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arXiv 2025年

作者： Shiraogawa, Takafumi Krug, Simon León Ehara, Masahiro von Lilienfeld, O. Anatole Institute for Molecular Science National Institutes of Natural Sciences 38 Nishigonaka Myodaiji Okazaki444-8585 Japan Research Center for Computational Science National Institutes of Natural Sciences 38 Nishigonaka Myodaiji Okazaki444-8585 Japan The Graduate University for Advanced Studies 38 Nishigonaka Myodaiji Okazaki444-8585 Japan Machine Learning Group Technische Universität Berlin Berlin10587 Germany Chemical Physics Theory Group Department of Chemistry University of Toronto St. George Campus TorontoM5S3H6 Ontario Canada Department of Materials Science and Engineering University of Toronto St. George Campus TorontoM5S 3E4 Ontario Canada Vector Institute for Artificial Intelligence TorontoM5S 1M1 Ontario Canada Berlin Institute for the Foundations of Learning and Data Berlin10587 Germany Department of Physics University of Toronto St. George Campus TorontoM5S 1A7 Ontario Canada Acceleration Consortium University of Toronto TorontoM5R 0A3 Ontario Canada

Understanding chemical compound space (CCS), a set of molecules and materials, is crucial for the rational discovery of molecules and materials. Concepts of symmetry have recently been introduced into CCS to account for near degeneracies and differences in electronic energies between iso-electronic materials. In this work, we present approximate relationships of response properties based on a first-principles view of CCS. They have been derived from perturbation theory and antisymmetry considerations involving nuclear charges. These rules allow approximate predictions of relative response properties of pairs of distinct compounds with opposite nuclear charge variations from a highly symmetric reference material, without the need for experiments or quantum chemical calculations of each compound. We numerically and statistically verified these rules for electric and magnetic response properties (electric dipole moment, polarizabilities, hyperpolarizabilities, and magnetizabilities) among charge-neutral and iso-electronic BN-doped polycyclic aromatic hydrocarbon derivatives of naphthalene, anthracene, and pyrene. Our analysis indicates that, despite their simplicity, antisymmetry rule-based predictions are remarkably accurate, enabling dimensionality reduction of CCS. Response properties in alchemical perturbation density functional theory were investigated to clarify the origin of this predictive power. © 2025, CC BY.

关键词： Naphthalene

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Scaling up the lattice dynamics of amorphous materials by orders of magnitude

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Physical Review B 2020年第2期102卷 024108-024108页

作者： Ivan Kriuchevskyi Vladimir V. Palyulin Rico Milkus Robert M. Elder Timothy W. Sirk Alessio Zaccone Department of Physics “A. Pontremoli” University of Milan via Celoria 16 20133 Milan Italy Centre for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Nobelya Ulitsa 3 Moscow 121205 Russia Department of Chemical Engineering and Biotechnology University of Cambridge Cambridge CB3 0AS United Kingdom Polymers Branch U.S. Army Research Laboratory Aberdeen Proving Ground Maryland 20783 USA Bennett Aerospace Inc. Cary North Carolina 27518 USA Center for Devices and Radiological Health U.S. Food and Drug Administration Silver Spring Maryland 20903 USA

We generalize the nonaffine theory of viscoelasticity for use with large, well-sampled systems of arbitrary chemical complexity. Having in mind predictions of mechanical and vibrational properties of amorphous systems with atomistic resolution, we propose an extension of the kernel polynomial method (KPM) for the computation of the vibrational density of states and the eigenmodes, including the Γ correlator of the affine force field, which is a key ingredient of lattice-dynamic calculations of viscoelasticity. We show that the results converge well to the solution obtained by direct diagonalization (DD) of the Hessian (dynamical) matrix. As is well known, the DD approach has prohibitively high computational requirements for systems with N=104 atoms or larger. Instead, the KPM approach developed here allows one to scale up lattice dynamic calculations of real materials up to 106 atoms, with a hugely more favorable (linear) scaling of computation time and memory consumption with N.

