Centering Ecological Goals in Automated Identification of Individual Animals

Active learning is now standard practice in labeling ecological data, enabling ecologists to quickly process large volumes of field data to understand and monitor natural environments. Current practices evaluate active learning inductively, estimating predictive performance on a held-out test set. We argue that this evaluation is misaligned with most ecological tasks, where the goal is to transductively label an entire pool of data as efficiently as possible. We demonstrate that ignoring the human-in-the-loop underestimates the importance of continuing to label, particularly for classes in the long tail which may be of disproportionate ecological importance (rare species, uncommon behaviors, etc.). Our analysis shows that, for this long tail, the transductive objective shifts importance from prediction to discovery: the true challenge becomes finding "needles in the haystack," examples of rare classes that are embedded within dense regions of abundant classes in the latent geometry, which we quantify with a novel metric of sampling difficulty. Finally, to translate these insights to practical ecological workflows, we propose a conservative hybrid stopping criterion inspired by ecological rarefaction curves, and show that combining predictive performance with discovery criteria reduces premature stopping on long-tailed pools, improving rare-class recovery when discovery, not classification, is the limiting factor.

Camera traps have become an essential tool for wildlife monitoring, motivating the development of computer vision methods for the automated extraction of information from these data. While most prior work has focused on species identification, many ecological applications also require estimating the number of unique individuals appearing across short image sequences. This task is particularly challenging because camera traps typically acquire bursts of images at approximately one frame per second, creating large temporal discontinuities that may make conventional multi-object tracking methods unreliable, and because manually collecting individual count annotations is prohibitively expensive. In this work, we describe the winning solution to the iWildCam 2021 Challenge, which introduced a benchmark for counting animals at the sequence level under realistic annotation constraints where count annotations are unavailable for training. Our approach, MaxBoxCount, combines a strong species classification pipeline with a simple yet effective counting heuristic based on MegaDetector detections to estimate the number of unique individuals without requiring count annotations. Code is available at https://github.com/alcunha/iwildcam2021ufam.

Reliable individual re-identification (re-ID) of wildlife is essential for population monitoring, behavioral tracking, and conservation policy evaluation, yet large-scale data collection remains labor-intensive, relying on manual efforts by ecologists or citizen scientists. We propose an autonomous drone navigation system that actively optimizes image capture for downstream re-ID, moving beyond passive aerial sensing. The system combines YOLOv11 object detection with a DINOv2-based pose classifier to guide real-time flight decisions: detecting animals, orienting to expose the lateral flank (the surface of interest for pattern-based re-ID), and approaching until the subject meets a minimum bounding-box threshold. Unlike prior drone systems that optimize for group-level behavioral video, ours targets the specific image-quality requirements of individual-identification models. We demonstrate feasibility through a case study on zebra using footage collected in Kenya, and show the approach generalizes to other species with diagnostic surface patterns, including giraffes, tigers, and elephants. Our work establishes a framework for task-aware embodied AI for ecological data collection, in which downstream re-ID requirements drive real-time perception and control.