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Clustering in Networks Via Kernel-ARMA Modeling and the Grassmannian: The Brain-Network Case

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arXiv 2020年

作者： Ye, Cong Slavakis, Konstantinos Patil, Pratik V. Nakuci, Johan Muldoon, Sarah F. Medaglia, John NY14260 United States Neuroscience Program University at Buffalo BuffaloNY14260 United States Department of Mathematics and the Computational and Data-Enabled Science and Engineering Program University at Buffalo SUNYNY14260 United States Department of Psychology Drexel University Perelman School of Medicine University of Pennsylvania PA19104 United States

This paper introduces a clustering framework for networks with nodes are annotated with time-series data. The framework addresses all types of network-clustering problems: State clustering, node clustering within states (a.k.a. topology identification or community detection), and even subnetwork-state-sequence identification/tracking. Via a bottom-up approach, features are first extracted from the raw nodal time-series data by kernel autoregressive-moving-average modeling to reveal non-linear dependencies and low-rank representations, and then mapped onto the Grassmann manifold (Grassmannian). All clustering tasks are performed by leveraging the underlying Riemannian geometry of the Grassmannian in a novel way. To validate the proposed framework, brain-network clustering is considered, where extensive numerical tests on synthetic and real functional Magnetic Resonance Imaging (fMRI) data demonstrate that the advocated learning framework compares favorably versus several state-of-the-art clustering schemes. Copyright © 2020, The Authors. All rights reserved.

关键词： Time series

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

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arXiv 2024年

作者： Evans, Matthew L. Bergsma, Johan Merkys, Andrius Andersen, Casper W. Andersson, Oskar B. Beltrán, Daniel Blokhin, Evgeny Boland, Tara M. Balderas, Rubén Castañeda Choudhary, Kamal Díaz, Alberto Díaz García, Rodrigo Domínguez Eckert, Hagen Eimre, Kristjan Montero, María Elena Fuentes Krajewski, Adam M. Mortensen, Jens Jørgen Duarte, José Manuel Nápoles Pietryga, Jacob Qi, Ji de Jesús Trejo Carrillo, Felipe Vaitkus, Antanas Yu, Jusong Zettel, Adam de Castro, Pedro Baptista Carlsson, Johan Cerqueira, Tiago F.T. Divilov, Simon Hajiyani, Hamidreza Hanke, Felix Jose, Kevin Oses, Corey Riebesell, Janosh Schmidt, Jonathan Winston, Donald Xie, Christen Yang, Xiaoyu Bonella, Sara Botti, Silvana Curtarolo, Stefano Draxl, Claudia Cobas, Luis Edmundo Fuentes Hospital, Adam Liu, Zi-Kui Marques, Miguel A.L. Marzari, Nicola Morris, Andrew J. Ong, Shyue Ping Orozco, Modesto Persson, Kristin A. Thygesen, Kristian S. Wolverton, Chris Scheidgen, Markus Toher, Cormac Conduit, Gareth J. Pizzi, Giovanni Gražulis, Saulius Rignanese, Gian-Marco Armiento, Rickard Chemin des Étoiles 8 Louvain-la-Neuve1348 Belgium Matgenix SRL 185 Rue Armand Bury Gozée6534 Belgium École Polytechnique Fédérale de Lausanne Avenue de Forel 3 Lausanne1015 Switzerland Institute of Biotechnology Life Sciences Center Vilnius University Sauletekio av. 7 VilniusLT-10257 Lithuania SINTEF P.O. Box 4760 Torgarden TrondheimNO-7465 Norway Materials Design and Informatics unit Department of Physics Chemistry and Biology Linköping University Sweden Baldiri i Reixac 10-12 Barcelona08028 Spain Tilde Materials Informatics Straßmannstraße 25 Berlin10249 Germany Materials Platform for Data Science Sepapaja 6 Tallinn15551 Estonia Computational Atomic-Scale Materials Design Technical University of Denmark Kgs. Lyngby Denmark Av. Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua Chih. 31136 Mexico Material Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Center for Extreme Materials Duke University DurhamNC27708 United States École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Universidad Autónoma de Chihuahua Facultad de Ciencias Quimicas Chihuahua31125 Mexico Department of Materials Science and Engineering The Pennsylvania State University University ParkPA16802 United States Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of NanoEngineering University of California 9500 Gilman Drive La Jolla San DiegoCA92093-0448 United States National Institute for Materials Science 1-2-1 Sengen Ibaraki Tsukuba305-0047 Japan Dassault Systèmes Germany GmbH Am Kabellager 11-13 Cologne51063 Germany CFisUC Department of Physics University of Coimbra Rua Larga Coimbra3004-516 Portugal Dassault Systèmes 22 Science Park CB4 0FJ United Kingdom Theory of Condensed Matter Cavendis

The Open databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development. © 2024, CC BY.

