureLM-audio, the first audio-language foundation model specifically designed for bioacoustics. Our carefully curated training dataset comprises text-audio pairs spanning a diverse range of bioacoustics, speech, and music data, designed to address the challenges posed by limited annotated datasets in the field. We demonstrate successful transfer of learned representations from music and speech to bioacoustics, and our model shows promising generalization to unseen taxa and tasks. Importantly, we test NatureLM-audio on a novel benchmark (BEANS-Zero) and it sets the new state of the art (SotA) on several bioacoustics tasks, including zero-shot classification of unseen species. To advance bioacoustics research, we also open-source the code for generating training and benchmark data, as well as for training the model.

We show that crowd counting can be viewed as a decomposable point querying process. This formulation enables arbitrary points as input and jointly reasons whether the points are crowd and where they locate. The querying processing, however, raises an underlying problem on the number of necessary querying points. Too few imply underestimation; too many increase computational overhead. To address this dilemma, we introduce a decomposable structure, i.e., the point-query quadtree, and propose a new counting model, termed Point quEry Transformer (PET). PET implements decomposable point querying via data-dependent quadtree splitting, where each querying point could split into four new points when necessary, thus enabling dynamic processing of sparse and dense regions. Such a querying process yields an intuitive, universal modeling of crowd as both the input and output are interpretable and steerable. We demonstrate the applications of PET on a number of crowd-related tasks, including fully-supervised crowd counting and localization, partial annotation learning, and point annotation refinement, and also report state-of-the-art performance. For the first time, we show that a single counting model can address multiple crowd-related tasks across different learning paradigms. Code is available at https://github.com/cxliu0/PET.

Wildlife trafficking remains a critical global issue, significantly impacting biodiversity, ecological stability, and public health. Despite efforts to combat this illicit trade, the rise of e-commerce platforms has made it easier to sell wildlife products, putting new pressure on wild populations of endangered and threatened species. The use of these platforms also opens a new opportunity: as criminals sell wildlife products online, they leave digital traces of their activity that can provide insights into trafficking activities as well as how they can be disrupted. The challenge lies in finding these traces. Online marketplaces publish ads for a plethora of products, and identifying ads for wildlife-related products is like finding a needle in a haystack. Learning classifiers can automate ad identification, but creating them requires costly, time-consuming data labeling that hinders support for diverse ads and research questions. This paper addresses a critical challenge in the data science pipeline for wildlife trafficking analytics: generating quality labeled data for classifiers that select relevant data. While large language models (LLMs) can directly label advertisements, doing so at scale is prohibitively expensive. We propose a cost-effective strategy that leverages LLMs to generate pseudo labels for a small sample of the data and uses these labels to create specialized classification models. Our novel method automatically gathers diverse and representative samples to be labeled while minimizing the labeling costs. Our experimental evaluation shows that our classifiers achieve up to 95% F1 score, outperforming LLMs at a lower cost. We present real use cases that demonstrate the effectiveness of our approach in enabling analyses of different aspects of wildlife trafficking.

The persisting threats on migratory bird populations highlight the urgent need for effective monitoring techniques that could assist in their conservation. Among these, passive acoustic monitoring is an essential tool, particularly for nocturnal migratory species that are difficult to track otherwise. This work presents the Nocturnal Bird Migration (NBM) dataset, a collection of 13,359 annotated vocalizations from 117 species of the Western Palearctic. The dataset includes precise time and frequency annotations, gathered by dozens of bird enthusiasts across France, enabling novel downstream acoustic analysis. In particular, we prove the utility of this database by training an original two-stage deep object detection model tailored for the processing of audio data. While allowing the precise localization of bird calls in spectrograms, this model shows competitive accuracy on the 45 main species of the dataset with state-of-the-art systems trained on much larger audio collections. These results highlight the interest of fostering similar open-science initiatives to acquire costly but valuable fine-grained annotations of audio files. All data and code are made openly available.

