arXiv subjects

Rainer Breitling

Publications and source records attributed to Rainer Breitling.

2 recordsLinked to original sources

arXiv2026

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 straightforward cross-model embedding initialization fails to improve downstream performance in BiGCARP, and show that deeper-layer embeddings capture a more contextual and faithful representation of the model's learned knowledge. Furthermore, we demonstrate that representations at different granularities encode complementary biological knowledge, and that combining them yields measurable performance gains in intermediate-level prediction tasks. Our findings highlight cross-granularity integration as a promising strategy for improving both the performance and interpretability of biological foundation models.

cs.LG↗

arXiv2026

Disentangling Similarity and Relatedness in Topic Models

The recent success of large pre-trained language models (PLMs) has motivated their integration into topic modeling. However, PLM-augmented topic models differ from classical co-occurrence models such as Latent Dirichlet Allocation (LDA) not only in performance, but also in the type of semantic structure they capture. We formalize this distinction along two psycholinguistic axes: thematic relatedness (dog/bone) and taxonomic similarity (dog/wolf). To measure both axes over topic words, we construct a large synthetic benchmark of word pairs using LLM-based annotation and train a neural scorer on it. Across multiple corpora and model families, the scorer places different topic-model families at distinct positions within the joint similarity-relatedness space. The two scores further predict downstream task performance: tasks requiring similarity benefit from similarity-rich topics, whereas tasks requiring relatedness benefit from the converse, and excessive emphasis on either axis degrades performance on tasks aligned with the opposing semantic structure. Neither axis is uniformly beneficial. Measuring both therefore provides a practical, model-agnostic diagnostic for evaluating the semantic structure captured by topic models.

cs.CL↗