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Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…

Soft Condensed Matter · Physics 2020-11-13 K. Koperwas , A. Grzybowski , M. Paluch

Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…

Biomolecules · Quantitative Biology 2023-07-20 Diego E. Kleiman , Hassan Nadeem , Diwakar Shukla

An automatic approach to counting any kind of cells could alleviate work of the experts and boost the research in fields such as regenerative medicine. In this paper, a method for microscopy cell counting using multiple frames (hence…

Computer Vision and Pattern Recognition · Computer Science 2018-02-01 Alexander Gomez Villa , Augusto Salazar , Igor Stefanini

This article proposes a novel density estimation based algorithm for carrying out supervised machine learning. The proposed algorithm features O(n) time complexity for generating a classifier, where n is the number of sampling instances in…

Machine Learning · Statistics 2007-11-06 Yen-Jen Oyang , Chien-Yu Chen , Darby Tien-Hao Chang , Chih-Peng Wu

The combination of data science and materials informatics has significantly propelled the advancement of multi-component compound synthesis research. This study employs atomic-level data to predict miscibility in binary compounds using…

Materials Science · Physics 2024-09-05 Chiwen Feng , Yanwei Liang , Jiaying Sun , Renhai Wang , Huaijun Sun , Huafeng Dong

The ability to efficiently predict adsorption properties of zeolites can be of large benefit in accelerating the design process of novel materials. The existing configuration space for these materials is wide, while existing molecular…

Materials Science · Physics 2024-03-29 Marko Petković , José Manuel Vicent-Luna , Vlado Menkovski , Sofía Calero

Generating molecular structures with desired properties is a critical task with broad applications in drug discovery and materials design. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to generate diverse,…

Machine Learning · Computer Science 2024-10-04 Huaisheng Zhu , Teng Xiao , Vasant G Honavar

Molecular property prediction is gaining increasing attention due to its diverse applications. One task of particular interests and importance is to predict quantum chemical properties without 3D equilibrium structures. This is practically…

Machine Learning · Computer Science 2021-06-17 Meng Liu , Cong Fu , Xuan Zhang , Limei Wang , Yaochen Xie , Hao Yuan , Youzhi Luo , Zhao Xu , Shenglong Xu , Shuiwang Ji

We introduce a local machine-learning method for predicting the electron densities of periodic systems. The framework is based on a numerical, atom-centred auxiliary basis, which enables an accurate expansion of the all-electron density in…

Chemical Physics · Physics 2021-11-10 Alan M. Lewis , Andrea Grisafi , Michele Ceriotti , Mariana Rossi

We use HIP-NN, a neural network architecture that excels at predicting molecular energies, to predict atomic charges. The charge predictions are accurate over a wide range of molecules (both small and large) and for a diverse set of charge…

The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…

Astrophysics of Galaxies · Physics 2022-10-05 Torben Villadsen , Niels F. W. Ligterink , Mie Andersen

We present a novel machine learning architecture for classification suggested by experiments on olfactory systems. The network separates input stimuli, represented as spatially distinct currents, via winnerless competition---a process based…

Biological Physics · Physics 2020-06-18 Jason A. Platt , Anna Miller , Lawson Fuller , Henry D. I. Abarbanel

Typically, the current dose prediction models are limited to small amounts of data and require re-training for a specific site, often leading to suboptimal performance. We propose a site-agnostic, 3D dose distribution prediction model using…

Particle dynamics and multi-agent systems provide accurate dynamical models for studying and forecasting the behavior of complex interacting systems. They often take the form of a high-dimensional system of differential equations…

Machine Learning · Computer Science 2023-08-09 Yuxuan Liu , Scott G. McCalla , Hayden Schaeffer

Predicting monomer reactivity ratios is crucial for controlling monomer sequence distribution in copolymers and their properties. Traditional experimental methods of determining reactivity ratios are time-consuming and resource-intensive,…

Chemical Physics · Physics 2025-12-24 Habibollah Safari , Mona Bavarian

This study introduces a novel point-wise diffusion model that processes spatio-temporal points independently to efficiently predict complex physical systems with shape variations. This methodological contribution lies in applying forward…

Computational Physics · Physics 2025-08-05 Jiyong Kim , Sunwoong Yang , Namwoo Kang

We present an adaptive sampling approach to 3D reconstruction of the welding joint using the point cloud that is generated by a laser sensor. We start with a randomized strategy to approximate the surface of the volume of interest through…

Robotics · Computer Science 2015-07-09 Soheil Keshmiri , Syeda Mariam Ahmed , Yue Wu , Chee Meng Chew , Chee Khiang Pang

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…

Biomolecules · Quantitative Biology 2023-03-08 Jiaqi Guan , Wesley Wei Qian , Xingang Peng , Yufeng Su , Jian Peng , Jianzhu Ma

We present Bayesian Diffusion Models (BDM), a prediction algorithm that performs effective Bayesian inference by tightly coupling the top-down (prior) information with the bottom-up (data-driven) procedure via joint diffusion processes. We…

Computer Vision and Pattern Recognition · Computer Science 2024-04-23 Haiyang Xu , Yu Lei , Zeyuan Chen , Xiang Zhang , Yue Zhao , Yilin Wang , Zhuowen Tu

This paper is concerned with distributed limited memory prediction for continuous-time linear stochastic systems with multiple sensors. A distributed fusion with the weighted sum structure is applied to the optimal local limited memory…

Other Computer Science · Computer Science 2010-02-18 Ha-ryong Song , Vladimir Shin
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