BarcodeMamba+: Advancing State-Space Models for Fungal Biodiversity Research

TL;DR

BarcodeMamba+ introduces a novel state-space model framework for fungal barcode classification, leveraging pretraining and specialized fine-tuning techniques to outperform existing methods in biodiversity monitoring tasks.

Contribution

It presents a new foundation model architecture for fungal taxonomy that effectively handles sparse labels and hierarchical data, with a comprehensive training paradigm and enhancements.

Findings

Outperforms existing methods across taxonomic levels

Effective in data-sparse, long-tailed taxonomic environments

Demonstrates superior generalization to unseen species

Abstract

Accurate taxonomic classification from DNA barcodes is a cornerstone of global biodiversity monitoring, yet fungi present extreme challenges due to sparse labelling and long-tailed taxa distributions. Conventional supervised learning methods often falter in this domain, struggling to generalize to unseen species and to capture the hierarchical nature of the data. To address these limitations, we introduce BarcodeMamba+, a foundation model for fungal barcode classification built on a powerful and efficient state-space model architecture. We employ a pretrain and fine-tune paradigm, which utilizes partially labelled data and we demonstrate this is substantially more effective than traditional fully-supervised methods in this data-sparse environment. During fine-tuning, we systematically integrate and evaluate a suite of enhancements--including hierarchical label smoothing, a weighted loss function, and a multi-head output layer from MycoAI--to specifically tackle the challenges of fungal taxonomy. Our experiments show that each of these components yields significant performance gains. On a challenging fungal classification benchmark with distinct taxonomic distribution shifts from the broad training set, our final model outperforms a range of existing methods across all taxonomic levels. Our work provides a powerful new tool for genomics-based biodiversity research and establishes an effective and scalable training paradigm for this challenging domain. Our code is publicly available at https://github.com/bioscan-ml/BarcodeMamba.