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Efficient design and discovery of target-driven molecules is a critical step in facilitating lead optimization in drug discovery. Current approaches to develop molecules for a target protein are intuition-driven, hampered by slow iterative…

Machine Learning · Computer Science 2022-05-24 Andrew D. McNaughton , Mridula S. Bontha , Carter R. Knutson , Jenna A. Pope , Neeraj Kumar

Large Language Models (LLMs) have exhibited remarkable performance across a wide range of domains, motivating research into their potential for recommendation systems. Early efforts have leveraged LLMs' rich knowledge and strong…

Information Retrieval · Computer Science 2025-04-03 Chao Sun , Yaobo Liang , Yaming Yang , Shilin Xu , Tianmeng Yang , Yunhai Tong

De novo drug design is a crucial component of modern drug development, yet navigating the vast chemical space to find synthetically accessible, high-affinity candidates remains a significant challenge. Reinforcement Learning (RL) enhances…

Machine Learning · Computer Science 2025-12-25 R Yadunandan , Nimisha Ghosh

Large language model reasoning is often treated as a monolithic capability, relying on binary preference supervision that fails to capture partial progress or fine-grained reasoning quality. We introduce Continuous Utility Direct Preference…

Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. Currently, the most widely used approach in biomolecular design is directed evolution,…

Machine Learning · Computer Science 2021-11-09 Alexander Whatley , Zhekun Luo , Xiangru Tang

The goal of most materials discovery is to discover materials that are superior to those currently known. Fundamentally, this is close to extrapolation, which is a weak point for most machine learning models that learn the probability…

Biomolecules · Quantitative Biology 2024-05-08 Hyunseung Kim , Haeyeon Choi , Dongju Kang , Won Bo Lee , Jonggeol Na

The inverse folding problem, aiming to design amino acid sequences that fold into desired three-dimensional structures, is pivotal for various biotechnological applications. Here, we introduce a novel approach leveraging Direct Preference…

Machine Learning · Computer Science 2025-06-04 Junde Xu , Zijun Gao , Xinyi Zhou , Jie Hu , Xingyi Cheng , Le Song , Guangyong Chen , Pheng-Ann Heng , Jiezhong Qiu

Direct Preference Optimization (DPO) has proven to be an effective solution for mitigating hallucination in Multimodal Large Language Models (MLLMs) by learning from preference pairs. One of its key challenges lies in how to transfer the…

Machine Learning · Computer Science 2026-05-07 Huatian Zhang , Zhendong Mao , Lei Zhang , Yongdong Zhang

Neural Combinatorial Optimization (NCO) has emerged as a promising approach for NP-hard problems. However, prevailing RL-based methods suffer from low sample efficiency due to sparse rewards and underused solutions. We propose Best-anchored…

Machine Learning · Computer Science 2025-06-03 Zijun Liao , Jinbiao Chen , Debing Wang , Zizhen Zhang , Jiahai Wang

As Large Language Models (LLMs) demonstrate remarkable capabilities learned from vast corpora, concerns regarding data privacy and safety are receiving increasing attention. LLM unlearning, which aims to remove the influence of specific…

Machine Learning · Computer Science 2025-10-07 Kai Qin , Jiaqi Wu , Jianxiang He , Haoyuan Sun , Yifei Zhao , Bin Liang , Yongzhe Chang , Tiantian Zhang , Houde Liu

Designing de novo 3D molecules with desirable properties remains a fundamental challenge in drug discovery and molecular engineering. While diffusion models have demonstrated remarkable capabilities in generating high-quality 3D molecular…

Machine Learning · Computer Science 2026-01-15 Lianghong Chen , Dongkyu Eugene Kim , Mike Domaratzki , Pingzhao Hu

Automated theorem proving (ATP) is one of the most challenging mathematical reasoning tasks for Large Language Models (LLMs). Most existing LLM-based ATP methods rely on supervised fine-tuning, which results in a limited alignment between…

Artificial Intelligence · Computer Science 2025-02-27 Shuming Shi , Ruobing Zuo , Gaolei He , Jianlin Wang , Chenyang Xu , Zhengfeng Yang

Direct Preference Optimization (DPO) and its variants have become the de facto standards for aligning large language models (LLMs) with human preferences or specific goals. However, DPO requires high-quality preference data and suffers from…

Machine Learning · Computer Science 2024-11-12 Zhuotong Chen , Fang Liu , Jennifer Zhu , Wanyu Du , Yanjun Qi

Direct Preference Optimization (DPO) is an effective framework for aligning large language models with human preferences, but it struggles with complex reasoning tasks. DPO optimizes for the likelihood of generating preferred over…

Artificial Intelligence · Computer Science 2026-04-23 Darsh Kachroo , Adriana Caraeni , Arjun Prasaath Anbazhagan , Brennan Lagasse , Kevin Zhu

Automating molecular design using deep reinforcement learning (RL) holds the promise of accelerating the discovery of new chemical compounds. Existing approaches work with molecular graphs and thus ignore the location of atoms in space,…

Machine Learning · Statistics 2021-03-02 Gregor N. C. Simm , Robert Pinsler , José Miguel Hernández-Lobato

Recent alignment methods based on Direct Preference Optimization (DPO) reformulate preference learning as supervised optimization over pairwise comparisons, offering improved efficiency and stability over reinforcement learning from human…

Machine Learning · Computer Science 2026-01-22 Yuhui Sun , Xiyao Wang , Zixi Li , YiTian Ding , Tianyang Ling , Jialuo Chen , Tianyi Yu , Zhenlong Yuan , Jinman Zhao

Direct Preference Optimization (DPO) simplifies reinforcement learning from human feedback (RLHF) for large language models (LLMs) by directly optimizing human preferences without an explicit reward model. We find that during DPO training,…

Computation and Language · Computer Science 2026-01-01 Junshu Pan , Wei Shen , Shulin Huang , Qiji Zhou , Yue Zhang

The fundamental goal of generative drug design is to propose optimized molecules that meet predefined activity, selectivity, and pharmacokinetic criteria. Despite recent progress, we argue that existing generative methods are limited in…

Chemical Physics · Physics 2020-12-17 Julien Horwood , Emmanuel Noutahi

Direct preference optimization (DPO) methods have shown strong potential in aligning text-to-image diffusion models with human preferences by training on paired comparisons. These methods improve training stability by avoiding the REINFORCE…

Computer Vision and Pattern Recognition · Computer Science 2025-10-22 Yi-Lun Wu , Bo-Kai Ruan , Chiang Tseng , Hong-Han Shuai

This work studies reinforcement learning (RL) in the context of multi-period supply chains subject to constraints, e.g., on production and inventory. We introduce Distributional Constrained Policy Optimization (DCPO), a novel approach for…

Machine Learning · Computer Science 2023-02-06 Jaime Sabal Bermúdez , Antonio del Rio Chanona , Calvin Tsay