WildlifeDatasets: An open-source toolkit for animal re-identification

In this paper, we present WildlifeDatasets (https://github.com/WildlifeDatasets/wildlife-datasets) - an open-source toolkit intended primarily for ecologists and computer-vision / machine-learning researchers. The WildlifeDatasets is written in Python, allows straightforward access to publicly available wildlife datasets, and provides a wide variety of methods for dataset pre-processing, performance analysis, and model fine-tuning. We showcase the toolkit in various scenarios and baseline experiments, including, to the best of our knowledge, the most comprehensive experimental comparison of datasets and methods for wildlife re-identification, including both local descriptors and deep learning approaches. Furthermore, we provide the first-ever foundation model for individual re-identification within a wide range of species - MegaDescriptor - that provides state-of-the-art performance on animal re-identification datasets and outperforms other pre-trained models such as CLIP and DINOv2 by a significant margin. To make the model available to the general public and to allow easy integration with any existing wildlife monitoring applications, we provide multiple MegaDescriptor flavors (i.e., Small, Medium, and Large) through the HuggingFace hub (https://huggingface.co/BVRA).

SeaTurtleID2022: A long-span dataset for reliable sea turtle re-identification

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%.

Unrolled three-operator splitting for parameter-map learning in Low Dose X-ray CT reconstruction

We propose a method for fast and automatic estimation of spatially dependent regularization maps for total variation-based (TV) tomography reconstruction. The estimation is based on two distinct sub-networks, with the first sub-network estimating the regularization parameter-map from the input data while the second one unrolling T iterations of the Primal-Dual Three-Operator Splitting (PD3O) algorithm. The latter approximately solves the corresponding TV-minimization problem incorporating the previously estimated regularization parameter-map. The overall network is then trained end-to-end in a supervised learning fashion using pairs of clean-corrupted data but crucially without the need of having access to labels for the optimal regularization parameter-maps.

SeaTurtleID: A novel long-span dataset highlighting the importance of timestamps in wildlife re-identification

This paper introduces SeaTurtleID, the first public large-scale, long-span dataset with sea turtle photographs captured in the wild. The dataset is suitable for benchmarking re-identification methods and evaluating several other computer vision tasks. The dataset consists of 7774 high-resolution photographs of 400 unique individuals collected within 12 years in 1081 encounters. Each photograph is accompanied by rich metadata, e.g., identity label, head segmentation mask, and encounter timestamp. The 12-year span of the dataset makes it the longest-spanned public wild animal dataset with timestamps. By exploiting this unique property, we show that timestamps are necessary for an unbiased evaluation of animal re-identification methods because they allow time-aware splits of the dataset into reference and query sets. We show that time-unaware splits can lead to performance overestimation of more than 100% compared to the time-aware splits for both feature- and CNN-based re-identification methods. We also argue that time-aware splits correspond to more realistic re-identification pipelines than the time-unaware ones. We recommend that animal re-identification methods should only be tested on datasets with timestamps using time-aware splits, and we encourage dataset curators to include such information in the associated metadata.

Optimization with learning-informed differential equation constraints and its applications

Inspired by applications in optimal control of semilinear elliptic partial differential equations and physics-integrated imaging, differential equation constrained optimization problems with constituents that are only accessible through data-driven techniques are studied. A particular focus is on the analysis and on numerical methods for problems with machine-learned components. For a rather general context, an error analysis is provided, and particular properties resulting from artificial neural network based approximations are addressed. Moreover, for each of the two inspiring applications analytical details are presented and numerical results are provided.