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

arXiv: https://arxiv.org/abs/2608.30337 · HTML: https://mlsanity.com/paper/2608.30337/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 36 references that are in the map.
- First posted on arXiv 31 Aug 2026.

## Builds on (most cited first, 4 of 4)

- [TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Second](https://mlsanity.com/paper/2207.01848/) (2022)
- [Transformers Can Do Bayesian Inference](https://mlsanity.com/paper/2112.10510/) (2021)
- [Learning from positive and unlabeled data: a survey](https://mlsanity.com/paper/1811.04820/) (2018)
- [A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification](https://mlsanity.com/paper/2511.04814/) (2025)

## Abstract (arXiv)

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.