On the Benefits of Uncertainty Estimation for Species Classification: A Case Study on Optimizing Expert re-Annotation

Dermatology models face distribution shifts in teledermatology settings, where submitted images differ from the training data in lighting, angle, distance, focus, and framing. These test-time images are ordinary clinical photographs, but some fall outside the model's training conditions, leading the model to often misclassify them due to shifts in acquisition between training and deployment. When multiple images of the same case exist (several photos of one patient or lesion), a natural way to improve accuracy is therefore to select the image the model is most likely to classify correctly. We call this task reliable-input selection. An oracle that, for each case, selects a correctly classified image when one exists raises weighted F1 by about 20 percentage points on average across six dermatology datasets and nine frozen backbones. This oracle is an upper bound that sees the labels, whereas a selector must choose blindly. Capturing this gain in practice is hard. A selector that needs no pretraining data applies to any frozen model, including those whose data is not public. It must judge reliability from quantities the model exposes at inference: its embeddings, their norms, and its confidence. We benchmark four such training-data-free selectors: the embedding norm, the neighborhood consensus among a case's images, the stability of the prediction under small perturbations, and the model's own confidence. No training-data-free selector substantially narrows this oracle gap. The best of them is the model's own confidence, but it recovers only a small part of the gap on the clinical datasets. A small labeled reference set does not help either: the best selector overall, a fusion of confidence and Mahalanobis distance, still leaves most of the gap. To our knowledge, this is the first study to introduce and benchmark reliable input selection, a clinically important, unsolved task.

Supervised deep learning methods enable the rapid processing of ecological image data, but depend on a costly annotation process. Consequently, training labels are commonly derived from volunteer citizen science projects. However, disagreement among volunteers introduces uncertainty in the "ground truth" data that are assumed to be correct for model training and validation. Using two datasets containing camera trap images with associated volunteer and expert classifications, we investigated the effects of training under higher ground truth uncertainty. We observed improved overall test accuracy, particularly for images that were more difficult for volunteers. Species-level accuracy also generally improved, but generalisation to a different dataset did not. The benefits of ground truth uncertainty were enhanced by pre-training on ImageNet. Pre-training also reduced the number of training epochs required; further reductions in computational cost, but not gains in accuracy, resulted from additional pre-training on other camera trap images. With unbalanced training data, we still observed a clear benefit of increased ground truth uncertainty for overall accuracy, especially on difficult images. Class imbalance improved accuracy for common species, reduced rare species accuracy, and changed patterns of misclassification to more closely resemble mistakes made by volunteers. Our findings have implications for applying deep learning across ecological image types with multiple labels. Practitioners can improve accuracy, especially on difficult examples, by including moderate levels of label disagreement during training and using models pre-trained on general image data. In addition to improving the use of citizen science-derived labels in model training, our study suggests avenues for more effectively integrating human and deep learning classifications in combined workflows. (abridged)

Identifying species in biology among tens of thousands of visually similar taxa while discovering unknown species in open-world environments remains a fundamental challenge in biodiversity research. Current methods treat identification and discovery as separate problems, with classification models assuming closed sets and discovery relying on threshold-based rejection. Here we present DeepTaxon, a retrieval-augmented multimodal framework that unifies species identification and discovery through interpretable reasoning over retrieved visual evidence. Given a query image, DeepTaxon retrieves the top-$k$ candidate species with $n$ exemplar images each from a retrieval index and performs chain-of-thought comparative reasoning. Critically, we redefine discovery as an explicit, retrieval-based decision problem rather than an implicit parametric memory problem. A sample is novel if and only if the retrieval index lacks sufficient evidence for identification, so each retrieval naturally yields a classification or discovery label without manual annotation, thereby providing automatic supervision for both tasks. We train the framework via supervised fine-tuning on synthetic retrieval-augmented data, followed by reinforcement learning on hard samples, converting high-recall retrieval into high-precision decisions that scale to massive taxonomic vocabularies. Extensive experiments on a large-scale in-distribution benchmark and six out-of-distribution datasets demonstrate consistent improvements in both identification and discovery. Ablation studies further reveal effective test-time scaling with candidate count $k$ and exemplar count $n$, strong zero-shot transfer to unseen domains, and consistent performance across retrieval encoders, establishing an interpretable solution for biodiversity research.