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Machine learning has the potential to automate molecular design and drastically accelerate the discovery of new functional compounds. Towards this goal, generative models and reinforcement learning (RL) using string and graph…

Machine Learning · Computer Science 2022-02-02 Daniel Flam-Shepherd , Alexander Zhigalin , Alán Aspuru-Guzik

Background: Identifying new indications for approved drugs is a complex and time-consuming process that requires extensive knowledge of pharmacology, clinical data, and advanced computational methods. Recently, deep learning (DL) methods…

Machine Learning · Computer Science 2025-11-13 Shuting Jin , Yi Jiang , Yimin Liu , Tengfei Ma , Dongsheng Cao , Leyi Wei , Xiangrong Liu , Xiangxiang Zeng

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

Realistic hair strand generation is crucial for applications like computer graphics and virtual reality. While diffusion models can generate hairstyles from text or images, these inputs lack precision and user-friendliness. Instead, we…

Computer Vision and Pattern Recognition · Computer Science 2025-08-05 Na Zhang , Moran Li , Chengming Xu , Han Feng , Xiaobin Hu , Jiangning Zhang , Weijian Cao , Chengjie Wang , Yanwei Fu

The goal of Sketch-Based Image Retrieval (SBIR) is using free-hand sketches to retrieve images of the same category from a natural image gallery. However, SBIR requires all test categories to be seen during training, which cannot be…

Computer Vision and Pattern Recognition · Computer Science 2020-09-21 Jiangtong Li , Zhixin Ling , Li Niu , Liqing Zhang

In the field of Structure-based Drug Design (SBDD), deep learning-based generative models have achieved outstanding performance in terms of docking score. However, further study shows that the existing molecular generative methods and…

Biomolecules · Quantitative Biology 2024-03-21 Bowen Gao , Minsi Ren , Yuyan Ni , Yanwen Huang , Bo Qiang , Zhi-Ming Ma , Wei-Ying Ma , Yanyan Lan

We propose a novel method that makes use of deep neural networks and gradient decent to perform automated design on complex real world engineering tasks. Our approach works by training a neural network to mimic the fitness function of a…

Machine Learning · Statistics 2017-10-31 Oliver Hennigh

Scene Designer is a novel method for searching and generating images using free-hand sketches of scene compositions; i.e. drawings that describe both the appearance and relative positions of objects. Our core contribution is a single…

Computer Vision and Pattern Recognition · Computer Science 2021-08-18 Leo Sampaio Ferraz Ribeiro , Tu Bui , John Collomosse , Moacir Ponti

Structure-Based drug design (SBDD) has emerged as a popular approach in drug discovery, leveraging three-dimensional protein structures to generate drug ligands. However, existing generative models encounter several key challenges: (1)…

Machine Learning · Computer Science 2025-11-27 Qingsong Zhong , Haomin Yu , Yan Lin , Wangmeng Shen , Long Zeng , Jilin Hu

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

Poetry generation, and creative language generation in general, usually suffers from the lack of large training data. In this paper, we present a novel framework to generate sonnets that does not require training on poems. We design a…

Computation and Language · Computer Science 2022-05-05 Yufei Tian , Nanyun Peng

The efficacy of a drug depends on its binding affinity to the therapeutic target and pharmacokinetics. Deep learning (DL) has demonstrated remarkable progress in predicting drug efficacy. We develop MolDesigner, a human-in-the-loop web…

Quantitative Methods · Quantitative Biology 2020-10-09 Kexin Huang , Tianfan Fu , Dawood Khan , Ali Abid , Ali Abdalla , Abubakar Abid , Lucas M. Glass , Marinka Zitnik , Cao Xiao , Jimeng Sun

The traditional more-is-better dose selection paradigm, developed based on cytotoxic chemotherapeutics, is often problematic When applied to the development of novel molecularly targeted agents (e.g., kinase inhibitors, monoclonal…

Methodology · Statistics 2022-11-04 Liyun Jiang , Ying Yuan

Engineering molecules to exhibit precise 3D intermolecular interactions with their environment forms the basis of chemical design. In ligand-based drug design, bioisosteric analogues of known bioactive hits are often identified by virtually…

Biomolecules · Quantitative Biology 2025-03-18 Keir Adams , Kento Abeywardane , Jenna Fromer , Connor W. Coley

Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently attracted great attention in drug R\&D. This paper…

Biomolecules · Quantitative Biology 2025-07-14 Peining Zhang , Daniel Baker , Minghu Song , Jinbo Bi

The process of screening molecules for desirable properties is a key step in several applications, ranging from drug discovery to material design. During the process of drug discovery specifically, protein-ligand docking, or chemical…

Machine Learning · Computer Science 2022-11-08 Ryien Hosseini , Filippo Simini , Austin Clyde , Arvind Ramanathan

We introduce a novel problem of scene sketch zero-shot learning (SSZSL), which is a challenging task, since (i) different from photo, the gap between common semantic domain (e.g., word vector) and sketch is too huge to exploit common…

Computer Vision and Pattern Recognition · Computer Science 2019-05-14 Yao Xie , Peng Xu , Zhanyu Ma

Synthesizability in generative molecular design remains a pressing challenge. Existing methods to assess synthesizability span heuristics-based methods, retrosynthesis models, and synthesizability-constrained molecular generation. The…

Biomolecules · Quantitative Biology 2024-07-18 Jeff Guo , Philippe Schwaller

In recent years, deep learning has demonstrated promising results in de novo drug design. However, the proposed techniques still lack an efficient exploration of the large chemical space. Most of these methods explore a small fragment of…

Quantitative Methods · Quantitative Biology 2024-01-17 Mohamed-Amine Chadi , Hajar Mousannif , Ahmed Aamouche

Video generation models have been used as a robot policy to predict the future states of executing a task conditioned on task description and observation. Previous works ignore their high computational cost and long inference time. To…

Computer Vision and Pattern Recognition · Computer Science 2026-03-17 Qikang Zhang , Yingjie Lei , Wei Liu , Daochang Liu