NeurIPS 2024 Workshop AIDrugX Submissions

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design
Chenyu Wang, Masatoshi Uehara, Yichun He, Amy Wang, Tommaso Biancalani, Avantika Lal, Tommi Jaakkola, Sergey Levine, Hanchen, Aviv Regev
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Disentangling the Peptide Space: A Contrastive Approach with Wasserstein Autoencoders
Mihir Agarwal, Progyan Das
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Training-Free Guidance with Applications to Protein Engineering
Lewis Cornwall, Joshua Meyers, James Day, Lilly S Wollman, Neil Dalchau, Aaron Sim
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Learning Protocols for Non-Equilibrium Conformational Free-Energy Estimation Using Optimal Transport and Conditional Flow Matching
Lars Holdijk, Michael M. Bronstein, Max Welling
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond
Zicheng Liu, Jiahui Li, Lei Xin, Siyuan Li, Chang Yu, Zelin Zang, Cheng Tan, Yufei Huang, yajingbai, Jun Xia, Stan Z. Li
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Molecular Generation with State Space Sequence Models
Anri Lombard, Shane Acton, Ulrich Armel Mbou Sob, Jan Buys
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks
Nayoung Kim, Seongsu Kim, Minsu Kim, Jinkyoo Park, Sungsoo Ahn
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Homomorphism Counts as Structural Encodings for Molecular Property Prediction
Linus Bao, Emily Jin, Michael M. Bronstein, Ismail Ilkan Ceylan, Matthias Lanzinger
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis
Soojung Yang, Juno Nam, Tynan Perez, Jinyeop Song, Xiaochen Du, Rafael Gomez-Bombarelli
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model
Sumin Ha, Jun Hyeong Kim, Yinhua Piao, Sun Kim
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Reinforcement Learning for Enhanced Targeted Molecule Generation Via Language Models
Salma J. Ahmed, Emad A. Mohammed
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Interpretable Causal Representation Learning for Biological Data in the Pathway Space
Jesus de la Fuente Cedeño, Robert Lehmann, Carlos Ruiz-Arenas, Irene Marín-Goñi, Jan Voges, Xabier Martinez de Morentin, David Gomez-Cabrero, Idoia Ochoa, Jesper Tegnér, Vincenzo Lagani, Mikel Hernaez
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
PLMFit: Benchmarking Transfer Learning with Protein Language Models for Protein Engineering
Thomas Bikias, Evangelos Stamkopoulos, Sai T. Reddy
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Improved Off-policy Reinforcement Learning in Biological Sequence Design
Hyeonah Kim, Minsu Kim, Taeyoung Yun, Sanghyeok Choi, Emmanuel Bengio, Alex Hernández-García, Jinkyoo Park
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Distilling Structural Representations into Protein Sequence Models
Jeffrey Ouyang-Zhang, Chengyue Gong, Yue Zhao, Philipp Kraehenbuehl, Adam Klivans, Daniel Jesus Diaz
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
Alexander Theus, Florian Barkmann, David Wissel, Valentina Boeva
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Mixture of Experts Enable Efficient and Effective Protein Understanding and Design
Ning Sun, Shuxian Zou, Tianhua Tao, Sazan Mahbub, Dian Li, Yonghao Zhuang, Hongyi Wang, Xingyi Cheng, Le Song, Eric P. Xing
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
TCRGenesis: Generation of SIINFEKL-specific T-cell receptor sequences using autoregressive Transformer
Yang An, Felix Drost, Adrian Straub, Annalisa Marsico, Dirk H Busch, Benjamin Schubert
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Modeling CAR Response at the Single-Cell Level Using Conditional OT
Alice Driessen, Jannis Born, Rocío Castellanos Rueda, Sai T. Reddy, Marianna Rapsomaniki
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Discrete Diffusion Schrödinger Bridge Matching for Graph Transformation
Jun Hyeong Kim, Seonghwan Kim, Seokhyun Moon, Hyeongwoo Kim, Jeheon Woo, Woo Youn Kim
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Language Models for Text-guided Protein Evolution
Zhanghan Ni, Shengchao Liu, Hongyu Guo, Anima Anandkumar
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Generative Flows on Synthetic Pathway for Drug Design
Seonghwan Seo, Minsu Kim, Tony Shen, Martin Ester, Jinkyoo Park, Sungsoo Ahn, Woo Youn Kim
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Modeling Complex System Dynamics with Flow Matching Across Time and Conditions
Martin Rohbeck, Charlotte Bunne, Edward De Brouwer, Jan-Christian Huetter, Anne Biton, Kelvin Y. Chen, Aviv Regev, Romain Lopez
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone
Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo
Jun Xia, Sizhe Liu, Jingbo Zhou, Shaorong Chen, hongxin xiang, Zicheng Liu, Yue Liu, Stan Z. Li
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Spotlight
- Readers: Everyone
JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling
Ameya Daigavane, Bodhi P. Vani, Saeed Saremi, Joshua A Rackers, Joseph Kleinhenz
- Published: 13 Oct 2024, Last Modified: 01 Dec 2024
- AIDrugX Poster
- Readers: Everyone