English
Related papers

Related papers: Empower Structure-Based Molecule Optimization with…

200 papers

Surgical triplet recognition, which involves identifying instrument, verb, target, and their combinations, is a complex surgical scene understanding challenge plagued by long-tailed data distribution. The mainstream multi-task learning…

Computer Vision and Pattern Recognition · Computer Science 2025-09-17 Yiyi Zhang , Yuchen Yuan , Ying Zheng , Jialun Pei , Jinpeng Li , Zheng Li , Pheng-Ann Heng

To solve large-scale or high-resolution topology optimization problem, a novel algorithm is developed based on modified bi-directional evolutionary structure optimization (BESO) and extended finite element method (XFEM). Within XFEM, a set…

Applied Physics · Physics 2026-04-07 Hongxin Wang , Jie Liu , Guilin Wen

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in…

Machine Learning · Computer Science 2025-10-29 Zihao Jing , Yan Sun , Yan Yi Li , Sugitha Janarthanan , Alana Deng , Pingzhao Hu

Recent advances in learnable evolutionary algorithms have demonstrated the importance of leveraging population distribution information and historical evolutionary trajectories. While significant progress has been made in continuous…

Neural and Evolutionary Computing · Computer Science 2024-12-10 Jiaxiang Huang , Licheng Jiao

Molecular optimization is a fundamental goal in the chemical sciences and is of central interest to drug and material design. In recent years, significant progress has been made in solving challenging problems across various aspects of…

Computational Engineering, Finance, and Science · Computer Science 2022-10-11 Wenhao Gao , Tianfan Fu , Jimeng Sun , Connor W. Coley

In therapeutic design, balancing various physiochemical properties is crucial for molecule development, similar to how Multiparameter Optimization (MPO) evaluates multiple variables to meet a primary goal. While many molecular features can…

Biomolecules · Quantitative Biology 2024-01-03 Agustin Kruel , Andrew D. McNaughton , Neeraj Kumar

Stochastic optimization of continuous objectives is at the heart of modern machine learning. However, many important problems are of discrete nature and often involve submodular objectives. We seek to unleash the power of stochastic…

Machine Learning · Computer Science 2017-11-07 Mohammad Reza Karimi , Mario Lucic , Hamed Hassani , Andreas Krause

Recent advances in language models have enabled framing molecule generation as sequence modeling. However, existing approaches often rely on single-objective reinforcement learning, limiting their applicability to real-world drug design,…

Machine Learning · Computer Science 2025-02-11 Diego Calanzone , Pierluca D'Oro , Pierre-Luc Bacon

Symbolic regression aims to discover human-interpretable equations that explain observational data. However, existing approaches rely heavily on discrete structure search (e.g., genetic programming), which often leads to high computational…

Machine Learning · Computer Science 2026-03-25 Fateme Memar , Tao Zhe , Dongjie Wang

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of…

Biomolecules · Quantitative Biology 2025-06-06 Keyue Qiu , Yuxuan Song , Zhehuan Fan , Peidong Liu , Zhe Zhang , Mingyue Zheng , Hao Zhou , Wei-Ying Ma

Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by the computational cost. To address this, a surge of deep…

Machine Learning · Computer Science 2026-03-02 Ziyang Yu , Wenbing Huang , Yang Liu

Graph-structured data are central to many scientific and industrial applications where the goal is to optimize expensive black-box objectives defined over graph structures or node configurations -- as seen in molecular design, supply…

Optimization and Control · Mathematics 2026-04-22 Yilin Xie , Shiqiang Zhang , Jixiang Qing , Ruth Misener , Calvin Tsay

Realizing high-throughput aberration-corrected Scanning Transmission Electron Microscopy (STEM) exploration of atomic structures requires rapid tuning of multipole probe correctors while compensating for the inevitable drift of the optical…

Machine Learning · Computer Science 2026-01-28 Utkarsh Pratiush , Austin Houston , Richard Liu , Gerd Duscher , Sergei Kalinin

Multi-objective optimization (MOO) has become an influential framework in many machine learning problems with multiple objectives such as learning with multiple criteria and multi-task learning (MTL). In this paper, we propose a new…

Machine Learning · Computer Science 2023-11-30 Peiyao Xiao , Hao Ban , Kaiyi Ji

Learning-enabled control systems increasingly rely on multiple sensing modalities (e.g., vision, audio, language, etc.) for perception and decision support. A key challenge is that multi-modal sensor training dynamics are often imbalanced:…

Machine Learning · Computer Science 2026-04-01 Heshan Fernando , Quan Xiao , Parikshit Ram , Yi Zhou , Horst Samulowitz , Nathalie Baracaldo , Tianyi Chen

Molecular property prediction is essential for applications such as drug discovery and toxicity assessment. While Graph Neural Networks (GNNs) have shown promising results by modeling molecules as molecular graphs, their reliance on…

Machine Learning · Computer Science 2025-04-09 Tianyi Jiang , Zeyu Wang , Shanqing Yu , Qi Xuan

Bayesian optimization (BO) is an efficient and flexible global optimization framework that is applicable to a very wide range of engineering applications. To leverage the capability of the classical BO, many extensions, including…

Machine Learning · Statistics 2021-09-01 Anh Tran , Mike Eldred , Scott McCann , Yan Wang

Despite recent advancements, most computational methods for molecule optimization are constrained to single- or double-property optimization tasks and suffer from poor scalability and generalizability to novel optimization tasks. Meanwhile,…

Machine Learning · Computer Science 2025-05-28 Vishal Dey , Xiao Hu , Xia Ning

Over the past two decades, descent methods have received substantial attention within the multiobjective optimization field. Nonetheless, both theoretical analyses and empirical evidence reveal that existing first-order methods for…

Optimization and Control · Mathematics 2024-11-13 Jian Chen , Liping Tang , Xinmin Yang

Distributionally robust optimization (DRO) problems are increasingly seen as a viable method to train machine learning models for improved model generalization. These min-max formulations, however, are more difficult to solve. We therefore…

Machine Learning · Statistics 2020-11-03 Soumyadip Ghosh , Mark Squillante , Ebisa Wollega