5 papers
Informational blueprints reveal condition-dependent gene regulatory architectures
Doruk Efe Gökmen, Rosalind Wenshan Pan, Tom Röschinger +4
While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. U…
Learning functional groups in complex microbiomes
Matthew S Schmitt, Kiseok Lee, Freddy Bunbury +3
From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven ap…
Graph Contrastive Learning versus Untrained Baselines: The Role of Dataset Size
Smayan Khanna, Doruk Efe Gökmen, Risi Kondor +1
Graph Contrastive Learning (GCL) has emerged as a leading paradigm for self-supervised learning on graphs, with strong performance reported on standardized datasets and growing app…
Melting of non reciprocal solids: how dislocations propel and fission in flowing crystals
Stéphane Guillet, Alexis Poncet, Marine Le Blay +3
When soft matter is driven out of equilibrium its constituents interact via effective interactions that escape Newton's action-reaction principle. Prominent examples include the hy…
Interpreting neural operators: how nonlinear waves propagate in non-reciprocal solids
Jonathan Colen, Alexis Poncet, Denis Bartolo +1
We present a data-driven pipeline for model building that combines interpretable machine learning, hydrodynamic theories, and microscopic models. The goal is to uncover the underly…