关键词： Dissipative dynamics Lattice dynamics Mechanical deformation Amorphous materials Polydisperse materials Polymer glasses Random & disordered media Viscoelasticity Molecular dynamics Numerical techniques

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Multivariate Analysis on Performance Gaps of Artificial Intelligence Models in Screening Mammography

arXiv

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arXiv 2023年

作者： Zhang, Linglin Brown-Mulry, Beatrice Nalla, Vineela Hwang, InChan Gichoya, Judy Wawira Gastounioti, Aimilia Banerjee, Imon Seyyed-Kalantari, Laleh Woo, MinJae Trivedi, Hari School of Data Science and Analytics Kennesaw State University 3391 Town Point Dr NW KennesawGA30144 United States Department of Information Technology Kennesaw State University 1100 South Marietta Pkwy MariettaGA30060 United States Department of Radiology and Imaging Sciences Emory University 1364 E Clifton Rd NE AtlantaGA30322 United States Computational Imaging Research Center Washington University in St. Louis School of Medicine 4525 Scott Avenue St. LouisMO63110 United States Department of Radiology Mayo Clinic Arizona 13400 E Shea Blvd ScottsdaleAZ85259 United States School of Computing and Augmented Intelligence Arizona State University 699 S Mill Ave TempeAZ85281 United States Department of Electrical Engineering and Computer Science York University 4700 Keele St TorontoONM3J 1P3 Canada

Although deep learning models for abnormality classification can perform well in screening mammography, the demographic, imaging, and clinical characteristics associated with increased risk of model failure remain unclear. This retrospective study uses the Emory BrEast Imaging dataset (EMBED) containing mammograms from 115,931 patients imaged at Emory Healthcare between 2013-2020, with Breast Imaging Reporting and data System (BI-RADS) assessment, region of interest coordinates for abnormalities, imaging features, pathologic outcomes, and patient demographics. Multiple deep learning models were trained to distinguish between abnormal tissue patches and randomly selected normal tissue patches from screening mammograms. We assessed model performance by subgroups defined by age, race, pathologic outcome, tissue density, and imaging characteristics and investigated their associations with false negatives and false positives. We also performed multivariate logistic regression to control for confounding between subgroups. The top-performing model, ResNet152V2, achieved accuracy of 92.6% (95%CI=92.0-93.2%), and area under the receiver operating characteristics curve 0.975 (95%CI=0.972-0.978). Before controlling for confounding, nearly all subgroups showed statistically significant differences in model performance. However, after controlling for confounding, we found lower false negative risk associates with Other race (RR=0.828;p= .050), biopsy-proven benign lesions (RR=0.927;p= .011), and mass (RR=0.921;p= .010) or asymmetry (RR=0.854;p= .040);higher false negative risk associates with architectural distortion (RR=1.037;p Copyright © 2023, The Authors. All rights reserved.

关键词： Mammography

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HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer

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Journal of Genetics and Genomics 2020年第8期47卷 435-448页

作者： Canhui Cao Ping Hong Xingyu Huang Da Lin Gang Cao Liming Wang Bei Feng Ping Wu Hui Shen Qian Xu Ci Ren Yifan Meng Wenhua Zhi Ruidi Yu Juncheng Wei Wencheng Ding Xun Tian Qinghua Zhang Wei Li Qinglei Gao Gang Chen Kezhen Li Wing-Kin Sung Zheng Hu Hui Wang Guoliang Li Peng Wu Department of Gynecologic Oncology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China Cancer Biology Research Center(Key Laboratory of the Ministry of Education) Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan430070China Agricultural Bioinformatics Key Laboratory of Hubei Province Hubei Engineering Technology Research Center of Agricultural Big DataCollege of InformaticsHuazhong Agricultural UniversityWuhan430070China State Key Laboratory of Agricultural Microbiology Huazhong Agricultural UniversityWuhan430070China Bio-Medical Center Huazhong Agricultural UniversityWuhan430070China College of Veterinary Medicine Huazhong Agricultural UniversityWuhan430070China Department of Obstetrics and Gynecology Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China Department of Obstetrics and Gynecology Key Laboratory for Molecular Diagnosis of Hubei ProvinceThe Central Hospital of WuhanTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430010China Department of Computational and Systems Biology Genome Institute of SingaporeSingapore Department of Gynecological Oncology The First Affiliated Hospital of Sun Yat-sen UniversityGuangzhou510080China

Integration of human papillomavirus(HPV)DNA into the human genome is a reputed key driver of cervical ***,the effects of HPV integration on chromatin structural organization and gene expression are largely *** studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome *** then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome,RNA,chromatin immunoprecipitation and high-throughput chromosome conformation capture(Hi-C)sequencing to identify the mechanisms of HPV integration in cervical *** analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities,with correlation found between three-dimensional(3D)structural change and gene ***,HPV integration divided one topologically associated domain(TAD)into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106,with a decrease in PEG3 expression and an increase in CCDC106 *** expression dysregulation was further confirmed using 10 samples from our cohort,which exhibited the same HPV-CCDC106 *** summary,we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure ***,this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.

