Ferguson Lab at the University of Chicago

DiAMoNDBack

DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces

LSS

mfGPR

Multi-fidelity Gaussian Process Regression

pines

Permutationally invariant networks for enhanced sampling (PINES)

Protein_design_mmdVAE_torch

molgen

Conditional Molecular Structure Generation

activeLearningPFASLinear

Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water

ActiveLearningCG

dMap_JAX

Diffusion maps using JAX

integrin_molgen

Deep generative modeling of large multi-molecular systems

mdn_propagator

Mixture Density Networks (MDNs) for learning simulation propagators

ChromSTEM-Denoising-Autoencoder

A denoising autoencoder using convolutional neural networks and molecular dynamics simulations to post-process ChromSTEM images and provide nucleosome-level resolution.

Limits-of-single-molecule-Takens-reconstruction-notebooks

mof-topology-prediction

snrv

WorkCurveOptim