Wildlife populations in Africa face severe threats, with vertebrate numbers declining by over 65% in the past five decades. In response, image classification using deep learning has emerged as a promising tool for biodiversity monitoring and conservation. This paper presents a comparative study of deep learning models for automatically classifying African wildlife images, focusing on transfer learning with frozen feature extractors. Using a public dataset of four species: buffalo, elephant, rhinoceros, and zebra; we evaluate the performance of DenseNet-201, ResNet-152, EfficientNet-B4, and Vision Transformer ViT-H/14. DenseNet-201 achieved the best performance among convolutional networks (67% accuracy), while ViT-H/14 achieved the highest overall accuracy (99%), but with significantly higher computational cost, raising deployment concerns. Our experiments highlight the trade-offs between accuracy, resource requirements, and deployability. The best-performing CNN (DenseNet-201) was integrated into a Hugging Face Gradio Space for real-time field use, demonstrating the feasibility of deploying lightweight models in conservation settings. This work contributes to African-grounded AI research by offering practical insights into model selection, dataset preparation, and responsible deployment of deep learning tools for wildlife conservation.

Animal Pose Estimation and Tracking (APT) is a critical task in detecting and monitoring the keypoints of animals across a series of video frames, which is essential for understanding animal behavior. Past works relating to animals have primarily focused on either animal tracking or single-frame animal pose estimation only, neglecting the integration of both aspects. The absence of comprehensive APT datasets inhibits the progression and evaluation of animal pose estimation and tracking methods based on videos, thereby constraining their real-world applications. To fill this gap, we introduce APTv2, the pioneering large-scale benchmark for animal pose estimation and tracking. APTv2 comprises 2,749 video clips filtered and collected from 30 distinct animal species. Each video clip includes 15 frames, culminating in a total of 41,235 frames. Following meticulous manual annotation and stringent verification, we provide high-quality keypoint and tracking annotations for a total of 84,611 animal instances, split into easy and hard subsets based on the number of instances that exists in the frame. With APTv2 as the foundation, we establish a simple baseline method named \posetrackmethodname and provide benchmarks for representative models across three tracks: (1) single-frame animal pose estimation track to evaluate both intra- and inter-domain transfer learning performance, (2) low-data transfer and generalization track to evaluate the inter-species domain generalization performance, and (3) animal pose tracking track. Our experimental results deliver key empirical insights, demonstrating that APTv2 serves as a valuable benchmark for animal pose estimation and tracking. It also presents new challenges and opportunities for future research. The code and dataset are released at https://github.com/ViTAE-Transformer/APTv2{https://github.com/ViTAE-Transformer/APTv2}.

The presence of species provides key insights into the ecological properties of a location such as land cover, climatic conditions or even soil properties. We propose a method to predict such ecological properties directly from remote sensing (RS) images by aligning them with species habitat descriptions. We introduce the EcoWikiRS dataset, consisting of high-resolution aerial images, the corresponding geolocated species observations, and, for each species, the textual descriptions of their habitat from Wikipedia. EcoWikiRS offers a scalable way of supervision for RS vision language models (RS-VLMs) for ecology. This is a setting with weak and noisy supervision, where, for instance, some text may describe properties that are specific only to part of the species' niche or is irrelevant to a specific image. We tackle this by proposing WINCEL, a weighted version of the InfoNCE loss. We evaluate our model on the task of ecosystem zero-shot classification by following the habitat definitions from the European Nature Information System (EUNIS). Our results show that our approach helps in understanding RS images in a more ecologically meaningful manner. The code and the dataset are available at https://github.com/eceo-epfl/EcoWikiRS.

