Data & Evaluation. Create new data engines. Create benchmarks that are formally verified. Unify scientific inverse problems into common frameworks.
Models & Architecture. Create new effective representations, such as for time series.
Inference & Search. Develop Bayesian inference methods using diffusion priors. Develop advanced LLM reasoning methods such as dynamic tree decomposition and self-training. Develop abstractions to simplify agent programming.
Foundation Models in the Scientific Loop: Design, Measure, Intepret
AI for Adaptive Experiment Design
AI for Robust Decision Making
Neurosymbolic AI for Safety-Critical Agile Control
Controlling the Structure of Inference and Learning in Neural Networks
Neurosymbolic Programming Summer School
Co-taught Architecture Search Module with Swarat Chaudhuri and Jennifer Sun.
Simple Agents Outperform Experts in Biomedical Imaging Workflow Optimization
Xuefei Wang, Kai A. Horstmann, Ethan Lin, Jonathan Chen, Alexander R. Farhang, Sophia Stiles, Atharva Sehgal, Jonathan Light, David Van Valen, Yisong Yue, Jennifer J. Sun
arXiv preprint arXiv:2512.06006, 2026
CellSAM: a foundation model for cell segmentation
Markus Marks, Uriah Israel, Rohit Dilip, Qilin Li, Changhua Yu, Emily Laubscher, Ahamed Iqbal, Elora Pradhan, Ada Ates, Martin Abt, Caitlin Brown, Edward Pao, Shenyi Li, Alexander Pearson-Goulart, Pietro Perona, Georgia Gkioxari, Ross Barnowski, Yisong Yue, David Van Valen
Nature Methods, 2025
KALIKO: Kalman-Implicit Koopman Operator Learning For Prediction of Nonlinear Dynamical Systems
Albert H Li, Ivan Dario Jimenez Rodriguez, Joel W Burdick, Yisong Yue, Aaron D Ames
arXiv preprint arXiv:2512.03256, 2025
Blade: A Derivative-free Bayesian Inversion Method using Diffusion Priors
Hongkai Zheng, Austin Wang, Zihui Wu, Zhengyu Huang, Ricardo Baptista, Yisong Yue
arXiv preprint arXiv:2510.10968, 2025
A Narwhal-Inspired Sensing-to-Control Framework for Small Fixed-Wing Aircraft
Fengze Xie, Xiaozhou Fan, Jacob Schuster, Yisong Yue, Morteza Gharib
arXiv preprint arXiv:2510.07160, 2025
Population Transformer: Learning Population-level Representations of Neural Activity
Geeling Chau, Christopher Wang, Sabera Talukder, Vighnesh Subramaniam, Saraswati Soedarmadji, Yisong Yue, Boris Katz, Andrei Barbu
International Conference on Learning Representations (ICLR), 2025Oral
InverseBench: Benchmarking Plug-and-Play Diffusion Models for Inverse Problems in Physical Sciences
Hongkai Zheng, Wenda Chu, Bingliang Zhang, Zihui Wu, Austin Wang, Berthy T. Feng, Caifeng Zou, Yu Sun, Nikola Kovachki, Zachary E. Ross, Katherine L. Bouman, Yisong Yue
International Conference on Learning Representations (ICLR), 2025Spotlight
Active Learning-Assisted Directed Evolution
Jason Yang, Ravi G. Lal, James C. Bowden, Raul Astudillo, Mikhail A. Hameedi, Sukhvinder Kaur, Matthew Hill, Yisong Yue, Frances H. Arnold
Nature Communications, 2025
SceneCraft: An LLM Agent for Synthesizing 3D Scene as Blender Code
Ziniu Hu, Ahmet Iscen, Aashi Jain, Thomas Kipf, Yisong Yue, David A. Ross, Cordelia Schmid, Alireza Fathi
International Conference on Machine Learning (ICML), 2024Oral
Neurosymbolic Programming
Swarat Chaudhuri, Kevin Ellis, Oleksandr Polozov, Rishabh Singh, Armando Solar-Lezama, Yisong Yue
Foundations and Trends in Programming Languages, 2021
Multi-dueling Bandits with Dependent Arms
Yanan Sui, Vincent Zhuang, Joel Burdick, Yisong Yue
Conference on Uncertainty in Artificial Intelligence (UAI), 2017
The K-armed Dueling Bandits Problem
Yisong Yue, Josef Broder, Robert Kleinberg, Thorsten Joachims
Conference on Learning Theory (COLT), 2009