Plug & Play Directed Evolution of Proteins with Gradient-based Discrete
MCMC

Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC

20 December 2022

Aidan Perreault

David J. Biagioni

Peter C. St. John

Papers citing "Plug & Play Directed Evolution of Proteins with Gradient-based Discrete MCMC"

12 / 12 papers shown

Title
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering Yizhen Luo Zikun Nie Massimo Hong Suyuan Zhao Hao Zhou Zaiqing Nie 33 0 0 30 Oct 2024
How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework Yinuo Ren Haoxuan Chen Grant M. Rotskoff Lexing Ying 47 3 0 04 Oct 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 60 31 0 03 Jun 2024
Three Pathways to Neurosymbolic Reinforcement Learning with Interpretable Model and Policy Networks Peter Graf Patrick Emami 26 2 0 07 Feb 2024
Training Discrete Energy-Based Models with Energy Discrepancy Tobias Schröder Zijing Ou Yingzhen Li Andrew B. Duncan 24 0 0 14 Jul 2023
Improving Protein Optimization with Smoothed Fitness Landscapes Andrew Kirjner Jason Yim Raman Samusevich Shahar Bracha Tommi Jaakkola Regina Barzilay Ila Fiete 13 16 0 02 Jul 2023
Protein Design with Guided Discrete Diffusion Nate Gruver Samuel Stanton Nathan C. Frey Tim G. J. Rudner I. Hotzel J. Lafrance-Vanasse A. Rajpal Kyunghyun Cho A. Wilson DiffM 42 101 0 31 May 2023
Discrete Langevin Sampler via Wasserstein Gradient Flow Haoran Sun H. Dai Bo Dai Haomin Zhou Dale Schuurmans BDL 42 19 0 29 Jun 2022
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval Pascal Notin M. Dias J. Frazer Javier Marchena-Hurtado Aidan N. Gomez D. Marks Y. Gal 55 177 0 27 May 2022
ReLSO: A Transformer-based Model for Latent Space Optimization and Generation of Proteins Egbert Castro Abhinav Godavarthi Julian Rubinfien Kevin B. Givechian Dhananjay Bhaskar Smita Krishnaswamy 38 5 0 24 Jan 2022
Unifying Likelihood-free Inference with Black-box Optimization and Beyond Dinghuai Zhang Jie Fu Yoshua Bengio Aaron Courville 31 13 0 06 Oct 2021
Design by adaptive sampling David H. Brookes Jennifer Listgarten TPM 39 65 0 08 Oct 2018