Hugo Markoff

Hugo Markoff, Stefan Hein Bengtson, Michael Ørsted

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.

Hugo Markoff, Jevgenijs Galaktionovs

Camera traps generate millions of wildlife images, yet many datasets contain species that are absent from existing classifiers. This work evaluates zero-shot approaches for organizing unlabeled wildlife imagery using self-supervised vision transformers, developed and tested within the Animal Detect platform for camera trap analysis. We compare unsupervised clustering methods (DBSCAN, GMM) across three architectures (CLIP, DINOv2, MegaDescriptor) combined with dimensionality reduction techniques (PCA, UMAP), and we demonstrate continuous 1D similarity ordering via t-SNE projection. On a 5-species test set with ground truth labels used only for evaluation, DINOv2 with UMAP and GMM achieves 88.6 percent accuracy (macro-F1 = 0.874), while 1D sorting reaches 88.2 percent coherence for mammals and birds and 95.2 percent for fish across 1,500 images. Based on these findings, we deployed continuous similarity ordering in production, enabling rapid exploratory analysis and accelerating manual annotation workflows for biodiversity monitoring.

Hugo Markoff, Jevgenijs Galaktionovs

State-of-the-art animal classification models like SpeciesNet provide predictions across thousands of species but use conservative rollup strategies, resulting in many animals labeled at high taxonomic levels rather than species. We present a hierarchical re-classification system for the Animal Detect platform that combines SpeciesNet EfficientNetV2-M predictions with CLIP embeddings and metric learning to refine high-level taxonomic labels toward species-level identification. Our five-stage pipeline (high-confidence acceptance, bird override, centroid building, triplet-loss metric learning, and adaptive cosine-distance scoring) is evaluated on a segment of the LILA BC Desert Lion Conservation dataset (4,018 images, 15,031 detections). After recovering 761 bird detections from "blank" and "animal" labels, we re-classify 456 detections labeled animal, mammal, or blank with 96.5% accuracy, achieving species-level identification for 64.9 percent