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The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…

Quantitative Methods · Quantitative Biology 2025-10-03 Ekaterina Podplutova , Anastasia Vepreva , Olga A. Konovalova , Vladimir Vinogradov , Dmitrii O. Shkil , Andrei Dmitrenko

Advances in generative artificial intelligence are transforming how metal-organic frameworks (MOFs) are designed and discovered. This Perspective introduces the shift from laborious enumeration of MOF candidates to generative approaches…

Is there a unified model for generating molecules considering different conditions, such as binding pockets and chemical properties? Although target-aware generative models have made significant advances in drug design, they do not consider…

Artificial Intelligence · Computer Science 2023-02-15 Zhangyang Gao , Yuqi Hu , Cheng Tan , Stan Z. Li

Generative transformers have shown their superiority in synthesizing high-fidelity and high-resolution images, such as good diversity and training stability. However, they suffer from the problem of slow generation since they need to…

Computer Vision and Pattern Recognition · Computer Science 2023-03-08 Jiacheng Li , Longhui Wei , ZongYuan Zhan , Xin He , Siliang Tang , Qi Tian , Yueting Zhuang

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to…

Quantitative Methods · Quantitative Biology 2022-01-27 Matthew Ragoza , Tomohide Masuda , David Ryan Koes

The field of image generation through generative modelling is abundantly discussed nowadays. It can be used for various applications, such as up-scaling existing images, creating non-existing objects, such as interior design scenes,…

Computer Vision and Pattern Recognition · Computer Science 2023-03-16 Giorgia Adorni , Felix Boelter , Stefano Carlo Lambertenghi

Attention-based Transformer models have been increasingly employed for automatic music generation. To condition the generation process of such a model with a user-specified sequence, a popular approach is to take that conditioning sequence…

Sound · Computer Science 2022-03-22 Yi-Jen Shih , Shih-Lun Wu , Frank Zalkow , Meinard Müller , Yi-Hsuan Yang

Discovering new physical products and processes often demands enormous experimentation and expensive simulation. To design a new product with certain target characteristics, an extensive search is performed in the design space by trying out…

Machine Learning · Statistics 2018-11-16 Phuoc Nguyen , Truyen Tran , Sunil Gupta , Santu Rana , Svetha Venkatesh

Learning based feature matching methods have been commonly studied in recent years. The core issue for learning feature matching is to how to learn (1) discriminative representations for feature points (or regions) within each intra-image…

Computer Vision and Pattern Recognition · Computer Science 2023-05-31 Bo Jiang , Shuxian Luo , Xiao Wang , Chuanfu Li , Jin Tang

Accurate protein structures are essential for understanding biological function, yet incorporating experimental data into protein generative models remains a major challenge. Most predictors of experimental observables are…

Machine Learning · Computer Science 2025-11-18 Nadav Bojan Sellam , Meital Bojan , Paul Schanda , Alex Bronstein

The discovery of new molecules based on the original chemical molecule distributions is of great importance in medicine. The graph transformer, with its advantages of high performance and scalability compared to traditional graph networks,…

Machine Learning · Computer Science 2025-04-30 Ji Shi , Chengxun Xie , Zhonghao Li , Xinming Zhang , Miao Zhang

Transformer model has been widely used on machine translation tasks and obtained state-of-the-art results. In this paper, we report an interesting phenomenon in its encoder-decoder multi-head attention: different attention heads of the…

Computation and Language · Computer Science 2019-11-22 Zewei Sun , Shujian Huang , Hao-Ran Wei , Xin-yu Dai , Jiajun Chen

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the…

Neurons and Cognition · Quantitative Biology 2024-03-19 Antonis Antoniades , Yiyi Yu , Joseph Canzano , William Wang , Spencer LaVere Smith

Discovering functional crystalline materials entails navigating an immense combinatorial design space. While recent advances in generative artificial intelligence have enabled the sampling of chemically plausible compositions and…

Machine Learning · Computer Science 2025-11-11 Hyunsoo Park , Aron Walsh

Transformer models have recently attracted much interest from computer vision researchers and have since been successfully employed for several problems traditionally addressed with convolutional neural networks. At the same time, image…

Computer Vision and Pattern Recognition · Computer Science 2021-07-13 Ricard Durall , Stanislav Frolov , Jörn Hees , Federico Raue , Franz-Josef Pfreundt , Andreas Dengel , Janis Keupe

De novo molecule design has become a highly active research area, advanced significantly through the use of state-of-the-art generative models. Despite these advances, several fundamental questions remain unanswered as the field…

Biomolecules · Quantitative Biology 2024-09-09 Heath Arthur-Loui , Amina Mollaysa , Michael Krauthammer

One of the most significant challenges in statistical signal processing and machine learning is how to obtain a generative model that can produce samples of large-scale data distribution, such as images and speeches. Generative Adversarial…

Computer Vision and Pattern Recognition · Computer Science 2020-05-28 Pegah Salehi , Abdolah Chalechale , Maryam Taghizadeh

Generating new molecules with specified chemical and biological properties via generative models has emerged as a promising direction for drug discovery. However, existing methods require extensive training/fine-tuning with a large dataset,…

Quantitative Methods · Quantitative Biology 2023-04-25 Zichao Wang , Weili Nie , Zhuoran Qiao , Chaowei Xiao , Richard Baraniuk , Anima Anandkumar

Creating diverse and high-quality 3D assets with an automatic generative model is highly desirable. Despite extensive efforts on 3D generation, most existing works focus on the generation of a single category or a few categories. In this…

Computer Vision and Pattern Recognition · Computer Science 2023-09-18 Ziang Cao , Fangzhou Hong , Tong Wu , Liang Pan , Ziwei Liu

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential…

Quantitative Methods · Quantitative Biology 2025-08-27 Mahsa Sheikholeslami , Navid Mazrouei , Yousof Gheisari , Afshin Fasihi , Matin Irajpour , Ali Motahharynia