Geodiff: A geometric diffusion model for molecular conformation generation

M Xu, L Yu, Y Song, C Shi, S Ermon, J Tang - arXiv preprint arXiv …, 2022 - arxiv.org
Predicting molecular conformations from molecular graphs is a fundamental problem in
cheminformatics and drug discovery. Recently, significant progress has been achieved with …

Geometric deep learning for drug discovery

M Liu, C Li, R Chen, D Cao, X Zeng - Expert Systems with Applications, 2023 - Elsevier
Drug discovery is a time-consuming and expensive process. With the development of
Artificial Intelligence (AI) techniques, molecular Geometric Deep Learning (GDL) has …

Learning gradient fields for molecular conformation generation

C Shi, S Luo, M Xu, J Tang - International conference on …, 2021 - proceedings.mlr.press
We study a fundamental problem in computational chemistry known as molecular
conformation generation, trying to predict stable 3D structures from 2D molecular graphs …

[HTML][HTML] Distinct biological ages of organs and systems identified from a multi-omics study

C Nie, Y Li, R Li, Y Yan, D Zhang, T Li, Z Li, Y Sun… - Cell reports, 2022 - cell.com
Biological age (BA) has been proposed to evaluate the aging status instead of chronological
age (CA). Our study shows evidence that there might be multiple" clocks" within the whole …

[HTML][HTML] Machine learning based energy-free structure predictions of molecules, transition states, and solids

D Lemm, GF Von Rudorff, OA Von Lilienfeld - Nature Communications, 2021 - nature.com
The computational prediction of atomistic structure is a long-standing problem in physics,
chemistry, materials, and biology. Conventionally, force-fields or ab initio methods determine …

Euclidean distance matrices: essential theory, algorithms, and applications

I Dokmanic, R Parhizkar, J Ranieri… - IEEE Signal Processing …, 2015 - ieeexplore.ieee.org
Euclidean distance matrices (EDMs) are matrices of the squared distances between points.
The definition is deceivingly simple; thanks to their many useful properties, they have found …

An end-to-end framework for molecular conformation generation via bilevel programming

M Xu, W Wang, S Luo, C Shi, Y Bengio… - International …, 2021 - proceedings.mlr.press
Predicting molecular conformations (or 3D structures) from molecular graphs is a
fundamental problem in many applications. Most existing approaches are usually divided …

Application of artificial intelligence for COVID-19 epidemic: an exploratory study, opportunities, challenges, and future prospects

JB Awotunde, SO Folorunso, RG Jimoh… - Artificial intelligence for …, 2021 - Springer
The occurrence of coronavirus (COVID-19) is greater than that of 2003 representing
respiratory infections syndrome (SARS). As of 12 August 2020, the reported cases are more …

DSOS and SDSOS optimization: more tractable alternatives to sum of squares and semidefinite optimization

AA Ahmadi, A Majumdar - SIAM Journal on Applied Algebra and Geometry, 2019 - SIAM
In recent years, optimization theory has been greatly impacted by the advent of sum of
squares (SOS) optimization. The reliance of this technique on large-scale semidefinite …

A data-enhanced distributionally robust optimization method for economic dispatch of integrated electricity and natural gas systems with wind uncertainty

B Zhao, T Qian, W Tang, Q Liang - Energy, 2022 - Elsevier
With growing penetrations of wind power in electricity systems, the coordinated dispatch of
integrated electricity and natural gas systems is becoming a popular research topic …