Cross-Granularity Representations for Biological Sequences: Insights from ESM and BiGCARP
Recent advances in general-purpose foundation models have stimulated the development of large biological sequence models. While natural language shows symbolic granularity (characters, words, sentences), biological sequences exhibit hierarchical granularity whose levels (nucleotides, amino acids, protein domains, genes) further encode biologically functional information. In this paper, we investigate the integration of cross-granularity knowledge from models through a case study of BiGCARP, a Pfam domain-level model for biosynthetic gene clusters, and ESM, an amino acid-level protein language model. Using representation analysis tools and a set of probe tasks, we first explain why a strai...
| Authors | Hanlin Xiao, Rainer Breitling, Eriko Takano et al. |
|---|---|
| Primary category | cs.LG |
| Published | 21 March 2026 |
| Last updated at source | 21 March 2026 |
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