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Lood van Niekerk

Research Assistant (2021—2022)

Lood van Niekerk was an MSc student with the group, after which he joined the group as a research assistant, splitting his time with the Debora Marks Lab at Harvard.

Publications while at OATMLNews items mentioning Lood van NiekerkReproducibility and CodeBlog Posts

Publications while at OATML:

ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design

Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high- quality expert annotations about mutation effects. We devise a robust evaluation framework that comb... [full abstract]

Pascal Notin, Aaron W. Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Hansen Spinner, Nathan Rollins, Ada Shaw, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Rose Orenbuch, Yarin Gal, Debora Marks
NeurIPS 2023

News items mentioning Lood van Niekerk:

OATML to co-organize the Machine Learning for Drug Discovery (MLDD) workshop at ICLR 2023

OATML to co-organize the Machine Learning for Drug Discovery (MLDD) workshop at ICLR 2023

21 Dec 2022

OATML students Pascal Notin and Clare Lyle, along with OATML group leader Yarin Gal, are co-organizing the Machine Learning for Drug Discovery (MLDD) workshop at ICLR 2023 jointly with collaborators at GSK, Genentech, Harvard, MIT and others. OATML students Neil Band, Freddie Bickford Smith, Jan Brauner, Lars Holdijk, Andrew Jesson, Andreas Kirsch, Shreshth Malik, Lood van Niekirk and Ruben Wietzman are part of the program committee.

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