16 papers
La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
Tomas Geffner, Kieran Didi, Zhonglin Cao +6
Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointl…
DiLaDiff: Distilled Latent-Augmented Diffusion for Language Modeling
Jean-Marie Lemercier, Tomas Geffner, Karsten Kreis +3
Diffusion language models intrinsically fail to capture correlations between decoded tokens, which leads to a harsh trade-off between sampling quality and throughput. To solve this…
Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute
Kieran Didi, Zuobai Zhang, Guoqing Zhou +11
Protein interaction modeling is central to protein design, which has been transformed by machine learning with applications in drug discovery and beyond. In this landscape, structu…
Demystifying Data-Driven Probabilistic Medium-Range Weather Forecasting
Jean Kossaifi, Nikola Kovachki, Morteza Mardani +15
The recent revolution in data-driven methods for weather forecasting has lead to a fragmented landscape of complex, bespoke architectures and training strategies, obscuring the fun…
Exploring Synthesizable Chemical Space with Iterative Pathway Refinements
Seul Lee, Karsten Kreis, Srimukh Prasad Veccham +5
A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effec…
Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
Danny Reidenbach, Zhonglin Cao, Zuobai Zhang +8
High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pair…