Xiaoyin Chen

Aligning Protein Conformation Ensemble Generation with Physical Feedback

Stephen Z. Lu

Aurelie Lozano

Vijil Chenthamarakshan

Payel Das

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-co… (see more)nsuming molecular dynamics (MD) simulations conducted in silico. Recent advances in generative modeling, particularly denoising diffusion models, have enabled efficient accurate protein structure prediction and conformation sampling by learning distributions over crystallographic structures. However, effectively integrating physical supervision into these data-driven approaches remains challenging, as standard energy-based objectives often lead to intractable optimization. In this paper, we introduce Energy-based Alignment (EBA), a method that aligns generative models with feedback from physical models, efficiently calibrating them to appropriately balance conformational states based on their energy differences. Experimental results on the MD ensemble benchmark demonstrate that EBA achieves state-of-the-art performance in generating high-quality protein ensembles. By improving the physical plausibility of generated structures, our approach enhances model predictions and holds promise for applications in structural biology and drug discovery.

2025-10-05

Proceedings of the 42nd International Conference on Machine Learning (published)

doi.org

proceedings.mlr.press

PipelineRL: Faster On-policy Reinforcement Learning for Long Sequence Generation

Alexandre Piché

Ehsan Kamalloo

Rafael Pardinas

Xiaoyin Chen

Dzmitry Bahdanau

Reinforcement Learning (RL) is increasingly utilized to enhance the reasoning capabilities of Large Language Models (LLMs). However, effecti… (see more)vely scaling these RL methods presents significant challenges, primarily due to the difficulty in maintaining high AI accelerator utilization without generating stale, off-policy data that harms common RL algorithms. This paper introduces PipelineRL, an approach designed to achieve a superior trade-off between hardware efficiency and data on-policyness for LLM training. PipelineRL employs concurrent asynchronous data generation and model training, distinguished by the novel in-flight weight updates. This mechanism allows the LLM generation engine to receive updated model weights with minimal interruption during the generation of token sequences, thereby maximizing both the accelerator utilization and the freshness of training data. Experiments conducted on long-form reasoning tasks using 128 H100 GPUs demonstrate that PipelineRL achieves approximately

2025-09-22

ArXiv (preprint)

doi.org

openreview.net

Latent Veracity Inference for Identifying Errors in Stepwise Reasoning

Minsu Kim

Jean-Pierre R. Falet

Oliver E. Richardson

Xiaoyin Chen

Moksh J. Jain

Sungjin Ahn

Sungsoo Ahn

Yoshua Bengio

Chain-of-Thought (CoT) reasoning has advanced the capabilities and transparency of language models (LMs); however, reasoning chains can cont… (see more)ain inaccurate statements that reduce performance and trustworthiness. To address this, we propose to augment each reasoning step in a CoT with a latent veracity (or correctness) variable. To efficiently explore this expanded space, we introduce Veracity Search (VS), a discrete search algorithm over veracity assignments. It performs otherwise intractable inference in the posterior distribution over latent veracity values by leveraging the LM's joint likelihood over veracity and the final answer as a proxy reward. This efficient inference-time verification method facilitates supervised fine-tuning of an Amortized Veracity Inference (AVI) machine by providing pseudo-labels for veracity. AVI generalizes VS, enabling accurate zero-shot veracity inference in novel contexts. Empirical results demonstrate that VS reliably identifies errors in logical (ProntoQA), mathematical (GSM8K), and commonsense (CommonsenseQA) reasoning benchmarks, with AVI achieving comparable zero-shot accuracy. Finally, we demonstrate the utility of latent veracity inference for providing feedback during self-correction and self-improvement.

2025-04-30

arXiv (published)

doi.org

arxiv.org

Self-Evolving Curriculum for LLM Reasoning

Nicolas Gontier

Ehsan Kamalloo

2025-04-30

arXiv (published)

doi.org

arxiv.org

HarmAug: Effective Data Augmentation for Knowledge Distillation of Safety Guard Models

Seanie Lee

Haebin Seong

Dong Bok Lee

Minki Kang

Xiaoyin Chen

Dominik Wagner

Yoshua Bengio

Juho Lee

Sung Ju Hwang

Safety guard models that detect malicious queries aimed at large language models (LLMs) are essential for ensuring the secure and responsibl… (see more)e deployment of LLMs in real-world applications. However, deploying existing safety guard models with billions of parameters alongside LLMs on mobile devices is impractical due to substantial memory requirements and latency. To reduce this cost, we distill a large teacher safety guard model into a smaller one using a labeled dataset of instruction-response pairs with binary harmfulness labels. Due to the limited diversity of harmful instructions in the existing labeled dataset, naively distilled models tend to underperform compared to larger models. To bridge the gap between small and large models, we propose HarmAug, a simple yet effective data augmentation method that involves jailbreaking an LLM and prompting it to generate harmful instructions. Given a prompt such as, "Make a single harmful instruction prompt that would elicit offensive content", we add an affirmative prefix (e.g., "I have an idea for a prompt:") to the LLM's response. This encourages the LLM to continue generating the rest of the response, leading to sampling harmful instructions. Another LLM generates a response to the harmful instruction, and the teacher model labels the instruction-response pair. We empirically show that our HarmAug outperforms other relevant baselines. Moreover, a 435-million-parameter safety guard model trained with HarmAug achieves an F1 score comparable to larger models with over 7 billion parameters, and even outperforms them in AUPRC, while operating at less than 25% of their computational cost.

2025-01-21

ICLR.cc/2025/Conference (poster)

doi.org

openreview.net

Structure Language Models for Protein Conformation Generation

Stephen Z. Lu

Hongyu Guo

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is cru… (see more)cial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

2025-01-21

ICLR.cc/2025/Conference (poster)

doi.org

openreview.net

Efficient Causal Graph Discovery Using Large Language Models

Yash More

2024-03-04

ICLR.cc/2024/Workshop/AGI (poster)