6 papers
Beyond Explainable AI (XAI): An Overdue Paradigm Shift and Post-XAI Research Directions
Saleh Afroogh, Syed Ishtiaque Ahmed, Petra Ahrweiler +46
This study provides a cross-disciplinary examination of Explainable Artificial Intelligence (XAI) approaches-focusing on deep neural networks (DNNs) and large language models (LLMs…
AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
Edward De Brouwer, Carl Edwards, Alexander Wu +9
Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior tha…
DC-W2S: Dual-Consensus Weak-to-Strong Training for Reliable Process Reward Modeling in Biological Reasoning
Chi-Min Chan, Ehsan Hajiramezanali, Xiner Li +6
In scientific reasoning tasks, the veracity of the reasoning process is as critical as the final outcome. While Process Reward Models (PRMs) offer a solution to the coarse-grained…
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,…
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…
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…