Fishes are integral to both ecological systems and economic sectors, and studying fish traits is crucial for understanding biodiversity patterns and macro-evolution trends. To enable the analysis of visual traits from fish images, we introduce the Fish-Visual Trait Analysis (Fish-Vista) dataset - a large, annotated collection of about 60K fish images spanning 1900 different species, supporting several challenging and biologically relevant tasks including species classification, trait identification, and trait segmentation. These images have been curated through a sophisticated data processing pipeline applied to a cumulative set of images obtained from various museum collections. Fish-Vista provides fine-grained labels of various visual traits present in each image. It also offers pixel-level annotations of 9 different traits for 2427 fish images, facilitating additional trait segmentation and localization tasks. The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-resolution dataset that can serve as a foundation for accelerating biological discoveries using advances in AI. Finally, we provide a comprehensive analysis of state-of-the-art deep learning techniques on Fish-Vista.

Multilingual language models have pushed state-of-the-art in cross-lingual NLP transfer. The majority of zero-shot cross-lingual transfer, however, use one and the same massively multilingual transformer (e.g., mBERT or XLM-R) to transfer to all target languages, irrespective of their typological, etymological, and phylogenetic relations to other languages. In particular, readily available data and models of resource-rich sibling languages are often ignored. In this work, we empirically show, in a case study for Faroese -- a low-resource language from a high-resource language family -- that by leveraging the phylogenetic information and departing from the 'one-size-fits-all' paradigm, one can improve cross-lingual transfer to low-resource languages. In particular, we leverage abundant resources of other Scandinavian languages (i.e., Danish, Norwegian, Swedish, and Icelandic) for the benefit of Faroese. Our evaluation results show that we can substantially improve the transfer performance to Faroese by exploiting data and models of closely-related high-resource languages. Further, we release a new web corpus of Faroese and Faroese datasets for named entity recognition (NER), semantic text similarity (STS), and new language models trained on all Scandinavian languages.

The current biodiversity loss crisis makes animal monitoring a relevant field of study. In light of this, data collected through monitoring can provide essential insights, and information for decision-making aimed at preserving global biodiversity. Despite the importance of such data, there is a notable scarcity of datasets featuring videos of birds, and none of the existing datasets offer detailed annotations of bird behaviors in video format. In response to this gap, our study introduces the first fine-grained video dataset specifically designed for bird behavior detection and species classification. This dataset addresses the need for comprehensive bird video datasets and provides detailed data on bird actions, facilitating the development of deep learning models to recognize these, similar to the advancements made in human action recognition. The proposed dataset comprises 178 videos recorded in Spanish wetlands, capturing 13 different bird species performing 7 distinct behavior classes. In addition, we also present baseline results using state of the art models on two tasks: bird behavior recognition and species classification.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

Insect-pests significantly impact global agricultural productivity and quality. Effective management involves identifying the full insect community, including beneficial insects and harmful pests, to develop and implement integrated pest management strategies. Automated identification of insects under real-world conditions presents several challenges, including differentiating similar-looking species, intra-species dissimilarity and inter-species similarity, several life cycle stages, camouflage, diverse imaging conditions, and variability in insect orientation. A deep-learning model, InsectNet, is proposed to address these challenges. InsectNet is endowed with five key features: (a) utilization of a large dataset of insect images collected through citizen science; (b) label-free self-supervised learning for large models; (c) improving prediction accuracy for species with a small sample size; (d) enhancing model trustworthiness; and (e) democratizing access through streamlined MLOps. This approach allows accurate identification (>96% accuracy) of over 2500 insect species, including pollinator (e.g., butterflies, bees), parasitoid (e.g., some wasps and flies), predator species (e.g., lady beetles, mantises, dragonflies) and harmful pest species (e.g., armyworms, cutworms, grasshoppers, stink bugs). InsectNet can identify invasive species, provide fine-grained insect species identification, and work effectively in challenging backgrounds. It also can abstain from making predictions when uncertain, facilitating seamless human intervention and making it a practical and trustworthy tool. InsectNet can guide citizen science data collection, especially for invasive species where early detection is crucial. Similar approaches may transform other agricultural challenges like disease detection and underscore the importance of data collection, particularly through citizen science efforts..

