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Generating molecules, both in a directed and undirected fashion, is a huge part of the drug discovery pipeline. Genetic algorithms (GAs) generate molecules by randomly modifying known molecules. In this paper we show that GAs are very…

Neural and Evolutionary Computing · Computer Science 2023-10-16 Austin Tripp , José Miguel Hernández-Lobato

Existing drug discovery pipelines take 5-10 years and cost billions of dollars. Computational approaches aim to sample from regions of the whole molecular and solid-state compounds called chemical space which could be on the order of 1060 .…

Emerging Technologies · Computer Science 2021-01-12 Junde Li , Rasit Topaloglu , Swaroop Ghosh

Topology design optimization offers tremendous opportunity in design and manufacturing freedoms by designing and producing a part from the ground-up without a meaningful initial design as required by conventional shape design optimization…

Machine Learning · Statistics 2019-01-10 Sharad Rawat , M. H. Herman Shen

We present a perspective on molecular machine learning (ML) in the field of chemical process engineering. Recently, molecular ML has demonstrated great potential in (i) providing highly accurate predictions for properties of pure components…

Chemical Physics · Physics 2025-09-01 Jan G. Rittig , Manuel Dahmen , Martin Grohe , Philippe Schwaller , Alexander Mitsos

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…

Machine Learning · Statistics 2021-05-28 Pietro Bongini , Monica Bianchini , Franco Scarselli

Molecular optimization, which aims to discover improved molecules from a vast chemical search space, is a critical step in chemical development. Various artificial intelligence technologies have demonstrated high effectiveness and…

Chemical Physics · Physics 2024-11-26 Xin Xia , Yajie Zhang , Xiangxiang Zeng , Xingyi Zhang , Chunhou Zheng , Yansen Su

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a…

Computation and Language · Computer Science 2024-10-11 Peng Zhou , Jianmin Wang , Chunyan Li , Zixu Wang , Yiping Liu , Siqi Sun , Jianxin Lin , Leyi Wei , Xibao Cai , Houtim Lai , Wei Liu , Longyue Wang , Yuansheng Liu , Xiangxiang Zeng

Personalized medicine is expected to maximize the intended drug effects and minimize side effects by treating patients based on their genetic profiles. Thus, it is important to generate drugs based on the genetic profiles of diseases,…

Machine Learning · Computer Science 2021-12-17 Sejin Park , Hyunju Lee

The functionality of catalysts, enzymes, and supramolecular assemblies emerges not from individual molecules alone, but from the subtle interplay between multiple components arranged in complex systems. Designing such systems is a grand…

Computational Physics · Physics 2026-04-15 Rhyan Barrett , Robin Curth , Julia Westermayr

We propose a hierarchical normalizing flow model for generating molecular graphs. The model produces new molecular structures from a single-node graph by recursively splitting every node into two. All operations are invertible and can be…

Chemical Physics · Physics 2021-06-11 Maksim Kuznetsov , Daniil Polykovskiy

Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous…

Molecular Networks · Quantitative Biology 2020-04-24 Mostafa Karimi , Arman Hasanzadeh , Yang shen

In topology optimization using deep learning, load and boundary conditions represented as vectors or sparse matrices often miss the opportunity to encode a rich view of the design problem, leading to less than ideal generalization results.…

Computational Engineering, Finance, and Science · Computer Science 2020-03-12 Zhenguo Nie , Tong Lin , Haoliang Jiang , Levent Burak Kara

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

Quantitative Methods · Quantitative Biology 2020-11-17 Matthew Ragoza , Tomohide Masuda , David Ryan Koes

The ability to design molecules while preserving similarity to a target molecule and/or property is crucial for various applications in drug discovery, chemical design, and biology. We introduce in this paper an efficient training-free…

Machine Learning · Computer Science 2025-11-18 Jiri Navratil , Jarret Ross , Payel Das , Youssef Mroueh , Samuel C Hoffman , Vijil Chenthamarakshan , Brian Belgodere

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…

Machine Learning · Computer Science 2019-01-30 Wengong Jin , Kevin Yang , Regina Barzilay , Tommi Jaakkola

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing…

Machine Learning · Computer Science 2020-02-28 Chence Shi , Minkai Xu , Zhaocheng Zhu , Weinan Zhang , Ming Zhang , Jian Tang

Modular design maximizes utility by using standardized components in large-scale systems. From a manufacturing perspective, it supports green technology by reducing material waste and improving reusability. Industrially, it offers economic…

Emerging Technologies · Computer Science 2025-03-18 Sumin Lee , Namwoo Kang

It is well known that Drug Design is often a costly process both in terms of time and economic effort. While good Quantitative Structure-Activity Relationship models (QSAR) can help predicting molecular properties without the need to…

Biomolecules · Quantitative Biology 2022-02-14 Dylan Savoia , Alessio Ragno , Roberto Capobianco

Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative…

Machine Learning · Computer Science 2024-07-02 Tianfan Fu , Cao Xiao , Xinhao Li , Lucas M. Glass , Jimeng Sun

Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to…

Machine Learning · Computer Science 2020-06-09 Daniel Schwalbe-Koda , Rafael Gómez-Bombarelli