Lillian Chong
337 posts
@ltchong
Moved to @ltchong.bsky.social. Professor, @PittChem. Computational biophysicist, @westpasoftware for rare event sampling, @ambermdprog force field developer.
Unsupervised learning of progress coordinates during weighted ensemble simulations: Application to millisecond protein folding - Improve rare events in protein folding (e.g., state transitions) through weighted ensemble simulation and an unsupervised deep learning model. - Use a convolutional VAE to compress contact maps into latent space, and applies a Local Outlier Factor to identify outlier conformations, which are then replicated in the simulation. - Training the CVAE on-the-fly works better than using a pretrained model. Preprint: biorxiv.org/content/10.110…
Unsupervised learning of progress coordinates during weighted ensemble simulations: Application to millisecond protein folding - Improve rare events in protein folding (e.g., state transitions) through weighted ensemble simulation and an unsupervised deep learning model. - Use a convolutional VAE to compress contact maps into latent space, and applies a Local Outlier Factor to identify outlier conformations, which are then replicated in the simulation. - Training the CVAE on-the-fly works better than using a pretrained model. Preprint: biorxiv.org/content/10.110…
#HighlightOfTheWeek Animated time-evolution of a 2D probability distribution obtained using WEDAP, a python package to plot molecular simulation data. Work by @darianyang and @ltchong. #compchem pubs.acs.org/doi/10.1021/ac…