关键词： Electronic data interchange

The Minimum Information about CLinical Artificial Intelligence Checklist for Generative Modeling Research (MI-CLAIM-GEN)

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arXiv 2024年

作者： Miao, Brenda Y. Chen, Irene Y. Williams, Christopher Y.K. Davidson, Jaysón Garcia-Agundez, Augusto Sun, Shenghuan Zack, Travis Saria, Suchi Arnaout, Rima Quer, Giorgio Sadaei, Hossein J. Torkamani, Ali Beaulieu-Jones, Brett Yu, Bin Gianfrancesco, Milena Butte, Atul J. Norgeot, Beau Sushil, Madhumita Bakar Computational Health Sciences Institute University of California San Francisco San FranciscoCA United States UCSF-UC Berkeley Joint Program in Computational Precision Health University of California Berkeley University of California San Francisco BerkeleyCA United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA United States Berkeley AI Research University of California Berkeley BerkeleyCA United States Department of Medicine Division of Rheumatology University of California San Francisco San FranciscoCA United States Helen Diller Family Comprehensive Cancer Center University of California San Francisco San FranciscoCA United States Center for Data-driven Insights and Innovation University of California Office of the President OaklandCA United States Bayesian Health New YorkNY10282 United States Department of Computer Science Johns Hopkins University Whiting School of Engineering BaltimoreMD United States Department of Health Policy & Management Johns Hopkins University Bloomberg School of Public Health BaltimoreMD United States Department of Medicine Johns Hopkins Medicine BaltimoreMD21205 United States Departments of Medicine Radiology and Pediatrics University of California San Francisco San FranciscoCA United States Scripps Research Translational Institute La Jolla CA United States Department of Integrative Structural and Computational Biology Scripps Research La Jolla CA92037 United States Department of Medicine University of Chicago ChicagoIL United States Department of Statistics University of California Berkeley BerkeleyCA United States Center for Computational Biology University of California Berkeley BerkeleyCA United States Qualified Health PBC Palo AltoCA United States

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research. © 2024, CC BY.

关键词： Generative adversarial networks

Generative models of simultaneously heavy-tailed distributions of inter-event times on nodes and edges

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arXiv 2020年

作者： dos Reis, Elohim Fonseca Li, Aming Masuda, Naoki Department of Mathematics State University of New York at Buffalo BuffaloNY United States Department of Zoology University of Oxford Oxford United Kingdom Department of Biochemistry University ofOxford Oxford United Kingdom Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY United States

Intervals between discrete events representing human activities, as well as other types of events, often obey heavy-tailed distributions, and their impacts on collective dynamics on networks such as contagion processes have been intensively studied. The literature supports that such heavy-tailed distributions are present for inter-event times associated with both individual nodes and individual edges in networks. However, the simultaneous presence of heavy-tailed distributions of inter-event times for nodes and edges is a non-trivial phenomenon, and its origin has been elusive. In the present study, we propose a generative model and its variants to explain this phenomenon. We assume that each node independently transits between a high-activity and low-activity state according to a continuous-time two-state Markov process and that, for the main model, events on an edge occur at a high rate if and only if both end nodes of the edge are in the high-activity state. In other words, two nodes interact frequently only when both nodes prefer to interact with others. The model produces distributions of inter-event times for both individual nodes and edges that resemble heavy-tailed distributions across some scales. It also produces positive correlation in consecutive inter-event times, which is another stylized observation for empirical data of human activity. We expect that our modeling framework provides a useful benchmark for investigating dynamics on temporal networks driven by non-Poissonian event sequences. Copyright © 2020, The Authors. All rights reserved.

关键词： Continuous time systems

Can Primal Methods Outperform Primal-dual Methods in Decentralized Dynamic Optimization?

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arXiv 2020年

作者： Yuan, Kun Xu, Wei Ling, Qing Department of Electrical and Computer Engineering University of California Los Angeles Department of Automation University of Science and Technology of China. School of Data and Computer Science Guangdong Province Key Laboratory of Computational Science Sun Yat-Sen University NSF China Grants Fundamental Research Funds Central Universities Asilomar Conference on Signals Systems and Computers Pacific Grove61573331 and 61973324 United States

In this paper, we consider the decentralized dynamic optimization problem defined over a multi-agent network. Each agent possesses a time-varying local objective function, and all agents aim to collaboratively track the drifting global optimal solution that minimizes the summation of all local objective functions. The decentralized dynamic optimization problem can be solved by primal or primal-dual methods, and when the problem degenerates to be static, it has been proved in literature that primal-dual methods are superior to primal ones. This motivates us to ask: are primal-dual methods necessarily better than primal ones in decentralized dynamic optimization? To answer this question, we investigate and compare convergence properties of the primal method, diffusion, and the primal-dual approach, decentralized gradient tracking (DGT). Theoretical analysis reveals that diffusion can outperform DGT in certain dynamic settings. We find that DGT and diffusion are significantly affected by the drifts and the magnitudes of optimal gradients, respectively. In addition, we show that DGT is more sensitive to the network topology, and a badly-connected network can greatly deteriorate its convergence performance. These conclusions provide guidelines on how to choose proper dynamic algorithms in various application scenarios. Numerical experiments are constructed to validate the theoretical analysis. Copyright © 2020, The Authors. All rights reserved.

