Beyond performance: How design choices shape chemical language models

Fender, I.; Gut, J. A.; Lemmin, T.

doi:10.1101/2025.05.23.655735

Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.05.23.655735

Beyond performance: How design choices shape chemical language models

Fender, I.·Gut, J. A.·Lemmin, T.

View original source ↗Export metadata ↓

Abstract

Chemical language models (CLMs) have shown strong performance in molecular property prediction and generation tasks. However, the impact of design choices, such as molecular representation format, tokenization strategy, and model architecture, on both performance and chemical interpretability remains underexplored. In this study, we systematically evaluate how these factors influence CLM performance and chemical understanding. We evaluated models through finetuning on downstream tasks and probing the structure of their latent spaces using simple classifiers and dimensionality reduction techniques. Despite similar performance on downstream tasks across model configurations, we observed substantial differences in the structure and interpretability of their internal representations. SMILES molecular representation format with atomwise tokenization strategy consistently produced more chemically meaningful embeddings, while models based on BART and RoBERTa architectures yielded comparably interpretable representations. These findings highlight that design choices meaningfully shape how chemical information is represented, even when external metrics appear unchanged. This insight can inform future model development, encouraging more chemically grounded and interpretable CLMs. Scientific ContributionThis study systematically evaluates how core design choices influence chemical language models. Although the performances on downstream tasks were often similar across configurations, we observed substantial differences in internal representations with atomwise tokenized SMILES representations producing more chemically structured latent spaces than representations based on SELFIES. By clarifying the effects of molecular representation format and tokenization strategy, our findings provide actionable guidance for the more informed and interpretable design of future CLMs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/655735v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@11c387org.highwire.dtl.DTLVardef@3be797org.highwire.dtl.DTLVardef@e197c2org.highwire.dtl.DTLVardef@b264e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

Explore related subjects

bioinformatics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Fender, I., Gut, J. A., Lemmin, T.. 2025-05-27. Beyond performance: How design choices shape chemical language models. https://doi.org/10.1101/2025.05.23.655735

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

spatialMET: an open and scalable framework for spatial metabolomics analysis

Mass spectrometry imaging (MSI) enables spatially resolved metabolomics in intact tissue sections, but analysis remains challenging at scale. Existing MSI workflows often require users to combine multiple software tools, while others rely on proprietary vendor software that limits interoperability and reproducibility. To address these challenges, we developed spatialMET, an open-source framework that provides an end-to-end workflow for MSI analysis. spatialMET provides a unified platform for preprocessing, spatial domain detection, and visualization. Downstream analyses include differential abundance testing, spatial autocorrelation and gradient analysis, dimensionality reduction, and correlation network analysis. Spatial domain detection uses hcdist, a C-based hierarchical clustering implementation that substantially reduces runtime and memory use relative to existing R-based approaches. spatialMET can be run through an interactive R Shiny application or as a standalone command-line workflow for larger datasets or high-performance computing environments. Applied to mouse small cell lung cancer MALDI-MSI data containing 284,673 pixels, spatialMET identified tumor-associated, stromal, and adjacent lung spatial domains that aligned with matched histology. Differential abundance analysis identified 117 m/z features that differed between tumor and stromal regions, while spatial autocorrelation analyses revealed spatially structured abundance patterns. Applying spatialMET to mouse lung adenocarcinoma data from an entire lung lobe containing 338,477 pixels further demonstrated scalability and captured spatial heterogeneity across tumor and surrounding lung tissue. In summary, spatialMET provides a scalable, open-source framework for end-to-end spatial metabolomics analysis, and it is distributed as a Docker container for reproducible deployment. Source code and installation instructions are available at https://github.com/biodatalab/spatialMET.

bioinformatics↗

bioRxiv2026

Probing the transcriptome response to shivering in skeletal muscle using a multilayered bioinformatics approach

Cold acclimation holds therapeutic potential for improving metabolic health. We previously demonstrated that repeated cold-induced shivering enhances insulin sensitivity in humans. However, the molecular pathways that underlie the skeletal muscle shivering response, and how these relate to beneficial physiological effects, remain poorly understood. In this study, we combined complementary bioinformatics approaches to allow in-depth analysis of the transcriptomic response of human skeletal muscle to repeated shivering. We identified a robust transcriptional signature and show a sex-specific component in the shivering skeletal muscle response, which seemed to diminish following cold adaptation. Our findings provide mechanistic insights into cold-induced muscle adaptations, shed light on potential interesting molecular targets for further investigation, and emphasize the importance of including both sexes in future cold acclimation studies.

bioinformatics↗

bioRxiv2026

An Information Geometry approach to model topological trajectories and Gene Expression Radius from UMAP geometry.

Understanding the relationship between gene expression dynamics and cellular identity remains a central challenge in single cell biology. Here, we introduce a novel computational and mathematical framework that integrates information geometry, fuzzy topology, and UMAP analysis to model gene expression landscapes derived from single cell RNA sequencing data. We formalize gene expression data as a fuzzy topological space, where interactions between expression points are governed by probabilistic distributions inspired by manifold learning approaches such as UMAP. Within this framework, we define an information geometric structure through a Fisher metric induced by these distributions, enabling the computation of geodesic trajectories that capture cellular differentiation processes. A key contribution of this work is the derivation of analytical conditions, expressed as expression radius formulas, that characterize local neighborhoods in gene expression space. These conditions allow for the identification of genes associated with stem cell states and predictions in transitional cell types in future work. Application of the proposed framework to single cell datasets reveals biologically meaningful gene sets enriched in key regulatory pathways and transcription factors, demonstrating the capacity of our approach to uncover latent structure in complex gene expression data. Our results suggest that integrating differential geometry with statistical learning theory offers a powerful paradigm for modeling genotype and phenotype relationships and cellular state transitions, with potential implications for precision medicine and systems biology.

bioinformatics↗