NeurIPS 2024 Workshop AIDrugX Submissions

3D Interaction Geometric Pre-training for Molecular Relational Learning
Namkyeong Lee, Yunhak Oh, Heewoong Noh, Gyoung S. Na, Tianfan Fu, Chanyoung Park
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences
Alan Nawzad Amin, Nate Gruver, Yucen Lily Li, Yilun Kuang, Hunter Elliott, Calvin McCarter, Aniruddh Raghu, Peyton Greenside, Andrew Gordon Wilson
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Leveraging Disease-Specific Topologies and Counterfactual Relationships in Knowledge Graphs for Inductive Reasoning in Drug Repurposing
Cerag Oguztuzun, Zhenxiang Gao, Hui Li, Rong Xu
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion
Anirban Sarkar, Ziqi Tang, Chris Z Zhao, Peter K Koo
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
A Large-Scale Foundation Model for RNA Function and Structure Prediction
Shuxian Zou, Tianhua Tao, Sazan Mahbub, Caleb Ellington, Robin Jonathan Algayres, Dian Li, Yonghao Zhuang, Hongyi Wang, Le Song, Eric P. Xing
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
HELM: Hierarchical Encoding for mRNA Language Modeling
Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi, Artem Moskalev, Rui Liao
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all
Ihab Bendidi, Shawn T. Whitfield, Kian Kenyon-Dean, Hanene Ben Yedder, Yassir El Mesbahi, Emmanuel Noutahi, Alisandra Kaye Denton
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis
Yan Wu, Esther Wershof, Sebastian M Schmon, Marcel Nassar, Błażej Osiński, Ridvan Eksi, Kun Zhang, Thore Graepel
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
Harnessing Preference Optimisation in Protein LMs for Hit Maturation in Cell Therapy
Katarzyna Janocha, Annabel Ling, Alice Godson, Yulia Lampi, Simon Bornschein, Nils Yannick Hammerla
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Correlational Lagrangian Schrodinger Bridge: Learning Dynamics with Population-Level Regularization
Yuning You, Ruida Zhou, Yang Shen
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Pharmacophore-based design by learning on voxel grids
Omar Mahmood, Pedro O. Pinheiro, Richard Bonneau, Saeed Saremi, Vishnu Sresht
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking
Yiliang Yuan, Mustafa Misir
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Best Practices for Multi-Fidelity Bayesian Optimization in Materials and Molecular Research
Victor Sabanza Gil, Riccardo Barbano, Daniel Pacheco Gutiérrez, Jeremy Scott Luterbacher, José Miguel Hernández-Lobato, Philippe Schwaller, Loïc Roch
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
FluxGAT: Integrating Flux Sampling with Graph Neural Networks for Unbiased Gene Essentiality Classification
Kieren Sharma, Zahraa S. Abdallah, Lucia Marucci
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning
Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K Gilson, Rose Yu
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules
Lucy Vost, Vijil Chenthamarakshan, Payel Das, Charlotte Deane
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs
Talip Ucar, Cedric Malherbe, Ferran Gonzalez
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
PepDoRA: A Unified Peptide Language Model via Weight-Decomposed Low-Rank Adaptation
Leyao Wang, Rishab Pulugurta, Pranay Vure, Yinuo Zhang, Aastha Pal, Pranam Chatterjee
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
A Deep Generative Model for the Design of Synthesizable Ionizable Lipids
Yuxuan Ou, Jingyi Zhao, Austin Tripp, Morteza Rasoulianboroujeni, José Miguel Hernández-Lobato
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Video Representation Learning of Cardiac MRI for Genetic Discovery
Matt Sooknah, Sivaramakrishnan Sankarapandian, Ramprakash Srinivasan, Johannes Riegler, Jun Xu
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale
Caleb Ellington, Ning Sun, Nicholas Ho, Tianhua Tao, Sazan Mahbub, Dian Li, Yonghao Zhuang, Hongyi Wang, Eric P. Xing, Le Song
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space
Jason Qin, Hans-Hermann Wessels, Carlos Fernandez-Granda, Yuhan Hao
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models
Conor F. Hayes, Andre R Goncalves, Steven Alan Magana-Zook, Ahmet Can Solak, Daniel faissol, Mikel Landajuela
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models
Dhruva Rajwade, Erica Wang, Aryan Satpathy, Alexander Brace, Hongyu Guo, Arvind Ramanathan, Shengchao Liu, Anima Anandkumar
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Latent Diffusion Models for Controllable RNA Sequence Generation
Kaixuan Huang, Yukang Yang, Kaidi Fu, Yanyi Chu, Le Cong, Mengdi Wang
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone