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This work explores the challenging problem of molecule design by framing it as a conditional generative modeling task, where target biological properties or desired chemical constraints serve as conditioning variables. We propose the Latent…

Deep generative models have gained significant advancements to accelerate drug discovery by generating bioactive chemicals against desired targets. Nevertheless, most generated compounds that have been validated for potent bioactivity often…

Quantitative Methods · Quantitative Biology 2024-01-03 Weixin Xie , Jianhang Zhang , Qin Xie , Chaojun Gong , Youjun Xu , Luhua Lai , Jianfeng Pei

A novel two-phase molecule inference framework, mol-infer, has recently been developed to infer chemical graphs with prescribed abstract structures and desired property values through mixed integer linear programming (MILP) under the…

Quantitative Methods · Quantitative Biology 2026-05-29 Jianshen Zhu , Raveena Rai , Taiyo Sohkawa , Naveed Ahmed Azam , Kazuya Haraguchi , Liang Zhao , Tatsuya Akutsu

3D data that contains rich geometry information of objects and scenes is valuable for understanding 3D physical world. With the recent emergence of large-scale 3D datasets, it becomes increasingly crucial to have a powerful 3D generative…

Computer Vision and Pattern Recognition · Computer Science 2020-12-29 Jianwen Xie , Zilong Zheng , Ruiqi Gao , Wenguan Wang , Song-Chun Zhu , Ying Nian Wu

Topological phases of matter$\unicode{x2013}$comprising both insulators and semimetals$\unicode{x2013}$offer great potential for quantum applications, but identifying new candidates remains challenging due to expensive first-principles…

Materials Science · Physics 2026-04-08 Xinyu Xu , Arif Ullah , Ming Yang

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports conditional generation of molecules over twelve properties, enabling flexible control across…

Machine Learning · Computer Science 2025-05-27 Raul Ortega-Ochoa , Tejs Vegge , Jes Frellsen

This paper presents the Model Gateway, a management platform for managing machine learning (ML) and scientific computational models in the drug discovery pipeline. The platform supports Large Language Model (LLM) Agents and Generative…

Software Engineering · Computer Science 2025-12-08 Yan-Shiun Wu , Nathan A. Morin

Artificial Intelligence (AI)-driven material design has been attracting great attentions as a groundbreaking technology across a wide spectrum of industries. Molecular design is particularly important owing to its broad application domains…

The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…

Atomic Physics · Physics 2025-05-20 Adarsh Singh

Efficient and accurate interatomic potential functions are critical to computational study of materials while searching for structures with desired properties. Traditionally, potential functions or energy landscapes are designed by experts…

Materials Science · Physics 2022-04-05 Andrew Eldridge , Alejandro Rodriguez , Ming Hu , Jianjun Hu

Data-driven materials design often encounters challenges where systems require or possess qualitative (categorical) information. Metal-organic frameworks (MOFs) are an example of such material systems. The representation of MOFs through…

Materials Science · Physics 2023-11-16 Yigitcan Comlek , Thang Duc Pham , Randall Snurr , Wei Chen

We search for new superhard B-N-O compounds with an iterative machine learning (ML) procedure, where ML models are trained using sample crystal structures from evolutionary algorithm. We first use cohesive energy to evaluate the…

Materials Science · Physics 2022-06-22 Wei-Chih Chen , Yogesh K. Vohra , Cheng-Chien Chen

Discovering the governing equations of a dynamical system from observed trajectories provides deeper insight into its structure than mere prediction of future states. We present a data-driven approach to model discovery based on…

Computer Vision and Pattern Recognition · Computer Science 2026-05-27 Martin Brückmann , Babette Dellen , Uwe Jaekel

High-entropy alloys are solid solutions of multiple principal elements, capable of reaching composition and feature regimes inaccessible for dilute materials. Discovering those with valuable properties, however, relies on serendipity, as…

Mathematical models are crucial for optimizing and controlling chemical processes, yet they often face significant limitations in terms of computational time, algorithm complexity, and development costs. Hybrid models, which combine…

Ion-conducting solid electrolytes are widely used for a variety of purposes. Therefore, designing highly ion-conductive materials is in strongly demand. Because of advancement in computers and enhancement of computational codes, theoretical…

Computational Physics · Physics 2020-03-23 Masayuki Karasuyama , Hiroki Kasugai , Tomoyuki Tamura , Kazuki Shitara

Accurate prediction of pure component physiochemical properties is crucial for process integration, multiscale modeling, and optimization. In this work, an enhanced framework for pure component property prediction by using explainable…

Applications · Statistics 2025-06-09 Jianfeng Jiao , Xi Gao , Jie Li

We show that density models describing multiple observables with (i) hard boundaries and (ii) dependence on external parameters may be created using an auto-regressive Gaussian mixture model. The model is designed to capture how observable…

Data Analysis, Statistics and Probability · Physics 2022-02-01 Stephen B. Menary , Darren D. Price

The development of machine learned potentials for catalyst discovery has predominantly been focused on very specific chemistries and material compositions. While effective in interpolating between available materials, these approaches…

Material scientists are increasingly adopting the use of machine learning (ML) for making potentially important decisions, such as, discovery, development, optimization, synthesis and characterization of materials. However, despite ML's…

Computational Physics · Physics 2019-03-12 Bhavya Kailkhura , Brian Gallagher , Sookyung Kim , Anna Hiszpanski , T. Yong-Jin Han