Despite progress in video understanding, current MLLMs struggle with counting tasks. Existing benchmarks are limited by short videos, close-set queries, lack of clue annotations, and weak multimodal coverage. In this paper, we introduce CG-AV-Counting, a manually-annotated clue-grounded counting benchmark with 1,027 multimodal questions and 5,845 annotated clues over 497 long videos. It supports both black-box and white-box evaluation, serving as a comprehensive testbed for both end-to-end and reasoning-based counting. To explore ways to improve model's counting capability, we propose AV-Reasoner, a model trained with GRPO and curriculum learning to generalize counting ability from related tasks. AV-Reasoner achieves state-of-the-art results across multiple benchmarks, demonstrating the effectiveness of reinforcement learning. However, experiments show that on out-of-domain benchmarks, reasoning in the language space fails to bring performance gains. The code and benchmark have been realeased on https://av-reasoner.github.io.

Camera traps are revolutionising wildlife monitoring by capturing vast amounts of visual data; however, the manual identification of individual animals remains a significant bottleneck. This study introduces a fully self-supervised approach to learning robust chimpanzee face embeddings from unlabeled camera-trap footage. Leveraging the DINOv2 framework, we train Vision Transformers on automatically mined face crops, eliminating the need for identity labels. Our method demonstrates strong open-set re-identification performance, surpassing supervised baselines on challenging benchmarks such as Bossou, despite utilising no labelled data during training. This work underscores the potential of self-supervised learning in biodiversity monitoring and paves the way for scalable, non-invasive population studies.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.

As Artificial Intelligence (AI) has developed rapidly over the past few decades, the new generation of AI, Large Language Models (LLMs) trained on massive datasets, has achieved ground-breaking performance in many applications. Further progress has been made in multimodal LLMs, with many datasets created to evaluate LLMs with vision abilities. However, none of those datasets focuses solely on marine mammals, which are indispensable for ecological equilibrium. In this work, we build a benchmark dataset with 1,423 images of 65 kinds of marine mammals, where each animal is uniquely classified into different levels of class, ranging from species-level to medium-level to group-level. Moreover, we evaluate several approaches for classifying these marine mammals: (1) machine learning (ML) algorithms using embeddings provided by neural networks, (2) influential pre-trained neural networks, (3) zero-shot models: CLIP and LLMs, and (4) a novel LLM-based multi-agent system (MAS). The results demonstrate the strengths of traditional models and LLMs in different aspects, and the MAS can further improve the classification performance. The dataset is available on GitHub: https://github.com/yeyimilk/LLM-Vision-Marine-Animals.git.

Human medical data can be challenging to obtain due to data privacy concerns, difficulties conducting certain types of experiments, or prohibitive associated costs. In many settings, data from animal models or in-vitro cell lines are available to help augment our understanding of human data. However, this data is known for having low etiological validity in comparison to human data. In this work, we augment small human medical datasets with in-vitro data and animal models. We use Invariant Risk Minimisation (IRM) to elucidate invariant features by considering cross-organism data as belonging to different data-generating environments. Our models identify genes of relevance to human cancer development. We observe a degree of consistency between varying the amounts of human and mouse data used, however, further work is required to obtain conclusive insights. As a secondary contribution, we enhance existing open source datasets and provide two uniformly processed, cross-organism, homologue gene-matched datasets to the community.

For many low-resource languages, the only available language models are large multilingual models trained on many languages simultaneously. However, using FLORES perplexity as a metric, we find that these models perform worse than bigrams for many languages (e.g. 24% of languages in XGLM 4.5B; 43% in BLOOM 7.1B). To facilitate research that focuses on low-resource languages, we pre-train and release Goldfish, a suite of monolingual autoregressive Transformer language models up to 125M parameters for 350 languages. The Goldfish reach lower FLORES perplexities than BLOOM, XGLM, and MaLA-500 on 98 of 204 FLORES languages, despite each Goldfish model being over 10x smaller. However, the Goldfish significantly underperform larger multilingual models on reasoning benchmarks, suggesting that for low-resource languages, multilinguality primarily improves general reasoning abilities rather than basic text generation. We release models trained on 5MB (350 languages), 10MB (288 languages), 100MB (166 languages), and 1GB (83 languages) of text data where available. The Goldfish models are available as baselines, fine-tuning sources, or augmentations to existing models in low-resource NLP research, and they are further useful for crosslinguistic studies requiring maximally comparable models across languages.

