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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

Modern generative models achieve excellent quality in a variety of tasks including image or text generation and chemical molecule modeling. However, existing methods often lack the essential ability to generate examples with requested…

Learning representations of molecular structures using deep learning is a fundamental problem in molecular property prediction tasks. Molecules inherently exist in the real world as three-dimensional structures; furthermore, they are not…

Machine Learning · Computer Science 2024-01-22 Daiki Koge , Naoaki Ono , Shigehiko Kanaya

Generating novel drug molecules with desired biological properties is a time consuming and complex task. Conditional generative adversarial models have recently been proposed as promising approaches for de novo drug design. In this paper,…

Quantitative Methods · Quantitative Biology 2021-10-26 Yuansan Liu , James Bailey

One of the major applications of generative models for drug Discovery targets the lead-optimization phase. During the optimization of a lead series, it is common to have scaffold constraints imposed on the structure of the molecules…

Quantitative Methods · Quantitative Biology 2021-01-05 Maxime Langevin , Herve Minoux , Maximilien Levesque , Marc Bianciotto

We seek to automate the design of molecules based on specific chemical properties. Our primary contributions are a simpler method for generating SMILES strings guaranteed to be chemically valid, using a combination of a new context-free…

Machine Learning · Computer Science 2018-11-29 Egor Kraev

Molecular property regression struggles with cases in chemically relevant target ranges that are underrepresented in datasets. Standard average error minimization approaches underperform in these highly relevant cases, and oversampling…

Machine Learning · Computer Science 2026-05-22 Brenda Nogueira , Gisela A. Gonzalez-Montiel , Meng Jiang , Nitesh V. Chawla , Nuno Moniz

The quest for accurate prediction of drug molecule properties poses a fundamental challenge in the realm of Artificial Intelligence Drug Discovery (AIDD). An effective representation of drug molecules emerges as a pivotal component in this…

Machine Learning · Computer Science 2024-04-22 Zhuoyuan Wang , Jiacong Mi , Shan Lu , Jieyue He

Developing new molecular compounds is crucial to address pressing challenges, from health to environmental sustainability. However, exploring the molecular space to discover new molecules is difficult due to the vastness of the space. Here…

Machine Learning · Computer Science 2025-05-23 Manuel Ruiz-Botella , Marta Sales-Pardo , Roger Guimerà

Deep generative neural networks have proven effective at both conditional and unconditional modeling of complex data distributions. Conditional generation enables interactive control, but creating new controls often requires expensive…

Machine Learning · Computer Science 2017-12-25 Jesse Engel , Matthew Hoffman , Adam Roberts

Autoregressive conditional image generation algorithms are capable of generating photorealistic images that are consistent with given textual or image conditions, and have great potential for a wide range of applications. Nevertheless, the…

Computer Vision and Pattern Recognition · Computer Science 2024-12-19 Qiaoying Qu , Shiyu Shen

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…

Machine Learning · Computer Science 2025-05-26 Jinho Chang , Jong Chul Ye

For a very long time, computational approaches to the design of new materials have relied on an iterative process of finding a candidate material and modeling its properties. AI has played a crucial role in this regard, helping to…

Deep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is possible to side-step expensive search procedures in…

Machine Learning · Statistics 2022-09-28 Nicola De Cao , Thomas Kipf

Scene Graph Generation (SGG) aims to explore the relationships between objects in images and obtain scene summary graphs, thereby better serving downstream tasks. However, the long-tailed problem has adversely affected the scene graph's…

Computer Vision and Pattern Recognition · Computer Science 2024-07-30 Yansheng Li , Tingzhu Wang , Kang Wu , Linlin Wang , Xin Guo , Wenbin Wang

The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design. However, despite the potential…

Machine Learning · Computer Science 2024-03-05 Yin Fang , Ningyu Zhang , Zhuo Chen , Lingbing Guo , Xiaohui Fan , Huajun Chen

In most scenarios, conditional image generation can be thought of as an inversion of the image understanding process. Since generic image understanding involves solving multiple tasks, it is natural to aim at generating images via…

Computer Vision and Pattern Recognition · Computer Science 2022-07-15 Ritika Chakraborty , Nikola Popovic , Danda Pani Paudel , Thomas Probst , Luc Van Gool

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…

Machine Learning · Computer Science 2020-04-21 Wengong Jin , Regina Barzilay , Tommi Jaakkola

We present Generative Semantic Segmentation (GSS), a generative learning approach for semantic segmentation. Uniquely, we cast semantic segmentation as an image-conditioned mask generation problem. This is achieved by replacing the…

Computer Vision and Pattern Recognition · Computer Science 2023-08-11 Jiaqi Chen , Jiachen Lu , Xiatian Zhu , Li Zhang

In the past decade, Artificial Intelligence driven drug design and discovery has been a hot research topic, where an important branch is molecule generation by generative models, from GAN-based models and VAE-based models to the latest…

Biomolecules · Quantitative Biology 2023-10-10 Siyuan Guo , Jihong Guan , Shuigeng Zhou
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