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Chemistry Journal Club
The PSML Nexus Chemistry Journal Club is a friendly get-together of a few graduate students and post-docs who are interested in the application of machine learning in their research. Generally, one participant takes the lead in each of these journal clubs and either discuss an article of their interest or a machine-learning technique that they would like to explore. Currently, the students meet every other Friday at 1:00 PM PST, but the schedule can be updated on demand. If you are interested to join these journal clubs, please send an email to
Carly Brennan (ckbrenna@uci.edu)
The schedule will be updated here each week before Friday.
Upcoming:
- April 9, 2021, 1:00PM - Project work: Data driven analysis of luciferase-luciferin pairs, discussion led by Carly Brennan
Past Sessions:
- March 12, 2021, 1:00PM - Project work: Using Machine Learning to Predict Building Block Yields for the Development of DNA Encoded Libraries, discussion led by Chris Zhang
- February 26, 2021, 1:00PM - Project work: Spin-polarized Kohn-Sham Regularizer, discussion led by Bhupalee Kalita
- February 12, 2021, 1:00PM - Project work: Label-free Cellular Characterization Using Time-Series Data, discussion led by Dan Seith
- January 29, 2021, 1:00PM - Project work: Unsupervised learning based prediction of dynamical coupling in SARS-C0V-2 spike protein, discussion led by Dhiman Ray
- November 13, 2020, 2:00PM - Journal article: Discovering de novo peptide substrates for enzymes using machine learning, discussion led by Carly Brennan.
- October 30, 2020, 2:00PM - Restricted Boltzmann Machines, discussion led by Bhupalee Kalita.
- October 2, 2020, 2:00 PM - Journal article: Mol2vec: Unsupervised Machine Learning Approach with ChemicalIntuition, the discussion will be led by Tommaso Galeazzo.
- September 18, 2020 - Journal article: Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes, discussion led by Dhiman Ray.
- September 4, 2020 - Project work: Use of network and machine learning methods to determine properties of the active site of the SARS-Cov-2 Main Protease (MPro), led by Elizabeth Deissner.
- August 21, 2020 - Journal article: Machine learning in thermodynamics: prediction of activity coefficients by matrix completion, discussion led by Bhupalee Kalita
- July 24, 2020 - Quarter-ending discussion
- July 10, 2020 - Auto differentiation using TensorFlow, with an application to calculating forces in a classical MD simulation, discussion led by Trevor Gokey
- June 26, 2020 - Journal article: Gaussian mixture-based enhanced sampling for statics and dynamics, discussion led by Dhiman Ray.
- June 12, 2020 - Journal article: Deep learning for chemical reaction prediction, discussion led by Tommaso Galeazzo.
- May 29, 2020 - Journal article: SchNet- A deep learning architecture for molecules and materials, discussion led by Bhupalee Kalita.
- May 15, 2020 - The theory behind time-lagged independent component analysis (TICA), discussion led by Dhiman Ray.