Ex-post harmonisation is one of many data preprocessing processes used to combine the increasingly vast and diverse sources of data available for research and analysis. Documenting provenance and ensuring the quality of multi-source datasets is vital for ensuring trustworthy scientific research and encouraging reuse of existing harmonisation efforts. However, capturing and communicating statistically relevant properties of harmonised datasets is difficult without a universal standard for describing harmonisation operations. Our paper combines mathematical and computer science perspectives to address this need. The Crossmaps Framework defines a new approach for transforming existing variables collected under a specific measurement or classification standard to an imputed counterfactual variable indexed by some target standard. It uses computational graphs to separate intended transformation logic from actual data transformations, and avoid the risk of syntactically valid data manipulation scripts resulting in statistically questionable data. In this paper, we introduce the Crossmaps Framework through the example of ex-post harmonisation of aggregated statistics in the social sciences. We define a new provenance task abstraction, the crossmap transform, and formalise two associated objects, the shared mass array and the crossmap. We further define graph, matrix and list encodings of crossmaps and discuss resulting implications for understanding statistical properties of ex-post harmonisation and designing error minimising workflows.

Cross-lingual transfer is a popular approach to increase the amount of training data for NLP tasks in a low-resource context. However, the best strategy to decide which cross-lingual data to include is unclear. Prior research often focuses on a small set of languages from a few language families and/or a single task. It is still an open question how these findings extend to a wider variety of languages and tasks. In this work, we analyze cross-lingual transfer for 266 languages from a wide variety of language families. Moreover, we include three popular NLP tasks: POS tagging, dependency parsing, and topic classification. Our findings indicate that the effect of linguistic similarity on transfer performance depends on a range of factors: the NLP task, the (mono- or multilingual) input representations, and the definition of linguistic similarity.

ImageNet-1K linear-probe transfer accuracy remains the default proxy for visual representation quality, yet it no longer predicts performance on scientific imagery. Across 46 modern vision model checkpoints, ImageNet top-1 accuracy explains only 34% of variance on ecology tasks and mis-ranks 30% of models above 75% accuracy. We present BioBench, an open ecology vision benchmark that captures what ImageNet misses. BioBench unifies 9 publicly released, application-driven tasks, 4 taxonomic kingdoms, and 6 acquisition modalities (drone RGB, web video, micrographs, in-situ and specimen photos, camera-trap frames), totaling 3.1M images. A single Python API downloads data, fits lightweight classifiers to frozen backbones, and reports class-balanced macro-F1 (plus domain metrics for FishNet and FungiCLEF); ViT-L models evaluate in 6 hours on an A6000 GPU. BioBench provides new signal for computer vision in ecology and a template recipe for building reliable AI-for-science benchmarks in any domain. Code and predictions are available at https://github.com/samuelstevens/biobench and results at https://samuelstevens.me/biobench.

This document describes the details and the motivation behind a new dataset we collected for the semi-supervised recognition challenge~semi-aves at the FGVC7 workshop at CVPR 2020. The dataset contains 1000 species of birds sampled from the iNat-2018 dataset for a total of nearly 150k images. From this collection, we sample a subset of classes and their labels, while adding the images from the remaining classes to the unlabeled set of images. The presence of out-of-domain data (novel classes), high class-imbalance, and fine-grained similarity between classes poses significant challenges for existing semi-supervised recognition techniques in the literature. The dataset is available here: https://github.com/cvl-umass/semi-inat-2020

