19 citations · 53 across the 27 of their papers we have counts for
28 papers
LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses
Betty Xiong, Jan-Christian Huetter, Gabriele Scalia +2
Predicting transcriptomic responses to small-molecule perturbations across cell lines is central to drug discovery, but exhaustive profiling of drug-cell combinations is infeasible…
HypoGeneAgent: A Hypothesis Language Agent for Gene-Set Cluster Resolution Selection Using Perturb-seq Datasets
Ying Yuan, Xing-Yue Monica Ge, Aaron Archer Waterman +8
Large-scale single-cell and Perturb-seq investigations routinely involve clustering cells and subsequently annotating each cluster with Gene-Ontology (GO) terms to elucidate the un…
Knowledgeable Language Models as Black-Box Optimizers for Personalized Medicine
Michael S. Yao, Osbert Bastani, Alma Andersson +3
The goal of personalized medicine is to discover a treatment regimen that optimizes a patient's clinical outcome based on their personal genetic and environmental factors. However,…
Iterative Distillation for Reward-Guided Fine-Tuning of Diffusion Models in Biomolecular Design
Xingyu Su, Xiner Li, Masatoshi Uehara +7
We address the problem of fine-tuning diffusion models for reward-guided generation in biomolecular design. While diffusion models have proven highly effective in modeling complex,…
Contextualizing biological perturbation experiments through language
Menghua Wu, Russell Littman, Jacob Levine +4
High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to w…
RAG-Enhanced Collaborative LLM Agents for Drug Discovery
Namkyeong Lee, Edward De Brouwer, Ehsan Hajiramezanali +3
Recent advances in large language models (LLMs) have shown great potential to accelerate drug discovery. However, the specialized nature of biochemical data often necessitates cost…
Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction
Sepideh Maleki, Jan-Christian Huetter, Kangway V. Chuang +3
Predicting transcriptional responses to novel drugs provides a unique opportunity to accelerate biomedical research and advance drug discovery efforts. However, the inherent comple…
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
Carl Edwards, Ziqing Lu, Ehsan Hajiramezanali +3
Bridging biomolecular modeling with natural language information, particularly through large language models (LLMs), has recently emerged as a promising interdisciplinary research…
A mechanistically interpretable neural network for regulatory genomics
Alex M. Tseng, Gokcen Eraslan, Tommaso Biancalani +1
Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scient…
Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design
Chenyu Wang, Masatoshi Uehara, Yichun He +7
Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation.…
Cell Morphology-Guided Small Molecule Generation with GFlowNets
Stephen Zhewen Lu, Ziqing Lu, Ehsan Hajiramezanali +4
High-content phenotypic screening, including high-content imaging (HCI), has gained popularity in the last few years for its ability to characterize novel therapeutics without prio…
Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding
Xiner Li, Yulai Zhao, Chenyu Wang +8
Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural…
Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review
Masatoshi Uehara, Yulai Zhao, Tommaso Biancalani +1
This tutorial provides a comprehensive survey of methods for fine-tuning diffusion models to optimize downstream reward functions. While diffusion models are widely known to provid…
Adding Conditional Control to Diffusion Models with Reinforcement Learning
Yulai Zhao, Masatoshi Uehara, Gabriele Scalia +4
Diffusion models are powerful generative models that allow for precise control over the characteristics of the generated samples. While these diffusion models trained on large data…
Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models
Masatoshi Uehara, Yulai Zhao, Ehsan Hajiramezanali +5
AI-driven design problems, such as DNA/protein sequence design, are commonly tackled from two angles: generative modeling, which efficiently captures the feasible design space (e.g…
Fine-Tuning of Continuous-Time Diffusion Models as Entropy-Regularized Control
Masatoshi Uehara, Yulai Zhao, Kevin Black +6
Diffusion models excel at capturing complex data distributions, such as those of natural images and proteins. While diffusion models are trained to represent the distribution in th…
Feedback Efficient Online Fine-Tuning of Diffusion Models
Masatoshi Uehara, Yulai Zhao, Kevin Black +6
Diffusion models excel at modeling complex data distributions, including those of images, proteins, and small molecules. However, in many cases, our goal is to model parts of the d…
Unsupervised Segmentation of Colonoscopy Images
Heming Yao, Jérôme Lüscher, Benjamin Gutierrez Becker +4
Colonoscopy plays a crucial role in the diagnosis and prognosis of various gastrointestinal diseases. Due to the challenges of collecting large-scale high-quality ground truth anno…
Conformalized Deep Splines for Optimal and Efficient Prediction Sets
Nathaniel Diamant, Ehsan Hajiramezanali, Tommaso Biancalani +1
Uncertainty estimation is critical in high-stakes machine learning applications. One effective way to estimate uncertainty is conformal prediction, which can provide predictive inf…
Complex Preferences for Different Convergent Priors in Discrete Graph Diffusion
Alex M. Tseng, Nathaniel Diamant, Tommaso Biancalani +1
Diffusion models have achieved state-of-the-art performance in generating many different kinds of data, including images, text, and videos. Despite their success, there has been li…
Towards Understanding and Improving GFlowNet Training
Max W. Shen, Emmanuel Bengio, Ehsan Hajiramezanali +3
Generative flow networks (GFlowNets) are a family of algorithms that learn a generative policy to sample discrete objects with non-negative reward . Learning objectives g…
Accurate and Efficient Structural Ensemble Generation of Macrocyclic Peptides using Internal Coordinate Diffusion
Colin A. Grambow, Hayley Weir, Nathaniel L. Diamant +3
Macrocyclic peptides are an emerging therapeutic modality, yet computational approaches for accurately sampling their diverse 3D ensembles remain challenging due to their conformat…
CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning
Colin A. Grambow, Hayley Weir, Christian N. Cunningham +2
Computational and machine learning approaches to model the conformational landscape of macrocyclic peptides have the potential to enable rational design and optimization. However,…
GraphGUIDE: interpretable and controllable conditional graph generation with discrete Bernoulli diffusion
Alex M. Tseng, Nathaniel Diamant, Tommaso Biancalani +1
Diffusion models achieve state-of-the-art performance in generating realistic objects and have been successfully applied to images, text, and videos. Recent work has shown that dif…