arXiv subjects

Natalia Flechas Manrique

Publications and source records attributed to Natalia Flechas Manrique.

3 recordsLinked to original sources

arXiv2026

ProtModernBERT: Compute-Efficient Protein Language Modeling

Large protein language models provide a powerful framework for learning sequence-function relationships and guiding experimental design. However, architectural improvements are underexplored, especially in low-compute regimes of relevance for resource-constrained research laboratories. We show that the training cost for encoder-only transformer architectures can be reduced by leveraging modern architectural refinements, offering an encouraging performance / compute-efficiency trade-off. We introduce ProtModernBERT, a modernized BERT-style model pre-trained on amino acid sequences, and compare it with ProtBert, Amplify, and ESM2 across a set of supervised structural tasks -encompassing secondary structure prediction, disorder prediction, and subcellular localization- and ProteinGym's zero-shot functional benchmark. We find that ProtModernBERT matches or closely tracks the performance of Amplify-120M and ProtBert with up to 80-90\% reduction in pre-training FLOPs, and narrows the gap to ESM2 when controlling for pre-training. Our analysis using a cluster-based validation protocol for hyperparameter selection and randomly initialized models disentangles the contributions of architecture and data, showing that modern components provide stronger inductive biases that are more consequential than parameter count in low-compute regimes.

cs.LG↗

arXiv2025

epiGPTope: A machine learning-based epitope generator and classifier

Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic epitope libraries is challenging due to the large combinatorial sequence space, $20^n$ combinations for linear epitopes of n amino acids, making screening and testing unfeasible, even with high throughput experimental techniques. In this study, we present a large language model, epiGPTope, pre-trained on protein data and specifically fine-tuned on linear epitopes, which for the first time can directly generate novel epitope-like sequences, which are found to possess statistical properties analogous to the ones of known epitopes. This generative approach can be used to prepare libraries of epitope candidate sequences. We further train statistical classifiers to predict whether an epitope sequence is of bacterial or viral origin, thus narrowing the candidate library and increasing the likelihood of identifying specific epitopes. We propose that such combination of generative and predictive models can be of assistance in epitope discovery. The approach uses only primary amino acid sequences of linear epitopes, bypassing the need for a geometric framework or hand-crafted features of the sequences. By developing a method to create biologically feasible sequences, we anticipate faster and more cost-effective generation and screening of synthetic epitopes, with relevant applications in the development of new biotechnologies.

cs.LG↗

arXiv2023

Enhancing Interpretability using Human Similarity Judgements to Prune Word Embeddings

Interpretability methods in NLP aim to provide insights into the semantics underlying specific system architectures. Focusing on word embeddings, we present a supervised-learning method that, for a given domain (e.g., sports, professions), identifies a subset of model features that strongly improve prediction of human similarity judgments. We show this method keeps only 20-40% of the original embeddings, for 8 independent semantic domains, and that it retains different feature sets across domains. We then present two approaches for interpreting the semantics of the retained features. The first obtains the scores of the domain words (co-hyponyms) on the first principal component of the retained embeddings, and extracts terms whose co-occurrence with the co-hyponyms tracks these scores' profile. This analysis reveals that humans differentiate e.g. sports based on how gender-inclusive and international they are. The second approach uses the retained sets as variables in a probing task that predicts values along 65 semantically annotated dimensions for a dataset of 535 words. The features retained for professions are best at predicting cognitive, emotional and social dimensions, whereas features retained for fruits or vegetables best predict the gustation (taste) dimension. We discuss implications for alignment between AI systems and human knowledge.

cs.CL↗