ICML Topological Deep Learning Challenge 2024: Beyond the Graph Domain

no code implementations • 8 Sep 2024 • Guillermo Bernárdez, Lev Telyatnikov, Marco Montagna, Federica Baccini, Mathilde Papillon, Miquel Ferriol-Galmés, Mustafa Hajij, Theodore Papamarkou, Maria Sofia Bucarelli, Olga Zaghen, Johan Mathe, Audun Myers, Scott Mahan, Hansen Lillemark, Sharvaree Vadgama, Erik Bekkers, Tim Doster, Tegan Emerson, Henry Kvinge, Katrina Agate, Nesreen K Ahmed, Pengfei Bai, Michael Banf, Claudio Battiloro, Maxim Beketov, Paul Bogdan, Martin Carrasco, Andrea Cavallo, Yun Young Choi, George Dasoulas, Matouš Elphick, Giordan Escalona, Dominik Filipiak, Halley Fritze, Thomas Gebhart, Manel Gil-Sorribes, Salvish Goomanee, Victor Guallar, Liliya Imasheva, Andrei Irimia, Hongwei Jin, Graham Johnson, Nikos Kanakaris, Boshko Koloski, Veljko Kovač, Manuel Lecha, Minho Lee, Pierrick Leroy, Theodore Long, German Magai, Alvaro Martinez, Marissa Masden, Sebastian Mežnar, Bertran Miquel-Oliver, Alexis Molina, Alexander Nikitin, Marco Nurisso, Matt Piekenbrock, Yu Qin, Patryk Rygiel, Alessandro Salatiello, Max Schattauer, Pavel Snopov, Julian Suk, Valentina Sánchez, Mauricio Tec, Francesco Vaccarino, Jonas Verhellen, Frederic Wantiez, Alexander Weers, Patrik Zajec, Blaž Škrlj, Nina Miolane

This paper describes the 2nd edition of the ICML Topological Deep Learning Challenge that was hosted within the ICML 2024 ELLIS Workshop on Geometry-grounded Representation Learning and Generative Modeling (GRaM).

Deep Learning Representation Learning

Scoreformer: A Surrogate Model For Large-Scale Prediction of Docking Scores

no code implementations • 13 Jun 2024 • Álvaro Ciudad, Adrián Morales-Pastor, Laura Malo, Isaac Filella-Mercè, Victor Guallar, Alexis Molina

In this study, we present ScoreFormer, a novel graph transformer model designed to accurately predict molecular docking scores, thereby optimizing high-throughput virtual screening (HTVS) in drug discovery.

Drug Discovery Graph Neural Network +1

Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks

no code implementations • 4 May 2023 • Isaac Filella-Merce, Alexis Molina, Marek Orzechowski, Lucía Díaz, Yang Ming Zhu, Julia Vilalta Mor, Laura Malo, Ajay S Yekkirala, Soumya Ray, Victor Guallar

To improve the applicability domain of GM methods, we have developed a workflow based on a variational autoencoder coupled with active learning steps.

Active Learning Drug Design +1