SNP2ARG: Inferring Ancestral Recombination Graphs with Deep Learning
Marçal Comajoan Cara, David Bonet, Cole Shanks, Daniel Mas Montserrat, Alexander Ioannidis
Oral and poster at the Annual Meeting of the Society for Molecular Biology & Evolution (SMBE), 2025, Beijing, China.
bioRxiv; GitHub.
ARGMix: Inferring Ancient Local Ancestry with Transformers in Ancestral Recombination Graphs
Cole Shanks, David Bonet, Marçal Comajoan Cara, Daniel Mas Montserrat, Alexander Ioannidis
Oral and poster at the Annual Meeting of the Society for Molecular Biology & Evolution (SMBE), 2025, Beijing, China.
bioRxiv; GitHub.
ARGformer: Learning on Ancestral Recombination Graphs with Transformers
David Bonet, Cole Shanks, Marçal Comajoan Cara, Daniel Mas Montserrat, Alexander Ioannidis
Poster at the Annual Meeting of the Society for Molecular Biology & Evolution (SMBE), 2025, Beijing, China.
bioRxiv; GitHub.
PM1: A Foundation Model Fusing Genotype, Phenotype, and Image for Precision Medicine
Marçal Comajoan Cara*, Margarita Geleta*, Christophe Thomassin*, David Bonet*, Aina Luis Vidal, Benet Oriol Sabat, Daniel Mas Montserrat, Alexander Ioannidis
Poster at the International Conference on Machine Learning (ICML) Workshop on Multimodal Foundation Models and Large Language Models for Life Sciences, 2025, Vancouver, Canada.
Paper; bioRxiv; GitHub.
Integrating Meta-Trained Hypernetworks with GBDTs and Retrieval for Tabular Data
Marçal Comajoan Cara*, David Bonet*, Álvaro Calafell, Daniel Mas Montserrat, Alexander Ioannidis
Spotlight paper with oral at the International Conference on Learning Representations (ICLR) Workshop on Weight Space Learning, 2025, Singapore.
Paper; arXiv; GitHub.
snputils: A Python Library for Genetic Variation and Population Structure
Marçal Comajoan Cara*, David Bonet*, Míriam Barrabés*, ..., Daniel Mas Montserrat, Alexander Ioannidis
Poster at the Annual Meeting of the American Society of Human Genetics (ASHG), 2024, Denver, Colorado, USA.
bioRxiv; website; GitHub.
PopGenAdapt: Semi-Supervised Domain Adaptation for Genotype-to-Phenotype Prediction in Underrepresented Populations
Marçal Comajoan Cara, Daniel Mas Montserrat, Alexander Ioannidis
Paper and oral at the Pacific Symposium on Biocomputing (PSB), 2024, Puako, Hawaii, USA.
Paper; bioRxiv; GitHub.
Quantum Vision Transformers for Quark-Gluon Classification
Marçal Comajoan Cara, ..., Sergei Gleyzer
Paper published in Axioms, 2024; 13(5):323.
Paper; arXiv; GitHub.
$\mathbb{Z}_2 \times \mathbb{Z}_2$ Equivariant Quantum Neural Networks: Benchmarking against Classical Neural Networks
Zhongtian Dong, Marçal Comajoan Cara, ..., Sergei Gleyzer
Paper published in Axioms, 2024; 13(3):188.
Paper; arXiv.
Hybrid Quantum Vision Transformers for Event Classification in High Energy Physics
Eyup Unlu, Marçal Comajoan Cara, ..., Sergei Gleyzer
Paper published in Axioms, 2024; 13(3):187.
Paper; arXiv.
A Comparison Between Invariant and Equivariant Classical and Quantum Graph Neural Networks
Roy Forestano, Marçal Comajoan Cara, ..., Sergei Gleyzer
Paper published in Axioms, 2024; 13(3):160.
Paper; arXiv.