Pedro O. Pinheiro

I am a research scientist at Genentech, Prescient Design team.

Previously, I was a research scientist at Deep Genomics and Element AI (where I work closely with people from Mila). I received a Ph.D. from École Polytechnique Fédérale de Lausanne (EPFL) and Idiap Research Institute (Switzerland), under supervision of Ronan Collobert. During my phd, I also spent time at Facebook AI Research (FAIR). Previously, I graduated with a MSc. in Image and Signal Processing from Institut National des Sciences Appliquées de Lyon (INSA), in France. I am originally form sunny Fortaleza, Brazil.

Email | LinkedIn

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Research

I am interested in machine learning and its applications, specifically deep learning methods for representation learning and generative modeling. Currently, I am interested in developing AI methods that can tackle complex scientific problems, such as molecular sciences and drug discovery.

Below is a list of some recent highlighted work. For a full list of publications, please see my Google Scholar page.

Score-based 3D molecule generation with neural fields
Matthieu Kirchmeyer*, Pedro O. Pinheiro*, Saeed Saremi
NeurIPS, 2024
paper | code

Structure-based drug design by denoising voxel grids
Pedro O. Pinheiro, Arian Jamasb, Omar Mahmood, Vishnu Sresht, Saeed Saremi
ICML, 2024
paper | code

3D Molecule generation by denoising voxel grids
Pedro O. Pinheiro, Joshua Rackers, Joseph Kleinhenz, Michael Maser, Omar Mahmood, Andrew Martin Watkins, Stephen Ra, Vishnu Sresht, Saeed Saremi
NeurIPS, 2023
paper | code

DyAb: sequence-based antibody design and property prediction in a low-data regime
Joshua Yao-Yu Lin, Jennifer L. Hofmann, Andrew Leaver-Fay,..., Pedro O. Pinheiro,..., Andrew Watkins, Kyunghyun Cho, and Nathan C. Frey
bioRxiv, 2025
paper

An RNA foundation model enables discovery of disease mechanisms and candidate therapeutics
Albi Celaj, Alice Jiexin Gao, Tammy T.Y. Lau, Erle M. Holgersen, ..., Pedro O. Pinheiro, ..., Brendan J. Frey
bioRxiv, 2023
paper