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Building virtual cells with generative models to simulate cellular behavior in silico is emerging as a promising paradigm for accelerating drug discovery. However, prior image-based generative approaches can produce implausible cell images…

Machine Learning · Computer Science 2026-05-22 Dongxia Wu , Shiye Su , Yuhui Zhang , Elaine Sui , Emma Lundberg , Emily B. Fox , Serena Yeung-Levy

Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…

Biomolecules · Quantitative Biology 2023-02-14 Gabriele Corso , Hannes Stärk , Bowen Jing , Regina Barzilay , Tommi Jaakkola

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

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 distribution that maximize certain properties: for example,…

Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates…

Biomolecules · Quantitative Biology 2021-11-02 Benson Chen , Xiang Fu , Regina Barzilay , Tommi Jaakkola

RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…

Machine Learning · Computer Science 2026-02-16 Milan Gautam , Ning Dai , Tianshuo Zhou , Bowen Xie , David Mathews , Liang Huang

We present ReCAD, a reinforcement learning (RL) framework that bootstraps pretrained large models (PLMs) to generate precise parametric computer-aided design (CAD) models from multimodal inputs by leveraging their inherent generative…

Computer Vision and Pattern Recognition · Computer Science 2025-12-09 Jiahao Li , Yusheng Luo , Yunzhong Lou , Xiangdong Zhou

Recent advancements in code generation have shown remarkable success across software domains, yet hardware description languages (HDLs) such as Verilog remain underexplored due to their concurrency semantics, syntactic rigidity, and…

Machine Learning · Computer Science 2025-08-27 Fu Teng , Miao Pan , Xuhong Zhang , Zhezhi He , Yiyao Yang , Xinyi Chai , Mengnan Qi , Liqiang Lu , Jianwei Yin

Rational design of covalent inhibitors requires simultaneously optimizing multiple properties, such as binding affinity, target selectivity, or electrophilic reactivity. This presents a multi-objective problem not easily addressed by…

Machine Learning · Computer Science 2026-04-23 Renee Gil

Molecule generation using generative AI is vital for drug discovery, yet class-specific datasets often contain fewer than 100 training examples. While fragment-based models handle limited data better than atom-based approaches, existing…

Artificial Intelligence · Computer Science 2025-11-27 Yuto Suzuki , Paul Awolade , Daniel V. LaBarbera , Farnoush Banaei-Kashani

Reinforcement Learning (RL) has proven highly effective in aligning Large Language Models (LLMs) with human preferences. Typical RL methods optimize under an overall sequence reward, which can lead to a suboptimal learning process. This…

Machine Learning · Computer Science 2025-02-26 Yanshi Li , Shaopan Xiong , Gengru Chen , Xiaoyang Li , Yijia Luo , Xingyuan Bu , Yingshui Tan , Wenbo Su , Bo Zheng

Although deep reinforcement learning (DRL) algorithms have made important achievements in many control tasks, they still suffer from the problems of sample inefficiency and unstable training process, which are usually caused by sparse…

Robotics · Computer Science 2020-02-28 Ke Lin , Liang Gong , Xudong Li , Te Sun , Binhao Chen , Chengliang Liu , Zhengfeng Zhang , Jian Pu , Junping Zhang

Accurate parameter estimation in electrochemical battery models is essential for monitoring and assessing the performance of lithium-ion batteries (LiBs). This paper presents a novel approach that combines deep reinforcement learning (DRL)…

Systems and Control · Electrical Eng. & Systems 2025-06-25 Mehmet Fatih Ozkan , Samuel Filgueira da Silva , Faissal El Idrissi , Prashanth Ramesh , Marcello Canova

Reinforcement learning (RL) offers a capable and intuitive structure for the fundamental sequential decision-making problem. Despite impressive breakthroughs, it can still be difficult to employ RL in practice in many simple applications.…

Artificial Intelligence · Computer Science 2024-01-18 Aida Afshar , Wenchao Li

This Research proposes a Novel Reinforcement Learning (RL) model to optimise malware forensics investigation during cyber incident response. It aims to improve forensic investigation efficiency by reducing false negatives and adapting…

Cryptography and Security · Computer Science 2025-01-14 Dipo Dunsin , Mohamed Chahine Ghanem , Karim Ouazzane , Vassil Vassilev

The goal of reinforcement learning (RL) is to let an agent learn an optimal control policy in an unknown environment so that future expected rewards are maximized. The model-free RL approach directly learns the policy based on data samples.…

Machine Learning · Statistics 2013-07-22 Syogo Mori , Voot Tangkaratt , Tingting Zhao , Jun Morimoto , Masashi Sugiyama

Lead optimization in drug discovery requires improving therapeutic properties while ensuring that molecular modifications correspond to feasible synthetic routes. Existing approaches either prioritize property scores without enforcing…

Machine Learning · Computer Science 2026-05-04 Tao Li , Kaiyuan Hou , Tuan Vinh , Monika Raj , Zhichun Guo , Carl Yang

Distributional reinforcement learning (DRL) enhances the understanding of the effects of the randomness in the environment by letting agents learn the distribution of a random return, rather than its expected value as in standard…

Optimization and Control · Mathematics 2024-03-26 Zifan Wang , Yulong Gao , Siyi Wang , Michael M. Zavlanos , Alessandro Abate , Karl H. Johansson

Multi-Chip-Modules (MCMs) reduce the design and fabrication cost of machine learning (ML) accelerators while delivering performance and energy efficiency on par with a monolithic large chip. However, ML compilers targeting MCMs need to…

RNA inverse folding, designing sequences to form specific 3D structures, is critical for therapeutics, gene regulation, and synthetic biology. Current methods, focused on sequence recovery, struggle to address structural objectives like…

Machine Learning · Computer Science 2026-01-28 Qi Si , Xuyang Liu , Penglei Wang , Xin Guo , Yuan Qi , Yuan Cheng