NeurIPS 2023 Workshop GenBio Submissions

TopoDiff: Improving Protein Backbone Generation with Topology-aware Latent Encoding
Yuyang Zhang, Zinnia Ma, Haipeng Gong
- Published: 27 Oct 2023, Last Modified: 29 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design
Wengong Jin, Caroline Uhler, Nir Hacohen
- Published: 27 Oct 2023, Last Modified: 06 Dec 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Causal Discovery in Gene Regulatory Networks with GFlowNet: Towards Scalability in Large Systems
Trang Nguyen, Alexander Tong, Kanika Madan, Yoshua Bengio, Dianbo Liu
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Integrating Protein Structure Prediction and Bayesian Optimization for Peptide Design
Negin Manshour, Fei He, Duolin Wang, Dong Xu
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Generative AI for designing and validating easily synthesizable and structurally novel antibiotics
Kyle Swanson, Gary Liu, Denise Catacutan, James Zou, Jonathan Stokes
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Generating Molecular Conformer Fields
Yuyang Wang, Ahmed Elhag, Navdeep Jaitly, Joshua Susskind, Miguel Bautista
- Published: 27 Oct 2023, Last Modified: 08 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Genomic language model predicts protein co-regulation and function
Yunha Hwang, Andre Cornman, Sergey Ovchinnikov, Peter Girguis
- Published: 27 Oct 2023, Last Modified: 28 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Identifying Neglected Hypotheses in Neurodegenerative Disease with Large Language Models
Spencer Hey, Darren Angle, Christopher Chatham
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods
Minsi Ren, Bowen Gao, Bo Qiang, Yanyan Lan
- Published: 27 Oct 2023, Last Modified: 18 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Generative Flow Networks Assisted Biological Sequence Editing
Pouya M. Ghari, Alex Tseng, Gökcen Eraslan, Romain Lopez, Tommaso Biancalani, Gabriele Scalia, Ehsan Hajiramezanali
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Exploring the building blocks of cell organization as high-order network motifs with graph isomorphism network
Yang Yu, Shuang Wang, Dong Xu, Juexin Wang
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Protein Discovery with Discrete Walk-Jump Sampling
Nathan Frey, Dan Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Vladimir Gligorijevic, Saeed Saremi
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Bowen Jing, Bonnie Berger, Tommi Jaakkola
- Published: 27 Oct 2023, Last Modified: 29 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
The Discovery of Binding Modes Requires Rethinking Docking Generalization
Gabriele Corso, Arthur Deng, Nicholas Polizzi, Regina Barzilay, Tommi Jaakkola
- Published: 27 Oct 2023, Last Modified: 29 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
CodonBERT: Large Language Models for mRNA design and optimization
Sizhen Li, Saeed Moayedpour, Ruijiang Li, Michael Bailey, Saleh Riahi, Milad Miladi, Jacob Miner, Dinghai Zheng, Jun Wang, Akshay Balsubramani, Khang Tran, Minnie, Monica Wu, Xiaobo Gu, Ryan Clinton, Carla Asquith, Joseph Skaleski, Lianne Boeglin, Sudha Chivukula, Anusha Dias et al. (4 additional authors not shown)
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Improving few-shot learning-based protein engineering with evolutionary sampling
Muhammad Zaki Jawaid, Aayushma Gautam, T. Gainous, Dan Hart, Robin Yeo, Timothy Daley
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models
Ziqi Chen, Bo Peng, srinivasan parthasarathy, Xia Ning
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Parameter-Efficient Fine-Tune on Open Pre-trained Transformers for Genomic Sequence
Huixin Zhan, Zijun Frank Zhang
- Published: 27 Oct 2023, Last Modified: 29 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Approximation of Intractable Likelihood Functions in Systems Biology via Normalizing Flows
Vincent Zaballa, Elliot Hui
- Published: 27 Oct 2023, Last Modified: 19 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
Wei Lu, Jixian Zhang, Huang Weifeng, Ziqiao Zhang, Chengtao Li, Shuangjia Zheng
- Published: 27 Oct 2023, Last Modified: 27 Oct 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
DGFN: Double Generative Flow Networks
Elaine Lau, Nikhil Murali Vemgal, Doina Precup, Emmanuel Bengio
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Contextualized Networks Reveal Heterogeneous Transcriptomic Regulation in Tumors at Sample-Specific Resolution
Caleb Ellington, Ben Lengerich, Thomas Watkins, Jiekun Yang, Hanxi Xiao, Manolis Kellis, Eric Xing
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation
Danny Reidenbach, Aditi Krishnapriyan
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
AMP-Diffusion: Integrating Latent Diffusion with Protein Language Models for Antimicrobial Peptide Generation
Tianlai Chen, Pranay Vure, Rishab Pulugurta, Pranam Chatterjee
- Published: 27 Oct 2023, Last Modified: 20 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
Chengyue Gong, Adam Klivans, Jordan Wells, James Loy, qiang liu, Alex Dimakis, Daniel Diaz
- Published: 27 Oct 2023, Last Modified: 20 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone