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Related papers: A Model to Search for Synthesizable Molecules

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Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although current graph…

Quantitative Methods · Quantitative Biology 2018-04-24 Yibo Li , Liangren Zhang , Zhenming Liu

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…

Biomolecules · Quantitative Biology 2024-09-27 Bowen Jing , Hannes Stärk , Tommi Jaakkola , Bonnie Berger

Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium…

Machine Learning · Statistics 2018-10-29 Niklas W. A. Gebauer , Michael Gastegger , Kristof T. Schütt

Finding drug-like compounds with high bioactivity is essential for drug discovery, but the task is complicated by the high cost of chemical synthesis and validation. With their outstanding performance in de novo drug design, deep generative…

Quantitative Methods · Quantitative Biology 2023-01-03 Yibo Li , Jianfeng Pei , Luhua Lai

We propose a new model for making generalizable and diverse retrosynthetic reaction predictions. Given a target compound, the task is to predict the likely chemical reactants to produce the target. This generative task can be framed as a…

Machine Learning · Computer Science 2019-10-23 Benson Chen , Tianxiao Shen , Tommi S. Jaakkola , Regina Barzilay

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

Structure-based drug design involves finding ligand molecules that exhibit structural and chemical complementarity to protein pockets. Deep generative methods have shown promise in proposing novel molecules from scratch (de-novo design),…

Quantitative Methods · Quantitative Biology 2021-11-09 Pavol Drotár , Arian Rokkum Jamasb , Ben Day , Cătălina Cangea , Pietro Liò

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 learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been…

Machine Learning · Computer Science 2021-09-29 Alexey Strokach , Philip M. Kim

Retrosynthesis is a major task for drug discovery. It is formulated as a graph-generating problem by many existing approaches. Specifically, these methods firstly identify the reaction center, and break target molecule accordingly to…

Machine Learning · Computer Science 2022-09-28 Jiahan Liu , Chaochao Yan , Yang Yu , Chan Lu , Junzhou Huang , Le Ou-Yang , Peilin Zhao

Recent advances in artificial intelligence have propelled the development of innovative computational materials modeling and design techniques. Generative deep learning models have been used for molecular representation, discovery, and…

Chemical Physics · Physics 2021-02-12 Navid Shervani-Tabar , Nicholas Zabaras

Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

Biomolecules · Quantitative Biology 2023-02-02 Masatsugu Yamada , Mahito Sugiyama

Generating novel molecules with optimal properties is a crucial step in many industries such as drug discovery. Recently, deep generative models have shown a promising way of performing de-novo molecular design. Although graph generative…

Machine Learning · Computer Science 2018-11-27 Rim Assouel , Mohamed Ahmed , Marwin H Segler , Amir Saffari , Yoshua Bengio

By linking conceptual theories with observed data, generative models can support reasoning in complex situations. They have come to play a central role both within and beyond statistics, providing the basis for power analysis in molecular…

Methodology · Statistics 2022-08-15 Kris Sankaran , Susan P. Holmes

Deep generative models produce data according to a learned representation, e.g. diffusion models, through a process of approximation computing possible samples. Approximation can be understood as reconstruction and the large datasets used…

Human-Computer Interaction · Computer Science 2023-09-25 Luís Arandas , Mick Grierson , Miguel Carvalhais

Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a…

Machine Learning · Computer Science 2020-09-03 Jaechang Lim , Sang-Yeon Hwang , Seungsu Kim , Seokhyun Moon , Woo Youn Kim

Drug discovery using deep learning has attracted a lot of attention of late as it has obvious advantages like higher efficiency, less manual guessing and faster process time. In this paper, we present a novel neural network for generating…

Biomolecules · Quantitative Biology 2021-10-08 Abhinav Sagar

Deep generative models have shown great promise when it comes to synthesising novel images. While they can generate images that look convincing on a higher-level, generating fine-grained details is still a challenge. In order to foster…

Computer Vision and Pattern Recognition · Computer Science 2019-01-15 Andrin Jenal , Nikolay Savinov , Torsten Sattler , Gaurav Chaurasia

We present a deep generative scene modeling technique for indoor environments. Our goal is to train a generative model using a feed-forward neural network that maps a prior distribution (e.g., a normal distribution) to the distribution of…

Computer Vision and Pattern Recognition · Computer Science 2018-08-08 Zaiwei Zhang , Zhenpei Yang , Chongyang Ma , Linjie Luo , Alexander Huth , Etienne Vouga , Qixing Huang

The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however,…

Machine Learning · Computer Science 2022-03-16 Minghao Guo , Veronika Thost , Beichen Li , Payel Das , Jie Chen , Wojciech Matusik