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Text-guided molecule generation is a task where molecules are generated to match specific textual descriptions. Recently, most existing SMILES-based molecule generation methods rely on an autoregressive architecture. In this work, we…

Machine Learning · Computer Science 2024-02-21 Haisong Gong , Qiang Liu , Shu Wu , Liang Wang

Deep learning has proven to yield fast and accurate predictions of quantum-chemical properties to accelerate the discovery of novel molecules and materials. As an exhaustive exploration of the vast chemical space is still infeasible, we…

Machine Learning · Statistics 2020-01-10 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

Materials-by-design has been historically challenging due to complex process-microstructure-property relations. Conventional analytical or simulation-based approaches suffer from low accuracy or long computational time and poor…

Materials Science · Physics 2023-10-24 Xiao Shang , Zhiying Liu , Jiahui Zhang , Tianyi Lyu , Yu Zou

Drug development is a critical but notoriously resource- and time-consuming process. In this manuscript, we develop a novel generative artificial intelligence (genAI) method DiffSMol to facilitate drug development. DiffSmol generates 3D…

Machine Learning · Computer Science 2025-02-11 Ziqi Chen , Bo Peng , Tianhua Zhai , Daniel Adu-Ampratwum , Xia Ning

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due…

Chemical Physics · Physics 2025-08-13 Lirong Wu , Junjie Wang , Zhifeng Gao , Xiaohong Ji , Rong Zhu , Xinyu Li , Linfeng Zhang , Guolin Ke , Weinan E

Topology optimization has emerged as a popular approach to refine a component's design and increase its performance. However, current state-of-the-art topology optimization frameworks are compute-intensive, mainly due to multiple finite…

Machine Learning · Computer Science 2022-10-27 Jaydeep Rade , Aditya Balu , Ethan Herron , Jay Pathak , Rishikesh Ranade , Soumik Sarkar , Adarsh Krishnamurthy

Diffusion models have emerged as powerful tools for molecular generation, particularly in the context of 3D molecular structures. Inspired by non-equilibrium statistical physics, these models can generate 3D molecular structures with…

Chemical Physics · Physics 2025-05-16 Amira Alakhdar , Barnabas Poczos , Newell Washburn

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining…

Machine Learning · Computer Science 2025-02-10 Shengchao Liu , Weitao Du , Zhiming Ma , Hongyu Guo , Jian Tang

Texture editing is a crucial task in 3D modeling that allows users to automatically manipulate the surface materials of 3D models. However, the inherent complexity of 3D models and the ambiguous text description lead to the challenge in…

Computer Vision and Pattern Recognition · Computer Science 2024-09-26 Shengqi Liu , Zhuo Chen , Jingnan Gao , Yichao Yan , Wenhan Zhu , Jiangjing Lyu , Xiaokang Yang

The crystallographic texture is a key organization feature of many technical and biological materials. In these materials, especially hierarchically structured ones, the preferential alignment of the nano constituents is heavily influencing…

Structure-based drug design (SBDD) is a critical task in drug discovery, requiring the generation of molecular information across two distinct modalities: discrete molecular graphs and continuous 3D coordinates. However, existing SBDD…

Computational Engineering, Finance, and Science · Computer Science 2025-03-28 Xiuyuan Hu , Guoqing Liu , Can Chen , Yang Zhao , Hao Zhang , Xue Liu

Large Language Models (LLMs) have significantly advanced molecular discovery, but existing multimodal molecular architectures fundamentally rely on autoregressive (AR) backbones. This strict left-to-right inductive bias is sub-optimal for…

Artificial Intelligence · Computer Science 2026-04-08 Seohyeon Shin , HanJun Choi , Jun-Hyung Park , Hong Kook Kim , Mansu Kim

Obtaining 3D conformations of realistic polyatomic molecules at the quantum chemistry level remains challenging, and although recent machine learning advances offer promise, predicting large-molecule structures still requires substantial…

Chemical Physics · Physics 2025-11-18 Yifei Zhu , Jiahui Zhang , Jiawei Peng , Mengge Li , Chao Xu , Zhenggang Lan

Molecule design is a multifaceted approach that leverages computational methods and experiments to optimize molecular properties, fast-tracking new drug discoveries, innovative material development, and more efficient chemical processes.…

Computation and Language · Computer Science 2024-08-23 Sakhinana Sagar Srinivas , Venkataramana Runkana

Molecule and text representation learning has gained increasing interest due to its potential for enhancing the understanding of chemical information. However, existing models often struggle to capture subtle differences between molecules…

Machine Learning · Computer Science 2025-10-31 Hyuntae Park , Yeachan Kim , SangKeun Lee

Recent progress in the text-driven 3D stylization of a single object has been considerably promoted by CLIP-based methods. However, the stylization of multi-object 3D scenes is still impeded in that the image-text pairs used for…

Computer Vision and Pattern Recognition · Computer Science 2023-12-08 Xuying Zhang , Bo-Wen Yin , Yuming Chen , Zheng Lin , Yunheng Li , Qibin Hou , Ming-Ming Cheng

The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due…

Biomolecules · Quantitative Biology 2025-10-23 Zaifei Yang , Hong Chang , Ruibing Hou , Shiguang Shan , Xilin Chen

Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific,…

Quantitative Methods · Quantitative Biology 2020-10-05 Samuel G. Finlayson , Matthew B. A. McDermott , Alex V. Pickering , Scott L. Lipnick , Isaac S. Kohane

Machine learning methods have been used to accelerate the molecule optimization process. However, efficient search for optimized molecules satisfying several properties with scarce labeled data remains a challenge for machine learning…

Biomolecules · Quantitative Biology 2022-12-20 Xin Xia , Yansen Su , Chunhou Zheng , Xiangxiang Zeng