Coarse composition suffices: tabular in-context learning for multi-activity antimicrobial peptide profiling

A sequence-only model for predicting antimicrobial peptide activity achieved an mAP-5 of 77.8%, outperforming previous methods without complex training.

Summary and findings

This study evaluates a sequence-only pipeline for predicting multi-label activity of antimicrobial peptides (AMPs) using 330 sequence descriptors. The model was tested on the ESCAPE benchmark with 82,359 peptides. The label-powerset TabPFN model achieved a mean average precision of 77.8%, surpassing the previous best of 72.1%.

Abstract

Antimicrobial peptides (AMPs) often act against multiple pathogen classes, making multi-label activity prediction a more realistic screening target than binary antimicrobial classification. The ESCAPE benchmark formalizes this setting, but leading approaches typically rely on multimodal, structure-conditioned deep models that are costly to train and tune. We show that a simple, sequence-only pipeline can match and surpass these methods by combining 330 interpretable sequence descriptors with TabPFN, a tabular foundation model that performs in-context prediction in a single forward pass without gradient-based training or hyperparameter search. On ESCAPE (82,359 peptides; five labels), a label-powerset TabPFN model achieves mAP-5=77.8%, improving on the previously best reported 72.1%. A probabilistic classifier chain is the first method to match or exceed the best published average precision on each of the five labels simultaneously. The gains persist under the prior state-of-the-art single-fold training protocol, indicating they are not a training-set-size artefact, and are largest for remote homologues (+11.2 points below 30% sequence identity). Ablations further show that predicted structure is unnecessary at inference and that performance is not driven by any single descriptor family: ten global physicochemical scalars recover 91% of full-feature performance. Finally, explicitly modelling label dependence yields targeted benefits for scarce activities and supports ranking which activity to assay next from partial positive evidence.

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