Visual Species Recognition with Large Multimodal Models as Post-Hoc Correctors

Camera traps often run in the field on edge hardware with limited or no connectivity, making small, locally-deployable vision-language models (VLMs) -- not frontier-scale ones -- the practically relevant class to evaluate for species identification. We test whether models in this deployment-relevant 2--8B range carry genuine taxonomic knowledge, evaluating four such VLMs (Qwen3-VL 2B/4B/8B, Gemma3 4B) against the domain-specific specialist BioCLIP (300M parameters) on a 96-species task, comparing clean iNaturalist photographs against camera-trap imagery from 6 LILA.science collections, on two independently-sampled evaluation sets. All models identify species far above chance, but every model -- general-purpose or specialist -- degrades sharply on field imagery (domain gaps of 9.6--26.6 percentage points, consistent across taxonomic levels and both evaluation sets), indicating the degradation reflects general image legibility rather than fine-grained discrimination failure. BioCLIP substantially outperforms every VLM tested (by 33.2--59.2 percentage points across an expanded 200-image sample for every model) despite its far smaller size, suggesting the gap reflects specialized training data rather than model scale; yet BioCLIP's own domain gap (18.0 points) is statistically indistinguishable from the best VLM's (22.3 points), suggesting the clean-to-field degradation itself is a property of the image-quality shift rather than a general-purpose-model weakness. Under open-set prompting, 5.9--9.6% of responses are syntactically valid but taxonomically nonexistent species names; the relative fabrication-rate ranking across models replicates exactly across both evaluation sets, a more robust finding than any single point estimate.

Vision-language models (VLMs) show promise for agricultural classification, but zero-shot performance on disease, pest, damage, quality, and species identification remains poor, and it is unclear whether this reflects weak visual features or a failure to connect them to domain knowledge. We build a benchmark of 116 datasets, 834 classes, and 8,324 images spanning these tasks to isolate where the gap arises. Linear probing shows VLM vision encoders already encode agricultural features nearly as separable as a self-supervised DINOv3 baseline, ruling out weak visual representations as the primary bottleneck. Conditioning each model on an oracle reference description (an upper bound on its parametric knowledge) closes most of the gap left by an unaided lower bound, showing VLMs already know more about agriculture than they show. To close this gap without an oracle description at inference time, we structure test-time reasoning around a fixed, per-task diagnostic rubric: the model generates $K$ candidate responses and a Probabilistic Pivot Tournament (PPT) verifier, scored pairwise against the rubric, selects the best one. This nearly doubles judged F1 over the lower bound and matches or exceeds the upper bound on several tasks, notably pushing Gemma 4 E4B-it's disease F1 to 0.71, above its own upper bound of 0.60. However, the verifier's letter-scale confidence score has the opposite of its intended effect: filtering to its most confident predictions does not improve accuracy and correlates negatively with correctness across every model and pool size tested, so the score cannot serve as a measure of predictive uncertainty, and most of the observed gain likely comes from rubric-grounded generation rather than pairwise verification.

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.