Publications
2026
Generative modeling of intrinsically disordered protein regions by reinforcing sparse autoencoder features
Jason X. Liu, Sebastian Ibarraran, Frank Hu, Soojung Yang, Xinyu A. Feng, Abigail Park, Anagha Aneesh, Lacramioara Bintu, Alexander R. Dunn, Grant M. Rotskoff
arXiv, 2026
LLM sequential decision making under uncertainty in biochemical domains
Mattias Akke, Soojung Yang, Jurgis Ruža, Sathya Edamadaka, Rafael Gómez-Bombarelli
arXiv, 2026
Earlier version: Bayesian Optimization for Biochemical Discovery with LLMs — NeurIPS AI4Science (Spotlight) & SPIGM Workshop, 2025.
Learning Collective Variables from BioEmu with Time-Lagged Generation
Seonghyun Park, Kiyoung Seong, Soojung Yang, Rafael Gómez-Bombarelli, Sungsoo Ahn
ICLR 2026
2025
Universally Converging Representations of Matter Across Scientific Foundation Models
Sathya Edamakada1, Soojung Yang1*, Ben Blaiszik, Ju Li, Rafael Gómez-Bombarelli*
NeurIPS AI4Mat Workshop, NeurIPS UniReps Workshop (Oral Spotlight), 1co-first, *co-corresponding
Guided Diffusion for A Priori Transition State Sampling
Hyukjun Lim1, Soojung Yang1*, Lucas Pinede1, Miguel Steiner, Yuanqi Du, Rafael Gómez-Bombarelli*
NeurIPS FPI & AI4Mat Workshop (Oral Spotlight), 1co-first, *co-corresponding
Unifying Force Prediction and Molecular Conformation Generation Through Representation Alignment
Lucas Pinede1, Soojung Yang*1, Juno Nam, Rafael Gómez-Bombarelli*
ICML GenBio Workshop, 1co-first, *co-corresponding
Scalable emulation of protein equilibrium ensembles with generative deep learning
Sarah Lewis1, Tim Hempel1, José Jiménez Luna1, Michael Gastegger1, Yu Xie1, Andrew Y. K. Foong1, Victor García Satorras1, Osama Abdin1, Bastiaan S. Veeling1, Iryna Zaporozhets, Yaoyi Chen, Soojung Yang, Arne Schneuing, Jigyasa Nigam, Federico Barbero, Vincent Stimper, Andrew Campbell, Jason Yim, Marten Lienen, Yu Shi, Shuxin Zheng, Hannes Schulz, Usman Munir, Cecilia Clementi, Frank Noé
Science (front cover!)
Transferable Learning of Reaction Pathways from Geometric Priors
Juno Nam, Miguel Steiner, Max Misterka, Soojung Yang, Avni Singhal, Rafael Gómez-Bombarelli
The Journal of Physical Chemistry Letters
Flow matching for accelerated simulation of atomic transport in crystalline materials
Juno Nam, Sulin Liu, Gavin Winter, KyuJung Jun, Soojung Yang, Rafael Gómez-Bombarelli
Nature Machine Intelligence
2024
Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis
Soojung Yang, Juno Nam, Tynan Perez, Jinyeop Song, Xiaochen Du, Rafael Gómez-Bombarelli
NeurIPS AIDrugX Workshop
Learning Collective Variables for Protein Folding with Labeled Data Augmentation through Geodesic Interpolation
Soojung Yang1, Juno Nam1, Johannes C. B. Dietschreit, Rafael Gómez-Bombarelli
JCTC, 1co-first
2023
Regularized indirect learning improves phage display ligand discovery
Joseph S. Brown, Yitong Tseo, Michael A. Lee, Jeffrey Y.-K. Wong, Soojung Yang, Yehlin Cho, Chae Rin Kim, Andrei Loas, Ratmir Derda, Rafael Gómez-Bombarelli, Bradley L. Pentelute
ChemRxiv
Chemically Transferable Generative Backmapping of Coarse-Grained Proteins
Soojung Yang, Rafael Gómez-Bombarelli
ICML
2022
PIGNet: A physics-informed deep learning model toward generalized drug-target interaction predictions
Seokhyun Moon1, Wonho Zhung1, Soojung Yang1, Jaechang Lim, Woo Youn Kim
Chemical Science, 1co-first
2021
Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation
Soojung Yang, Doyeong Hwang, Seul Lee, Seongok Ryu, Sung Ju Hwang
NeurIPS
2020
Comprehensive Study on Molecular Supervised Learning with Graph Neural Networks
Doyeong Hwang, Soojung Yang , Yongchan Kwon , Kyung Hoon Lee, Grace Lee, Hanseok Jo, Seyeol Yoon, Seongok Ryu
J Chem Inf Model
A comprehensive study on the prediction reliability of graph neural networks for virtual screening
Soojung Yang, Kyung Hoon Lee, Seongok Ryu
arXiv