Nematode worms are one of most abundant metazoan groups on the earth, occupying diverse ecological niches. Accurate recognition or identification of nematodes are of great importance for pest control, soil ecology, bio-geography, habitat conservation and against climate changes. Computer vision and image processing have witnessed a few successes in species recognition of nematodes; however, it is still in great demand. In this paper, we identify two main bottlenecks: (1) the lack of a publicly available imaging dataset for diverse species of nematodes (especially the species only found in natural environment) which requires considerable human resources in field work and experts in taxonomy, and (2) the lack of a standard benchmark of state-of-the-art deep learning techniques on this dataset which demands the discipline background in computer science. With these in mind, we propose an image dataset consisting of diverse nematodes (both laboratory cultured and naturally isolated), which, to our knowledge, is the first time in the community. We further set up a species recognition benchmark by employing state-of-the-art deep learning networks on this dataset. We discuss the experimental results, compare the recognition accuracy of different networks, and show the challenges of our dataset. We make our dataset publicly available at: https://github.com/xuequanlu/I-Nema

This study explores strategies for efficiently classifying scientific full texts using both small, BERT-based models and local large language models like Llama-3.1 8B. We focus on developing methods for selecting subsets of input sentences to reduce input size while simultaneously enhancing classification performance. To this end, we compile a novel dataset consisting of full-text scientific papers from the field of invasion biology, specifically addressing the impacts of invasive species. These papers are aligned with publicly available impact assessments created by researchers for the International Union for Conservation of Nature (IUCN). Through extensive experimentation, we demonstrate that various sources like human evidence annotations, LLM-generated annotations or explainability scores can be used to train sentence selection models that improve the performance of both encoder- and decoder-based language models while optimizing efficiency through the reduction in input length, leading to improved results even if compared to models like ModernBERT that are able to handle the complete text as input. Additionally, we find that repeated sampling of shorter inputs proves to be a very effective strategy that, at a slightly increased cost, can further improve classification performance.

Non-human primates are our closest living relatives, and analyzing their behavior is central to research in cognition, evolution, and conservation. Computer vision could greatly aid this research, but existing methods often rely on human-centric pretrained models and focus on single datasets, which limits generalization. We address this limitation by shifting from a model-centric to a data-centric approach and introduce PriVi, a large-scale primate-centric video pretraining dataset. PriVi contains 424 hours of curated video, combining 174 hours from behavioral research across 11 settings with 250 hours of diverse web-sourced footage, assembled through a scalable data curation pipeline. We pretrain V-JEPA on PriVi to learn primate-specific representations and evaluate it using a lightweight frozen classifier. Across four benchmark datasets, ChimpACT, BaboonLand, PanAf500, and ChimpBehave, our approach consistently outperforms prior work, including fully finetuned baselines, and scales favorably with fewer labels. These results demonstrate that primate-centric pretraining substantially improves data efficiency and generalization, making it a promising approach for low-label applications. Code, models, and the majority of the dataset will be made available.

We present CrossSum, a large-scale cross-lingual abstractive summarization dataset comprising 1.7 million article-summary samples in 1500+ language pairs. We create CrossSum by aligning identical articles written in different languages via cross-lingual retrieval from a multilingual summarization dataset. We propose a multi-stage data sampling algorithm to effectively train a cross-lingual summarization model capable of summarizing an article in any target language. We also propose LaSE, a new metric for automatically evaluating model-generated summaries and showing a strong correlation with ROUGE. Performance on ROUGE and LaSE indicate that pretrained models fine-tuned on CrossSum consistently outperform baseline models, even when the source and target language pairs are linguistically distant. To the best of our knowledge, CrossSum is the largest cross-lingual summarization dataset and the first-ever that does not rely solely on English as the pivot language. We are releasing the dataset, alignment and training scripts, and the models to spur future research on cross-lingual abstractive summarization. The resources can be found at https://github.com/csebuetnlp/CrossSum.