NeurIPS 2024 Workshop AIDrugX Submissions

PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models
Eli M Carrami, Sahand Sharifzadeh
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Deep Interactions for Multimodal Molecular Property Prediction
Patrick Soga, Zhenyu Lei, Camille L. Bilodeau, Jundong Li
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics
Alejandro Velez-Arce, Kexin Huang, Michelle M Li, xiang lin, Wenhao Gao, Bradley Pentelute, Tianfan Fu, Manolis Kellis, Marinka Zitnik
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Orthrus: Towards Evolutionary and Functional RNA Foundation Models
Philip Fradkin, Ruian Shi, Keren Isaev, Brendan Frey, Quaid Morris, Leo J Lee, BO WANG
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Learning Molecular Representation in a Cell
Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, Anne E Carpenter, Meng Jiang, Shantanu Singh
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Representation Learning based Target Discovery from UKBB MRI data
Sivaramakrishnan Sankarapandian, Ramprakash Srinivasan, Matt Sooknah, Elena Sorokin, Jun Xu
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Learning to refine domain knowledge for biological network inference
Peiwen Li, Menghua Wu
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Diverse Genomic Embedding Benchmark for functional evaluation across the tree of life.
Jacob West-Roberts, Joshua Kravitz, Nishant Jha, Andre Cornman, Yunha Hwang
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions
Wei Lu, Jixian Zhang, Jiahua Rao, Zhongyue Zhang, Shuangjia Zheng
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
BindingGYM: A Large-Scale Mutational Dataset Toward Deciphering Protein-Protein Interactions
Wei Lu, Jixian Zhang, Ming Gu, Shuangjia Zheng
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Improving Molecular Graph Generation with Flow Matching and Optimal Transport
Xiaoyang Hou, Tian Zhu, Milong Ren, Dongbo Bu, Xin Gao, Chunming Zhang, Shiwei Sun
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach
Jingyi Zhao, Yuxuan Ou, Austin Tripp, Morteza Rasoulianboroujeni, José Miguel Hernández-Lobato
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
A Deep Learning Approach for RNA-Compound Interaction Prediction with Binding Site Interpretability
Haelee Bae, Hojung Nam
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
Jiaqing Xie, Yue Zhao, Tianfan Fu
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph
Kexin Huang, Tony Zeng, Soner Koc, Alexandra Pettet, Martin Jinye Zhang, Jure Leskovec
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Generalized Flow Matching for Transition Dynamics Modeling
Haibo Wang, Yuxuan Qiu, Yanze Wang, Rob Brekelmans, Yuanqi Du
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Understanding the Sources of Performance in Deep Drug Response Models Reveals Insights and Improvements
Nikhil Branson, Pedro R. Cutillas, Conrad Bessant
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Effective Protein-Protein Interaction Exploration with PPIretrieval
Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics
Chenqing Hua, Yong Liu, Dinghuai Zhang, Odin Zhang, Sitao Luan, Kevin K Yang, Guy Wolf, Doina Precup, Shuangjia Zheng
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Computational Antigen Optimization through Symbolic Optimization and Affinity Maturation Simulation
Jonathan G. Faris, Mikel Landajuela, Kayla G. Sprenger, Daniel faissol, Felipe Leno da Silva
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states
Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Lee Diamant, Missarova Alsu, Minsheng Hao, Hanchen, Hector Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
MeMDLM: De Novo Membrane Protein Design with Masked Discrete Diffusion Protein Language Models
Shrey Goel, Vishrut Thoutam, Edgar Mariano Marroquin, Aaron Gokaslan, Arash Firouzbakht, Sophia Vincoff, Volodymyr Kuleshov, Huong T. Kratochvil, Pranam Chatterjee
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Applications of Modular Co-Design for De Novo 3D Molecule Generation
Danny Reidenbach, Filipp Nikitin, Olexandr Isayev, Saee Gopal Paliwal
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Alignment-based and protein foundation models for viral evolution, vaccines and vectors
Sarah Gurev, Noor Youssef, Navami Jain, Debora Susan Marks
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models
Jeff Guo, Philippe Schwaller
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone