Hierarchy-Guided Multimodal Representation Learning for Taxonomic Inference

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.

Label-free clustering of frozen pretrained visual embeddings offers a scalable route to biodiversity monitoring, but image-only fine-grained taxonomy exhibits a consistent coarse-to-fine failure mode: clusters recover broad taxonomic structure yet plateau at species level. We study this behaviour on BIOSCAN-5M through an information-calibrated clustering analysis. BioCLIP~2 features with UMAP and HDBSCAN reach $0.79$ AMI at family and $0.67$ at genus, substantially improving over the prior image baseline and remaining competitive with oracle-$K$, graph-based, and learned clustering heads on the same frozen features. To diagnose whether the remaining plateau is method-limited or information-limited, we introduce InfoTaxa, which combines clustering efficiency---the fraction of probe-estimated image information recovered by an unsupervised partition---with paired DNA as an audit signal only, not an inference input. The density pipeline recovers approximately $0.90$ and $0.81$ of the image-available information at order and family, respectively. Held-out late-fusion probes show that adding DNA to the image embedding reduces species-level prediction error by approximately two bits. Robustness analyses cover multiple image encoders, described-species and rare-class subsets, probe diagnostics, and held-out-species coarse-rank generalisation and same-species retrieval. Thus, in the tested setting, species-level label-free clustering is both clustering-limited and representation-limited: improved clustering may recover additional image-exposed structure, but cannot close the DNA-audited information gap alone.

Taxonomies provide key information about the semantic relationships between concepts and the inherent organization of vision and language. Despite their impressive capabilities, large multimodal models (LMMs) often lack taxonomic knowledge, leading to low hierarchical visual recognition (HVR) consistency. These models typically only rely on language modeling objectives during fine-tuning and lack explicit taxonomy-aware regularization. To address this, we propose Hierarchical Representation Regularization ($HiR^2$), a simple plug-and-play regularizer that improves hierarchical consistency in LMMs. Specifically, we introduce a semantic-aware visual tree construction framework that extracts coarse-to-fine visual features from intermediate LLM layers guided by textual cues. The regularizer combines two complementary objectives: a taxonomic entailment loss that enforces hierarchy via hyperbolic entailment cones in the Lorentz model, and a discriminative dispersive loss that promotes angular separation of semantically similar embeddings on the unit sphere without disturbing the radial hierarchical structure. Extensive experiments demonstrate that $HiR^2$ effectively captures taxonomic structures across diverse LMMs and fine-tuning methods. Code is available at https://github.com/PKU-ICST-MIPL/HiR2_ICML2026.