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Living systems continually respond to signals from the surrounding environment. Survival requires that their responses adapt quickly and robustly to the changes in the environment. One particularly challenging example is olfactory…

Neurons and Cognition · Quantitative Biology 2024-10-08 Kiri Choi , Will Rosenbluth , Isabella R. Graf , Nirag Kadakia , Thierry Emonet

Functional groups (FGs) are molecular substructures that are served as a foundation for analyzing and predicting chemical properties of molecules. Automatic discovery of FGs will impact various fields of research, including medicinal…

Machine Learning · Computer Science 2019-10-11 Phillip Pope , Soheil Kolouri , Mohammad Rostrami , Charles Martin , Heiko Hoffmann

In the last few years, we have seen the transformative impact of deep learning in many applications, particularly in speech recognition and computer vision. Inspired by Google's Inception-ResNet deep convolutional neural network (CNN) for…

Machine Learning · Statistics 2018-08-15 Garrett B. Goh , Charles Siegel , Abhinav Vishnu , Nathan O. Hodas , Nathan Baker

Chemists have been pursuing the general mathematical laws to explain and predict molecular properties for a long time. However, most of the traditional quantitative structure-activity relationship (QSAR) models have limited application…

Chemical Physics · Physics 2023-05-30 Lu Xu , Qin Yang

Prediction of toxicity levels of chemical compounds is an important issue in Quantitative Structure-Activity Relationship (QSAR) modeling. Although toxicity prediction has achieved significant progress in recent times through deep learning,…

Machine Learning · Computer Science 2019-07-22 Abdul Karim , Jaspreet Singh , Avinash Mishra , Abdollah Dehzangi , M. A. Hakim Newton , Abdul Sattar

Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…

Machine Learning · Computer Science 2017-03-31 Joseph Gomes , Bharath Ramsundar , Evan N. Feinberg , Vijay S. Pande

Virtual screening can accelerate drug discovery by identifying promising candidates for experimental evaluation. Machine learning is a powerful method for screening, as it can learn complex structure-property relationships from experimental…

Machine Learning · Computer Science 2021-02-22 Simon Axelrod , Rafael Gomez-Bombarelli

Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review…

Machine Learning · Computer Science 2024-11-13 Chenqing Hua

Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…

Quantitative Methods · Quantitative Biology 2023-04-07 Xinye Xiong , Bingxin Zhou , Yu Guang Wang

This work targets the problem of odor source localization by multi-agent systems. A hierarchical cooperative control has been put forward to solve the problem of locating source of an odor by driving the agents in consensus when at least…

Systems and Control · Computer Science 2017-11-13 Abhinav Sinha , Rishemjit Kaur , Ritesh Kumar , Amol P. Bhondekar

According to density functional theory, any chemical property can be inferred from the electron density, making it the most informative attribute of an atomic structure. In this work, we demonstrate the use of established physical methods…

Materials Science · Physics 2023-09-12 Ethan M. Sunshine , Muhammed Shuaibi , Zachary W. Ulissi , John R. Kitchin

Prediction of molecular properties, including physico-chemical properties, is a challenging task in chemistry. Herein we present a new state-of-the-art multitask prediction method based on existing graph neural network models. We have used…

Machine Learning · Computer Science 2019-10-31 Fabio Capela , Vincent Nouchi , Ruud Van Deursen , Igor V. Tetko , Guillaume Godin

Deep learning based methods have been widely applied to predict various kinds of molecular properties in the pharmaceutical industry with increasingly more success. Solvation free energy is an important index in the field of organic…

Chemical Physics · Physics 2021-05-06 Ramin Ansari , Amirata Ghorbani

Hypergraphs, increasingly utilised to model complex and diverse relationships in modern networks, have gained significant attention for representing intricate higher-order interactions. Among various challenges, cohesive subgraph discovery…

Social and Information Networks · Computer Science 2025-07-14 Dahee Kim , Hyewon Kim , Song Kim , Minseok Kim , Junghoon Kim , Yeon-Chang Lee , Sungsu Lim

Accurate prediction of physical properties is critical for discovering and designing novel materials. Machine learning technologies have attracted significant attention in the materials science community for their potential for large-scale…

Materials Science · Physics 2021-11-24 Boyu Zhang , Mushen Zhou , Jianzhong Wu , Fuchang Gao

Identifying objects in an image and their mutual relationships as a scene graph leads to a deep understanding of image content. Despite the recent advancement in deep learning, the detection and labeling of visual object relationships…

Computer Vision and Pattern Recognition · Computer Science 2021-07-13 Rajat Koner , Poulami Sinhamahapatra , Volker Tresp

Machine Learning tools are nowadays widely applied extensively to the prediction of the properties of molecular materials, using datasets extracted from high-throughput computational models. In several cases of scientific and technological…

Materials Science · Physics 2021-02-10 Fabio Le Piane , Matteo Baldoni , Francesco Mercuri

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…

Chemical Physics · Physics 2025-02-04 Ming Han , Ge Sun , Juan J. de Pablo

Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal…

Machine Learning · Computer Science 2025-07-04 Runzhong Wang , Rui-Xi Wang , Mrunali Manjrekar , Connor W. Coley

Odor identification is an important area in a wide range of industries like cosmetics, food, beverages and medical diagnosis among others. Odor detection could be done through an array of gas sensors conformed as an electronic nose where a…

Machine Learning · Computer Science 2019-05-06 Jose de Jesus Rubio , Ramon Silva Ortigoza , Francisco Jacob Avila , Adolfo Melendez , Juan Manuel Stein