Publications

You can also find my articles on my Google Scholar profile.

Journal Articles

BioBrigit, a Hybrid Machine Learning and Knowledge-Based Approach to Model Metal Pathways in Proteins: Application to a Dicopper Tyrosinase

Published in ACS Omega, 2025

This paper presents a new prediction tool for identifying metal ion diffusion pathways within proteins, and demonstrates its capabilities by considering the use case of a dicopper tyrosinase.

Recommended citation: Fernández-Díaz R, Roldán-Martín L, Sodupe M, Sánchez-Aparicio JE, Maréchal JD. BioBrigit, a Hybrid Machine Learning and Knowledge-Based Approach to Model Metal Pathways in Proteins: Application to a Dicopper Tyrosinase. ACS omega. 2025 Jun 6.
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AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors

Published in Bioinformatics, 2024

This paper discusses the design of an AutoML tool for building peptide bioactivity predictors and how to ensure their robust evaluation through homology partitioning.

Recommended citation: Fernández-Díaz R, Cossio-Pérez R, Agoni C, Lam HT, Lopez V, Shields DC. AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors. Bioinformatics. 2024 Sep;40(9):btae555.
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Conference Papers

A new framework for evaluating model out-of-distribution generalisation for the biochemical domain

Published in The Thirteenth International Conference on Learning Representations, 2025

This paper discusses a new framework for evaluating model performance in new data. It offers metrics for choosing the best similarity function for a given biochemical prediction task and for estimating model performance conditioned on a deployment distribution.

Recommended citation: Fernandez-Diaz R, Lam HT, López V, Shields DC. A new framework for evaluating model out-of-distribution generalisation for the biochemical domain. In The Thirteenth International Conference on Learning Representations.
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