关键词： Diffusion

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Ball k-means

arXiv 2020年

作者： Xia, Shuyin Peng, Daowan Meng, Deyu Zhang, Changqing Wang, Guoyin Chen, Zizhong Wei, Wei Department of Chongqing Key Laboratory of Computational Intelligence Chongqing University of Posts and Telecommunications Chongqing400065 China National Engineering Laboratory for Algorithm and Analysis Technologiy on Big Data Xian Jiaotong University Xi'an710049 China College of Intelligence and Computing Tianjin University 300072 China Department of Computer Science and Engineering University of California Riverside 900 University Avenue RiversideCA92521 United States School of Computer Science and Engineering Xi'an University of Technology Xi'an710048 China

This paper presents a novel accelerated exact k-means algorithm called the Ball k-means algorithm, which uses a ball to describe a cluster, focusing on reducing the point-centroid distance computation. The Ball k-means can accurately find the neighbor clusters for each cluster resulting distance computations only between a point and its neighbor clusters centroids instead of all centroids. Moreover, each cluster can be divided into a stable area and an active area, and the later one can be further divided into annulus areas. The assigned cluster of the points in the stable area is not changed in the current iteration while the points in the annulus area will be adjusted within a few neighbor clusters in the current iteration. Also, there are no upper or lower bounds in the proposed Ball k-means. Furthermore, reducing centroid-centroid distance computation between iterations makes it efficient for large k clustering. The fast speed, no extra parameters and simple design of the Ball k-means make it an all-around replacement of the naive k-means algorithm. Copyright © 2020, The Authors. All rights reserved.

关键词： K-means clustering

Genes and comorbidities of thyroid cancer

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Informatics in Medicine Unlocked 2021年 25卷

作者： Ljubic, Branimir Pavlovski, Martin Roychoudhury, Shoumik Van Neste, Christophe Salhi, Adil Essack, Magbubah Bajic, Vladimir B. Obradovic, Zoran Temple University Center for Data Analytics and Biomedical Informatics (DABI) Philadelphia 19122 PA United States Rutgers University the Office of Advanced Research Computing (OARC) Piscataway 08854 NJ United States Center for Medical Genetics (CMGG) Ghent University Ghent Belgium King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Center (CBRC) Computer Electrical and Mathematical Science and Engineering (CEMSE) Division Thuwal Saudi Arabia

Introduction: Thyroid cancer represents 3.1 % of diagnosed cancers in the United States. The objective of this research was to identify comorbidities and discover additional genes potentially related to thyroid cancer and improve current knowledge of genetics and comorbidities associated with this cancer. Methods: Healthcare Cost and Utilization Project (HCUP) California State Inpatient database (SID) was used to extract and rank the comorbidities of thyroid cancer. The text mining software - BeFree was utilized to identify and extract genes associated with thyroid cancer and the comorbidities from PubMed abstracts and the DisGeNET expert-curated repositories. Results: Female patients had 4,485, and male patients 2912 different comorbidities in early stages of thyroid cancer. Females had 3,587, and males 2817 different comorbidities in advanced stages. Through PubMed utilizing the BeFree method, 504 different genes associated with thyroid cancer were discovered, as well as five genes on DisGeNET. The most often genes on PubMed, associated with thyroid cancer were: BRAF, RET, SLC5A5, RAS, and PTEN. Genes found via DisGeNET were BRAF, RET, KRAS, NRAS, and PRKAR1A. Conclusion: Identified genes and comorbidities, as potential additional risk factors for thyroid cancer, not previously known, could improve the early diagnosis and the survival of patients with thyroid cancer. Genes discovered in this research in association with thyroid cancer could be used to direct decision making for optimal, more personalized treatment of thyroid cancer. © 2021

关键词： Biomedical informatics Comorbidities DisGeNET Genes Text mining Thyroid cancer

Small inter-event times govern epidemic spreading on networks

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Physical Review Research 2020年第2期2卷 023163-023163页

作者： Naoki Masuda Petter Holme Department of Mathematics University at Buffalo State University of New York Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York Buffalo New York 14260-5030 USA Tokyo Tech World Research Hub Initiative (WRHI) Institute of Innovative Research Tokyo Institute of Technology Yokohama 226-8503 Japan

Many aspects of human and animal interaction, such as the frequency of contacts of an individual, the number of interaction partners, and the time between the contacts of two individuals, are characterized by heavy-tailed distributions. These distributions affect the spreading of, e.g., infectious diseases or rumors, often because of impacts of the right tail of the distributions (i.e., the large values). In this paper we show that when it comes to inter-event time distributions, it is not the tail but the small values that control spreading dynamics. We investigate this effect both analytically and numerically for different versions of the susceptible-infected-recovered model on different types of networks.

关键词： Epidemic Epidemic evolution Epidemic growth Epidemic prevalence

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

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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