Portrait of Almer Van Der Sloot is unavailable

Almer Van Der Sloot

almer.van-der-sloot@mila.quebec
Scientific Facilitator, Scientific Direction

Publications

Protein Language Models: Is Scaling Necessary?
Quentin Fournier
Robert M. Vernon
Almer van der Sloot
Benjamin Schulz
Sarath Chandar
Christopher James Langmead
2024-09-23
bioRxiv (preprint)
doi.org
Protein Language Models: Is Scaling Necessary?
Quentin Fournier
Robert M. Vernon
Almer van der Sloot
Benjamin Schulz
Sarath Chandar
Christopher James Langmead
Public protein sequence databases contain samples from the fitness landscape explored by nature. Protein language models (pLMs) pre-trained … (see more)on these sequences aim to capture this landscape for tasks like property prediction and protein design. Following the same trend as in natural language processing, pLMs have continuously been scaled up. However, the premise that scale leads to better performance assumes that source databases provide accurate representation of the underlying fitness landscape, which is likely false. By developing an efficient codebase, designing a modern architecture, and addressing data quality concerns such as sample bias, we introduce AMPLIFY, a best-in-class pLM that is orders of magnitude less expensive to train and deploy than previous models. Furthermore, to support the scientific community and democratize the training of pLMs, we have open-sourced AMPLIFY’s pre-training codebase, data, and model checkpoints.
2024-09-23
bioRxiv (preprint)
doi.org
RECOVER identifies synergistic drug combinations in vitro through sequential model optimization
Paul Bertin
Jarrid Rector-Brooks
Deepak Sharma
Thomas Gaudelet
Andrew Anighoro
Torsten Gross
Francisco Martínez-Peña
Eileen L. Tang
M.S. Suraj
Cristian Regep
Jeremy B.R. Hayter
Maksym Korablyov
Nicholas Valiante
Almer van der Sloot
Mike Tyers
Charles E.S. Roberts
Michael M. Bronstein
Luke L. Lairson
Jake P. Taylor-King
Yoshua Bengio
2023-09-27
Cell Reports Methods (published)
doi.org