Daily Papers

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.

Invasive species in water bodies pose a major threat to the environment and biodiversity globally. Due to increased transportation and trade, non-native species have been introduced to new environments, causing damage to ecosystems and leading to economic losses in agriculture, forestry, and fisheries. Therefore, there is a pressing need for risk assessment and management techniques to mitigate the impact of these invasions. This study aims to develop a new physics-inspired model to forecast maritime shipping traffic and thus inform risk assessment of invasive species spread through global transportation networks. Inspired by the gravity model for international trades, our model considers various factors that influence the likelihood and impact of vessel activities, such as shipping flux density, distance between ports, trade flow, and centrality measures of transportation hubs. Additionally, by analyzing the risk network of invasive species, we provide a comprehensive framework for assessing the invasion threat level given a pair of origin and destination. Accordingly, this paper introduces transformers to gravity models to rebuild the short- and long-term dependencies that make the risk analysis feasible. Thus, we introduce a physics-inspired framework that achieves an 89% segmentation accuracy for existing and non-existing trajectories and an 84.8% accuracy for the number of vessels flowing between key port areas, representing more than 10% improvement over the traditional deep-gravity model. Along these lines, this research contributes to a better understanding of invasive species risk assessment. It allows policymakers, conservationists, and stakeholders to prioritize management actions by identifying high-risk invasion pathways. Besides, our model is versatile and can include new data sources, making it suitable for assessing species invasion risks in a changing global landscape.

Wood species identification plays a crucial role in various industries, from ensuring the legality of timber products to advancing ecological conservation efforts. This paper introduces WoodYOLO, a novel object detection algorithm specifically designed for microscopic wood fiber analysis. Our approach adapts the YOLO architecture to address the challenges posed by large, high-resolution microscopy images and the need for high recall in localization of the cell type of interest (vessel elements). Our results show that WoodYOLO significantly outperforms state-of-the-art models, achieving performance gains of 12.9% and 6.5% in F2 score over YOLOv10 and YOLOv7, respectively. This improvement in automated wood cell type localization capabilities contributes to enhancing regulatory compliance, supporting sustainable forestry practices, and promoting biodiversity conservation efforts globally.

Accurate identification of crop and weed species is critical for precision agriculture and sustainable farming. However, it remains a challenging task due to a variety of factors -- a high degree of visual similarity among species, environmental variability, and a continued lack of large, agriculture-specific image data. We introduce iNatAg, a large-scale image dataset which contains over 4.7 million images of 2,959 distinct crop and weed species, with precise annotations along the taxonomic hierarchy from binary crop/weed labels to specific species labels. Curated from the broader iNaturalist database, iNatAg contains data from every continent and accurately reflects the variability of natural image captures and environments. Enabled by this data, we train benchmark models built upon the Swin Transformer architecture and evaluate the impact of various modifications such as the incorporation of geospatial data and LoRA finetuning. Our best models achieve state-of-the-art performance across all taxonomic classification tasks, achieving 92.38\% on crop and weed classification. Furthermore, the scale of our dataset enables us to explore incorrect misclassifications and unlock new analytic possiblities for plant species. By combining large-scale species coverage, multi-task labels, and geographic diversity, iNatAg provides a new foundation for building robust, geolocation-aware agricultural classification systems. We release the iNatAg dataset publicly through AgML (https://github.com/Project-AgML/AgML), enabling direct access and integration into agricultural machine learning workflows.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

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.

Traditionally, bioacoustics has relied on spectrograms and continuous, per-frame audio representations for the analysis of animal sounds, also serving as input to machine learning models. Meanwhile, the International Phonetic Alphabet (IPA) system has provided an interpretable, language-independent method for transcribing human speech sounds. In this paper, we introduce ISPA (Inter-Species Phonetic Alphabet), a precise, concise, and interpretable system designed for transcribing animal sounds into text. We compare acoustics-based and feature-based methods for transcribing and classifying animal sounds, demonstrating their comparable performance with baseline methods utilizing continuous, dense audio representations. By representing animal sounds with text, we effectively treat them as a "foreign language," and we show that established human language ML paradigms and models, such as language models, can be successfully applied to improve performance.

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.

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.

Knowledge of tree species distribution is fundamental to managing forests. New deep learning approaches promise significant accuracy gains for forest mapping, and are becoming a critical tool for mapping multiple tree species at scale. To advance the field, deep learning researchers need large benchmark datasets with high-quality annotations. To this end, we present the PureForest dataset: a large-scale, open, multimodal dataset designed for tree species classification from both Aerial Lidar Scanning (ALS) point clouds and Very High Resolution (VHR) aerial images. Most current public Lidar datasets for tree species classification have low diversity as they only span a small area of a few dozen annotated hectares at most. In contrast, PureForest has 18 tree species grouped into 13 semantic classes, and spans 339 km^2 across 449 distinct monospecific forests, and is to date the largest and most comprehensive Lidar dataset for the identification of tree species. By making PureForest publicly available, we hope to provide a challenging benchmark dataset to support the development of deep learning approaches for tree species identification from Lidar and/or aerial imagery. In this data paper, we describe the annotation workflow, the dataset, the recommended evaluation methodology, and establish a baseline performance from both 3D and 2D modalities.

Identification of tree species plays a key role in forestry related tasks like forest conservation, disease diagnosis and plant production. There had been a debate regarding the part of the tree to be used for differentiation, whether it should be leaves, fruits, flowers or bark. Studies have proven that bark is of utmost importance as it will be present despite seasonal variations and provides a characteristic identity to a tree by variations in the structure. In this paper, a deep learning based approach is presented by leveraging the method of computer vision to classify 50 tree species, on the basis of bark texture using the BarkVN-50 dataset. This is the maximum number of trees being considered for bark classification till now. A convolutional neural network(CNN), ResNet101 has been implemented using transfer-learning based technique of fine tuning to maximise the model performance. The model produced an overall accuracy of >94% during the evaluation. The performance validation has been done using K-Fold Cross Validation and by testing on unseen data collected from the Internet, this proved the model's generalization capability for real-world uses.

We introduce MABe22, a large-scale, multi-agent video and trajectory benchmark to assess the quality of learned behavior representations. This dataset is collected from a variety of biology experiments, and includes triplets of interacting mice (4.7 million frames video+pose tracking data, 10 million frames pose only), symbiotic beetle-ant interactions (10 million frames video data), and groups of interacting flies (4.4 million frames of pose tracking data). Accompanying these data, we introduce a panel of real-life downstream analysis tasks to assess the quality of learned representations by evaluating how well they preserve information about the experimental conditions (e.g. strain, time of day, optogenetic stimulation) and animal behavior. We test multiple state-of-the-art self-supervised video and trajectory representation learning methods to demonstrate the use of our benchmark, revealing that methods developed using human action datasets do not fully translate to animal datasets. We hope that our benchmark and dataset encourage a broader exploration of behavior representation learning methods across species and settings.

Automatic snake species recognition is important because it has vast potential to help lower deaths and disabilities caused by snakebites. We introduce our solution in SnakeCLEF 2022 for fine-grained snake species recognition on a heavy long-tailed class distribution. First, a network architecture is designed to extract and fuse features from multiple modalities, i.e. photograph from visual modality and geographic locality information from language modality. Then, logit adjustment based methods are studied to relieve the impact caused by the severe class imbalance. Next, a combination of supervised and self-supervised learning method is proposed to make full use of the dataset, including both labeled training data and unlabeled testing data. Finally, post processing strategies, such as multi-scale and multi-crop test-time-augmentation, location filtering and model ensemble, are employed for better performance. With an ensemble of several different models, a private score 82.65%, ranking the 3rd, is achieved on the final leaderboard.

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.

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.

