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Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling.…

Machine Learning · Computer Science 2025-05-28 Hexiong Yang , Mingrui Chen , Huaibo Huang , Junxian Duan , Jie Cao , Zhen Zhou , Ran He

One of the most important and difficult parts of constructing a multidimensional numerical simulation of flame acceleration and deflagration-to-detonation transition (DDT) in a reacting flow is finding a reliable and affordable model of the…

Fluid Dynamics · Physics 2017-09-04 Carolyn R. Kaplan , Alp Ozgen , Elaine S. Oran

Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited…

Machine Learning · Computer Science 2023-10-23 Yaorui Shi , An Zhang , Enzhi Zhang , Zhiyuan Liu , Xiang Wang

In this article, a stochastic gradient based online learning algorithm for Extreme Learning Machines (ELM) is developed (SG-ELM). A stability criterion based on Lyapunov approach is used to prove both asymptotic stability of estimation…

Neural and Evolutionary Computing · Computer Science 2015-01-19 Vijay Manikandan Janakiraman , XuanLong Nguyen , Dennis Assanis

Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…

Chemical Physics · Physics 2021-04-15 Lennard Böselt , Moritz Thürlemann , Sereina Riniker

Methane pyrolysis provides a scalable alternative to conventional hydrogen production methods, avoiding greenhouse gas emissions. However, high operating temperatures limit economic feasibility on an industrial scale. A major scientific…

We propose masked particle modeling (MPM) as a self-supervised method for learning generic, transferable, and reusable representations on unordered sets of inputs for use in high energy physics (HEP) scientific data. This work provides a…

High Energy Physics - Phenomenology · Physics 2024-07-12 Tobias Golling , Lukas Heinrich , Michael Kagan , Samuel Klein , Matthew Leigh , Margarita Osadchy , John Andrew Raine

With recent advances in sequencing technologies, large amounts of epigenomic data have become available and computational methods are contributing significantly to the progress of epigenetic research. As an orthogonal approach to methods…

Genomics · Quantitative Biology 2019-11-05 Alexander Lück , Verena Wolf

Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learning theory, chemical reaction network theory, and statistical…

Molecular Networks · Quantitative Biology 2023-11-08 William Poole , Thomas E. Ouldridge , Manoj Gopalkrishnan

This paper presents a proper generalized decomposition (PGD) based reduced-order model of hierarchical deep-learning neural networks (HiDeNN). The proposed HiDeNN-PGD method keeps both advantages of HiDeNN and PGD methods. The automatic…

Numerical Analysis · Mathematics 2022-01-12 Lei Zhang , Ye Lu , Shaoqiang Tang , Wing Kam Liu

In chemical processing and bioprocessing, conventional online sensors are limited to measure only basic process variables like pressure and temperature, pH, dissolved O and CO$_2$ and viable cell density (VCD). The concentration of other…

Quantitative Methods · Quantitative Biology 2020-05-07 Semion Rozov

Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…

Quantitative Methods · Quantitative Biology 2025-12-23 Mamoru Saita , Yutaka Hori

[Context] The stochasticity of grain chemistry requires special care in modeling. Previously methods based on the modified rate equation, the master equation, the moment equation, and Monte Carlo simulations have been used. [Aims] We…

Astrophysics of Galaxies · Physics 2012-01-05 Fujun Du , Berengere Parise

Finding amorphous polymers with higher thermal conductivity is important, as they are ubiquitous in heat transfer applications. With recent progress in material informatics, machine learning approaches have been increasingly adopted for…

Materials Science · Physics 2021-09-08 Ruimin Ma , Hanfeng Zhang , Jiaxin Xu , Yoshihiro Hayashi , Ryo Yoshida , Junichiro Shiomi , Tengfei Luo

Since the internal temperature is less accessible than surface temperature, there is an urgent need to develop accurate and real-time estimation algorithms for better thermal management and safety. This work presents a novel framework for…

Systems and Control · Electrical Eng. & Systems 2025-09-15 Yusheng Zheng , Wenxue Liu , Yunhong Che , Ferdinand Grimm , Jingyuan Zhao , Xiaosong Hu , Simona Onori , Remus Teodorescu , Gregory J. Offer

The chemistry of an astrophysical environment is closely coupled to its dynamics, the latter often found to be complex. Hence, to properly model these environments a 3D context is necessary. However, solving chemical kinetics within a 3D…

Computational Physics · Physics 2024-05-07 S. Maes , F. De Ceuster , M. Van de Sande , L. Decin

Prediction and control of chemical mixing are vital for many scientific areas such as subsurface reactive transport, climate modeling, combustion, epidemiology, and pharmacology. Due to the complex nature of mixing in heterogeneous and…

Machine Learning · Computer Science 2021-12-15 N. V. Jagtap , M. K. Mudunuru , K. B. Nakshatrala

New experimental data are collected for methyl-cyclohexane (MCH) autoignition in a heated rapid compression machine (RCM). Three mixtures of MCH/O2/N2/Ar at equivalence ratios of $\phi$=0.5, 1.0, and 1.5 are studied and the ignition delays…

Chemical Physics · Physics 2017-06-12 Bryan W. Weber , WIlliam J. Pitz , Marco Mehl , Emma Silke , Alexander C. Davis , Chih-Jen Sung

Accurate simulations of molecules require high-level electronic-structure theory in combination with rigorous methods for approximating the quantum dynamics. Machine-learning approaches can significantly reduce the computational expense of…

Chemical Physics · Physics 2026-02-24 Valerii Andreichev , Jindra Dušek , Markus Meuwly , Jeremy O. Richardson

Recently, there has been a growing interest in applying machine learning methods to problems in engineering mechanics. In particular, there has been significant interest in applying deep learning techniques to predicting the mechanical…

Machine Learning · Computer Science 2023-03-15 Saeed Mohammadzadeh , Peerasait Prachaseree , Emma Lejeune