关键词： Cervical cancer HPV integration Fusion gene Hi-C Enhancer TAD

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Prediction of Oral Food Challenge Outcomes via Ensemble Learning

arXiv

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arXiv 2022年

作者： Zhang, Justin Lee, Deborah Jungles, Kylie Shaltis, Diane Najarian, Kayvan Ravikumar, Rajan Sanders, Georgiana Gryak, Jonathan Department of Electrical and Computer Engineering University of Michigan Ann ArborMI United States Department of Internal Medicine University of Michigan Ann ArborMI United States Department of Pediatrics University of Michigan Ann ArborMI United States Department of Computational Medicine and Bioinformatics University of Michigan Ann ArborMI United States Michigan Institute for Data Science University of Michigan Ann ArborMI United States Department of Emergency Medicine University of Michigan Ann ArborMI United States Department of Computer Science and Engineering University of Michigan Ann ArborMI United States Max Harry Weil Institute for Critical Care Research and Innovation University of Michigan Ann ArborMI United States Mary H. Weiser Food Allergy Center University of Michigan Ann ArborMI United States Department of Computer Science Queens College City University of New York New YorkNY United States

Oral Food Challenges (OFCs) are essential to accurately diagnosing food allergy due to the limitations of existing clinical testing. However, some patients are hesitant to undergo OFCs, while those willing suffer from limited access to allergists in rural/community healthcare settings. Despite its success in predicting patient outcomes in other clinical settings, few applications of machine learning to food allergy have been developed. Thus, in this study, we seek to leverage machine learning methodologies for OFC outcome prediction. Retrospective data was gathered from 1,112 patients who collectively underwent a total of 1,284 OFCs, and consisted of clinical factors including serum-specific Immunoglobulin E (IgE), total IgE, skin prick tests (SPTs), comorbidities, sex, and age. Using these features, multiple machine learning models were constructed to predict OFC outcomes for three common allergens: peanut, egg, and milk. The best performing model for each allergen was an ensemble of random forest (egg) or Learning Using Concave and Convex Kernels (LUCCK) (peanut, milk) models, which achieved an Area under the Curve (AUC) of 0.91, 0.96, and 0.94, in predicting OFC outcomes for peanut, egg, and milk, respectively. Moreover, all such models had sensitivity and specificity values ≥ 89%. Model interpretation via SHapley Additive exPlanations (SHAP) indicates that specific IgE, along with wheal and flare values from SPTs, are highly predictive of OFC outcomes. The results of this analysis suggest that ensemble learning has the potential to predict OFC outcomes and reveal relevant clinical factors for further study. Copyright © 2022, The Authors. All rights reserved.

关键词： Machine learning

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Optimizing Laser Pulses for Narrow-Band Inverse Compton Sources in the High-Intensity Regime

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Physical Review Letters 2019年第20期122卷 204802-204802页

作者： Daniel Seipt Vasily Yu. Kharin Sergey G. Rykovanov Helmholtz-Institut Jena Fröbelstieg 3 07743 Jena Germany Center for Ultrafast Optical Science University of Michigan Ann Arbor Michigan 48109 USA Research Institute Moscow R&D Lab Moscow Bersenevskaya nab. 6 119072 Russia Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Nobel Str. 3 Skolkovo Russia

Scattering of ultraintense short laser pulses off relativistic electrons allows one to generate a large number of X- or gamma-ray photons with the expense of the spectral width—temporal pulsing of the laser inevitable leads to considerable spectral broadening. In this Letter, we describe a simple method to generate optimized laser pulses that compensate the nonlinear spectrum broadening and can be thought of as a superposition of two oppositely linearly chirped pulses delayed with respect to each other. We develop a simple analytical model that allows us to predict the optimal parameters of such a two-pulse—the delay, amount of chirp, and relative phase—for generation of a narrow-band γ-ray spectrum. Our predictions are confirmed by numerical optimization and simulations including three-dimensional effects.

关键词： Gamma-ray generation in plasmas High intensity laser-plasma interactions Strong electromagnetic field effects Radiation from moving charges

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Optimizing Laser Pulses for Narrowband Inverse Compton Sources in the High-Intensity Regime

arXiv

引用

arXiv 2019年

作者： Seipt, Daniel Yu. Kharin, Vasily Rykovanov, Sergey G. Helmholtz-Institut Jena Fröbelstieg 3 Jena07743 Germany Center for Ultrafast Optical Science University of Michigan Ann Arbor MI48109 United States Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Nobel Str. 3 Skolkovo Russia

Scattering of ultraintense short laser pulses off relativistic electrons allows one to generate a large number of X- or gamma-ray photons with the expense of the spectral width—temporal pulsing of the laser inevitable leads to considerable spectral broadening. In this Letter, we describe a simple method to generate optimized laser pulses that compensate the nonlinear spectrum broadening, and can be thought of as a superposition of two oppositely linearly chirped pulses delayed with respect to each other. We develop a simple analytical model that allow us to predict the optimal parameters of such a two-pulse—the delay, amount of chirp and relative phase—for generation of a narrowband γ-ray spectrum. Our predictions are confirmed by numerical optimization and simulations including 3D effects. Copyright © 2019, The Authors. All rights reserved.

关键词： Gamma rays

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Concept transfer of synaptic diversity from biological to artificial neural networks

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Nature communications 2025年第1期16卷 5112页

作者： Martin Hofmann Moritz Franz Peter Becker Christian Tetzlaff Patrick Mäder Data-intensive Systems and Visualization Group (dAI.SY) Technische Universität Ilmenau Max-Planck-Ring 14 Ilmenau 98693 Thuringia Germany. martin.hofmann@tu-ilmenau.de. Group of Computational Synaptic Physiology Department for Neuro- and Sensory Physiology University Medical Center Göttingen Humboldtallee 23 Göttingen 37073 Lower Saxony Germany. Campus-Institut Data Science (CIDAS) University of Göttingen Goldschmidtstraße 1 Göttingen 37077 Lower Saxony Germany. Data-intensive Systems and Visualization Group (dAI.SY) Technische Universität Ilmenau Max-Planck-Ring 14 Ilmenau 98693 Thuringia Germany. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e Leipzig 04103 Saxony Germany. Faculty of Biological Sciences Friedrich Schiller University Fürstengraben 1 Jena 07745 Thuringia Germany.

Recent developments in artificial neural networks have drawn inspiration from biological neural networks, leveraging the concept of the artificial neuron to model the learning abilities of biological nerve cells. However, while neuroscience has provided new insights into the mechanisms of biological neural networks, only a limited number of these concepts have been directly applied to artificial neural networks, with no guarantee of improved performance. Here, we address the discrepancy between the inhomogeneous and dynamic structures of biological neural networks and the largely homogeneous and fixed topologies of artificial neural networks. Specifically, we demonstrate successful integration of concepts of synaptic diversity, including spontaneous spine remodeling, synaptic plasticity diversity, and multi-synaptic connectivity, into artificial neural networks. Our findings reveal increased learning speed, prediction accuracy, and resilience to gradient inversion attacks. Our publicly available drop-in replacement code enables easy incorporation of these proposed concepts into existing networks.

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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USID and Pycroscopy - Open frameworks for storing and analyzing spectroscopic and imaging data

arXiv

引用

arXiv 2019年

作者： Somnath, Suhas Smith, Chris R. Laanait, Nouamane Vasudevan, Rama K. Ievlev, Anton Belianinov, Alex Lupini, Andrew R. Shankar, Mallikarjun Kalinin, Sergei V. Jesse, Stephen Advanced Data and Workflows Group National Center for Computational Sciences Center for Nanophase Materials Sciences Computational Chemical and Materials Sciences Computational Science and Engineering Division Oak Ridge National Laboratory Oak RidgeTN37831 United States

Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific research requires an evolution of the associated computing and data infrastructure, bridging scientific instrumentation with super- and cloud-computing. Here, we describe Universal Spectroscopy and Imaging data (USID), a data model capable of representing data from most common instruments, modalities, dimensionalities, and sizes. We pair this schema with the hierarchical data file format (HDF5) to maximize compatibility, exchangeability, traceability, and reproducibility. We discuss a family of community-driven, open-source, and free python software packages for storing, processing and visualizing data. The first is pyUSID which provides the tools to read and write USID HDF5 files in addition to a scalable framework for parallelizing data analysis. The second is Pycroscopy, which provides algorithms for scientific analysis of nanoscale imaging and spectroscopy modalities and is built on top of pyUSID and USID. The instrument-agnostic nature of USID facilitates the development of analysis code independent of instrumentation and task in Pycroscopy which in turn can bring scientific communities together and break down barriers in the age of open-science. The interested reader is encouraged to be a part of this ongoing community-driven effort to collectively accelerate materials research and discovery through the realms of big data. Copyright © 2019, The Authors. All rights reserved.

关键词： Open systems

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