Robust visual recognition in underwater environments remains a significant challenge due to complex distortions such as turbidity, low illumination, and occlusion, which severely degrade the performance of standard vision systems. This paper introduces AQUA20, a comprehensive benchmark dataset comprising 8,171 underwater images across 20 marine species reflecting real-world environmental challenges such as illumination, turbidity, occlusions, etc., providing a valuable resource for underwater visual understanding. Thirteen state-of-the-art deep learning models, including lightweight CNNs (SqueezeNet, MobileNetV2) and transformer-based architectures (ViT, ConvNeXt), were evaluated to benchmark their performance in classifying marine species under challenging conditions. Our experimental results show ConvNeXt achieving the best performance, with a Top-3 accuracy of 98.82% and a Top-1 accuracy of 90.69%, as well as the highest overall F1-score of 88.92% with moderately large parameter size. The results obtained from our other benchmark models also demonstrate trade-offs between complexity and performance. We also provide an extensive explainability analysis using GRAD-CAM and LIME for interpreting the strengths and pitfalls of the models. Our results reveal substantial room for improvement in underwater species recognition and demonstrate the value of AQUA20 as a foundation for future research in this domain. The dataset is publicly available at: https://huggingface.co/datasets/taufiktrf/AQUA20.

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.

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.

Trapped ions form an advanced technology platform for quantum information processing with long qubit coherence times, high-fidelity quantum logic gates, optically active qubits, and a potential to scale up in size while preserving a high level of connectivity between qubits. These traits make them attractive not only for quantum computing but also for quantum networking. Dedicated, special-purpose trapped-ion processors in conjunction with suitable interconnecting hardware can be used to form quantum repeaters that enable high-rate quantum communications between distant trapped-ion quantum computers in a network. In this regard, hybrid traps with two distinct species of ions, where one ion species can generate ion-photon entanglement that is useful for optically interfacing with the network and the other has long memory lifetimes, useful for qubit storage, have been proposed for entanglement distribution. We consider an architecture for a repeater based on such dual-species trapped-ion systems. We propose and analyze a protocol based on spatial and temporal mode multiplexing for entanglement distribution across a line network of such repeaters. Our protocol offers enhanced rates compared to rates previously reported for such repeaters. We determine the ion resources required at the repeaters to attain the enhanced rates, and the best rates attainable when constraints are placed on the number of repeaters and the number of ions per repeater. Our results bolster the case for near-term trapped-ion systems as quantum repeaters for long-distance quantum communications.

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.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

The Numerical Flow Iteration (NuFI) method has recently been proposed as a memory-slim solution method for the Vlasov--Poisson system. It stores the temporal evolution of the electric field, instead of the distribution functions, and reconstructs the solution in each time step by following the characteristics backwards in time and reconstructing the solution from the initial distribution. NuFI has been shown to be more accurate than other state-of-the-art Vlasov solvers given the same amount of degrees of freedom as well as interpolation order, essentially making NuFI a high-fidelity but low-memory cost scheme. In this paper, we build on the Hamiltonian structure of the full Vlasov--Maxwell system to extend NuFI to handle electro-magnetic kinetic plasma dynamics. We show that the advanced structure-preserving properties of NuFI are preserved when extending to the electro-magnetic case.

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.

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}.

Visual animal biometrics is rapidly gaining popularity as it enables a non-invasive and cost-effective approach for wildlife monitoring applications. Widespread usage of camera traps has led to large volumes of collected images, making manual processing of visual content hard to manage. In this work, we develop a framework for automatic detection and recognition of individuals in different patterned species like tigers, zebras and jaguars. Most existing systems primarily rely on manual input for localizing the animal, which does not scale well to large datasets. In order to automate the detection process while retaining robustness to blur, partial occlusion, illumination and pose variations, we use the recently proposed Faster-RCNN object detection framework to efficiently detect animals in images. We further extract features from AlexNet of the animal's flank and train a logistic regression (or Linear SVM) classifier to recognize the individuals. We primarily test and evaluate our framework on a camera trap tiger image dataset that contains images that vary in overall image quality, animal pose, scale and lighting. We also evaluate our recognition system on zebra and jaguar images to show generalization to other patterned species. Our framework gives perfect detection results in camera trapped tiger images and a similar or better individual recognition performance when compared with state-of-the-art recognition techniques.