Taxonomy-aware deep learning for hierarchical marine species classification in underwater imagery

Fine-grained recognition of marine organisms is important for ecological research, biodiversity monitoring, and habitat conservation. However, existing methods often focus on the target organism alone, which can overlook informative cues from the surrounding environment. Moreover, biological taxonomy is often underused during model training, despite providing meaningful hierarchical information for distinguishing visually similar taxa. To address these limitations, we propose MATANet, a Multi-Context Attention and Taxonomy-Aware Network for ROI-guided fine-grained marine organism recognition. Inspired by expert taxonomic identification, MATANet jointly models target appearance, environmental context, and taxonomic information. Specifically, MCEAM uses the target organism representation as a query to attend to informative cues from surrounding regions. In addition, biological taxonomy is used as auxiliary supervision through level-wise taxonomic CE, encouraging predictions that are more consistent with the taxonomic hierarchy. Experiments on FathomNet 2025 and FishCLEF2015 demonstrate that MATANet consistently outperforms representative benchmark models for fine-grained marine organism recognition. The official challenge evaluation further supports the practical effectiveness of the proposed framework on held-out test data. Additional evaluations on FAIR1M v2.0 assess the transferability of MATANet to another visual recognition domain, while experiments using automatically detected ROIs examine its practical applicability and robustness in detection-based recognition settings.

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.

Marine plankton underpin aquatic food webs and play a key role in global CO2 sequestration, making reliable species identification critical for understanding ocean health and climate feedbacks. Existing classification models perform well on individual collections but fail to generalize across instruments and environments due to isolated training datasets and inconsistent labels. To address this, we introduce Planktonzilla-17M, a unified dataset consolidating publicly available plankton image collections spanning thirteen imaging systems. It comprises 17.4 million images with standardized taxonomy and geo-environmental metadata, including 3.74 million plankton images spanning over 602 taxonomic classes, of which 201 are identified at the species level, making it the largest and most comprehensive plankton image dataset to date. Using this large-scale dataset, we perform a controlled comparison between supervised and CLIP-style image--text training on a shared ViT backbone. We find that a supervised classifier matches or exceeds CLIP-style training when trained using taxonomic lineage as text. We further observe that BioCLIP and BioCLIP2 perform poorly on plankton in zero-shot and few-shot settings. Leveraging Planktonzilla-17M improves plankton classification performance, highlighting the limitations of current biological foundation models in marine imaging domains.