NeurIPS 2023 Workshop GenBio Submissions

De Novo Drug Design with Joint Transformers
Adam Izdebski, Ewelina Weglarz-Tomczak, Ewa Szczurek, Jakub Tomczak
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
$\textit{In vitro}$ validated antibody design against multiple therapeutic antigens using generative inverse folding
Amir Shanehsazzadeh
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
AntiFold: Improved antibody structure design using inverse folding
Magnus Høie, Alissa Hummer, Tobias Olsen, Morten Nielsen, Charlotte Deane
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Targeting tissues via dynamic human systems modeling in generative design
Zachary Fox, Nolan English, Belinda Akpa
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Conditional Generation of Antigen Specific T-cell Receptor Sequences
Dhuvarakesh Karthikeyan, Colin Raffel, Benjamin Vincent, Alex Rubinsteyn
- Published: 27 Oct 2023, Last Modified: 30 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
An Energy Based Model for Incorporating Sequence Priors for Target-Specific Antibody Design
Yining Huang, Steffanie Paul, Debora Marks
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Inpainting Protein Sequence and Structure with ProtFill
Elizaveta Kozlova, Arthur Valentin, Daniel Nakhaee-Zadeh Gutierrez
- Published: 27 Oct 2023, Last Modified: 20 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Fine-tuning protein Language Models by ranking protein fitness
Minji Lee, Kyungmin Lee, Jinwoo Shin
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
regLM: Designing realistic regulatory DNA with autoregressive language models
Avantika Lal, Tommaso Biancalani, Gökcen Eraslan
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Analysis of cellular phenotypes with unbiased image-based generative models
Ruben Fonnegra, Mohammad Sanian, Zitong Chen, Lassi Paavolainen, Juan Caicedo
- Published: 27 Oct 2023, Last Modified: 28 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Unexplored regions of the protein sequence-structure map revealed at scale by a library of “foldtuned” language models
Arjuna Subramanian, Matt Thomson
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Through the looking glass: navigating in latent space to optimize over combinatorial synthesis libraries
Aryan Pedawi, Saulo De Oliveira, Henry van den Bedem
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Transition Path Sampling with Boltzmann Generator-based MCMC Moves
Michael Plainer, Hannes Stark, Charlotte Bunne, Stephan Günnemann
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation
Divya Nori, Simon Mathis, Amir Shanehsazzadeh
- Published: 27 Oct 2023, Last Modified: 20 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Alex Lu, Nicolo Fusi, Ava Amini, Kevin Yang
- Published: 27 Oct 2023, Last Modified: 29 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Sampling Protein Language Models for Functional Protein Design
Jeremie Theddy Darmawan, Yarin Gal, Pascal Notin
- Published: 27 Oct 2023, Last Modified: 30 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Autoregressive fragment-based diffusion for pocket-aware ligand design
Mahdi Ghorbani, Leo Gendelev, Paul Beroza, Michael Keiser
- Published: 03 Nov 2023, Last Modified: 29 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Generative design for gene therapy: An $\textit{in vivo}$ validated method
Farhan Damani, David Brookes, Jeffrey Chan, Rishi Jajoo, Alexander Mijalis, Joyce Samson, Flaviu Vadan, Cameron Webster, Stephen Malina, Sam Sinai
- Published: 27 Oct 2023, Last Modified: 28 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Bending and Binding: Predicting Protein Flexibility upon Ligand Interaction using Diffusion Models
Xuejin Zhang, Tomas Geffner, Matt McPartlon, Mehmet Akdel, Dylan Abramson, Graham Holt, Alexander Goncearenco, Luca Naef, Michael Bronstein
- Published: 27 Oct 2023, Last Modified: 28 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Epitope-specific antibody design using diffusion models on the latent space of ESM embeddings
Tomer Cohen, Dina Schneidman-Duhovny
- Published: 27 Oct 2023, Last Modified: 22 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Harmonic Prior Self-conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design
Hannes Stark, Bowen Jing, Regina Barzilay, Tommi Jaakkola
- Published: 27 Oct 2023, Last Modified: 28 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Combining Structure and Sequence for Superior Fitness Prediction
Steffanie Paul, Aaron Kollasch, Pascal Notin, Debora Marks
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
Ian Dunn, David Koes
- Published: 27 Oct 2023, Last Modified: 21 Nov 2023
- GenBio@NeurIPS2023 Spotlight
- Readers: Everyone
Machine learning derived embeddings of bulk multi-omics data enable clinically significant representations in a pan-cancer cohort
Sanjay Nagaraj, ZACHARY MCCAW, Theofanis Karaletsos, Daphne Koller, Anna Shcherbina
- Published: 27 Oct 2023, Last Modified: 23 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Charles Harris, Kieran Didi, Arian Jamasb, Chaitanya Joshi, Simon Mathis, Pietro Lio, Tom Blundell
- Published: 27 Oct 2023, Last Modified: 30 Nov 2023
- GenBio@NeurIPS2023 Poster
- Readers: Everyone