34 citations · 38 across the 4 of their papers we have counts for
4 papers
A standard transformer and attention with linear biases for molecular conformer generation
Viatcheslav Gurev, Timothy Rumbell
Sampling low-energy molecular conformations, spatial arrangements of atoms in a molecule, is a critical task for many different calculations performed in the drug discovery and opt…
BMFM-RNA: whole-cell expression decoding improves transcriptomic foundation models
Michael M. Danziger, Bharath Dandala, Viatcheslav Gurev +12
Transcriptomic foundation models pretrained with masked language modeling can achieve low pretraining loss yet produce poor cell representations for downstream tasks. We introduce…
Novel and flexible parameter estimation methods for data-consistent inversion in mechanistic modeling
Timothy Rumbell, Jaimit Parikh, James Kozloski +1
Predictions for physical systems often rely upon knowledge acquired from ensembles of entities, e.g., ensembles of cells in biological sciences. For qualitative and quantitative an…
Beyond Backprop: Online Alternating Minimization with Auxiliary Variables
Anna Choromanska, Benjamin Cowen, Sadhana Kumaravel +8
Despite significant recent advances in deep neural networks, training them remains a challenge due to the highly non-convex nature of the objective function. State-of-the-art metho…