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Optimal designs are usually model-dependent and likely to be sub-optimal if the postulated model is not correctly specified. In practice, it is common that a researcher has a list of candidate models at hand and a design has to be found…

Statistics Theory · Mathematics 2023-03-29 Mingyao Ai , Holger Dette , Zhengfu Liu , Jun Yu

Computational protein design, i.e. inferring novel and diverse protein sequences consistent with a given structure, remains a major unsolved challenge. Recently, deep generative models that learn from sequences alone or from sequences and…

Biomolecules · Quantitative Biology 2021-11-15 Igor Melnyk , Payel Das , Vijil Chenthamarakshan , Aurelie Lozano

A rational design of new therapeutic drugs aims to find a molecular structure with desired biological functionality, e.g., an ability to activate or suppress a specific protein via binding to it. Molecular docking is a common technique for…

Neural generative models can be used to learn complex probability distributions from data, to sample from them, and to produce probability density estimates. We propose a computational framework for developing neural generative models…

Machine Learning · Computer Science 2022-01-06 Alexander Ororbia , Daniel Kifer

Toolpath optimization of metal-based additive manufacturing processes is currently hampered by the high-dimensionality of its design space. In this work, a reinforcement learning platform is proposed that dynamically learns toolpath…

Artificial Intelligence · Computer Science 2020-10-01 Mojtaba Mozaffar , Ablodghani Ebrahimi , Jian Cao

Designing de-novo molecules with desired property profiles requires efficient exploration of the vast chemical space ranging from $10^{23}$ to $10^{60}$ possible synthesizable candidates. While various deep generative models have been…

Machine Learning · Computer Science 2025-08-25 Kamran Chitsaz , Roshan Balaji , Quentin Fournier , Nirav Pravinbhai Bhatt , Sarath Chandar

Template-based molecular generation offers a promising avenue for drug design by ensuring generated compounds are synthetically accessible through predefined reaction templates and building blocks. In this work, we tackle three core…

We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…

Statistical Mechanics · Physics 2020-06-01 Stephen Whitelam , Isaac Tamblyn

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

Deep generative models of molecules have grown immensely in popularity, trained on relevant datasets, these models are used to search through chemical space. The downstream utility of generative models for the inverse design of novel…

Machine Learning · Computer Science 2023-05-11 Daniel Flam-Shepherd , Kevin Zhu , Alán Aspuru-Guzik

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

Most design methods contain a forward framework, asking for primary specifications of a building to generate an output or assess its performance. However, architects urge for specific objectives though uncertain of the proper design…

Computer Vision and Pattern Recognition · Computer Science 2021-06-10 Zohreh Shaghaghian , Wei Yan

With the rising demands for robust structural health monitoring procedures for aerospace structures, the scope of intelligent algorithms and learning techniques is expanding. Supervised algorithms have shown promising results in the field…

Signal Processing · Electrical Eng. & Systems 2023-08-11 Mahindra Rautela , Amin Maghareh , Shirley Dyke , S. Gopalakrishnan

Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural…

Biomolecules · Quantitative Biology 2025-05-07 Cheng Ge , Han-Shen Tae , Zhenqiang Zhang , Lu Lu , Zhijie Huang , Yilin Wang , Tao Jiang , Wenqing Cai , Shan Chang , David J. Adams , Rilei Yu

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in…

Biomolecules · Quantitative Biology 2023-05-24 Zaixi Zhang , Qi Liu

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

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…

Machine Learning · Computer Science 2024-03-08 Bo Qiang , Yiran Zhou , Yuheng Ding , Ningfeng Liu , Song Song , Liangren Zhang , Bo Huang , Zhenming Liu

Mechanical product engineering often must comply with manufacturing or geometric constraints related to the shaping process. Mechanical design hence should rely on robust and fast tools to explore complex shapes, typically for design for…

Computational Engineering, Finance, and Science · Computer Science 2020-10-23 Waad Almasri , Dimitri Bettebghor , Fakhreddine Ababsa , Florence Danglade

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

The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…

Atomic Physics · Physics 2025-05-20 Adarsh Singh