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arXiv 2020年

作者： Zhan, Xiu-Xiu Li, Ziyu Masuda, Naoki Holme, Petter Wang, Huijuan Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Mekelweg 4 Delft2628 CD Netherlands Department of Mathematics University at Buffalo State University of New York Buffalo New YorkNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York Buffalo New YorkNY14260-2900 United States Institute of Innovative Research Tokyo Institute of Technology Yokohama226-8503 Japan

Link prediction can be used to extract missing information, identify spurious interactions as well as forecast network evolution. Network embedding is a methodology to assign coordinates to nodes in a low-dimensional vector space. By embedding nodes into vectors, the link prediction problem can be converted into a similarity comparison task. Nodes with similar embedding vectors are more likely to be connected. Classic network embedding algorithms are random-walk-based. They sample trajectory paths via random walks and generate node pairs from the trajectory paths. The node pair set is further used as the input for a Skip-Gram model, a representative language model that embeds nodes (which are regarded as words) into vectors. In the present study, we propose to replace random walk processes by a spreading process, namely the susceptible-infected (SI) model, to sample paths. Specifically, we propose two SI-spreading-based algorithms, SINE and TSINE, to embed static and temporal networks, respectively. The performance of our algorithms is evaluated by the missing link prediction task in comparison with state-of-the-art static and temporal network embedding algorithms. Results show that SINE and TSINE outperform the baselines across all six empirical datasets. We further find that the performance of SINE is mostly better than TSINE, suggesting that temporal information does not necessarily improve the embedding for missing link prediction. Moreover, we study the effect of the sampling size, quantified as the total length of the trajectory paths, on the performance of the embedding algorithms. The better performance of SINE and TSINE requires a smaller sampling size in comparison with the baseline algorithms. Hence, SI-spreading-based embedding tends to be more applicable to large-scale networks. Copyright © 2020, The Authors. All rights reserved.

关键词： Network embeddings

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Bounded Manifold Completion

arXiv

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arXiv 2019年

作者： Gajamannage, Kelum Paffenroth, Randy Department of Mathematics and Statistics Texas A&M University–Corpus Christi Corpus ChristiTX78412 United States Department of Mathematical Sciences Department of Computer Science and Data Science Program Worcester Polytechnic Institute WorcesterMA01609 United States

Nonlinear dimensionality reduction or, equivalently, the approximation of high-dimensional data using a low-dimensional nonlinear manifold is an active area of research. In this paper, we will present a thematically different approach to detect the existence of a low-dimensional manifold of a given dimension that lies within a set of bounds derived from a given point cloud. A matrix representing the appropriately defined distances on a low-dimensional manifold is low-rank, and our method is based on current techniques for recovering a partially observed matrix from a small set of fully observed entries that can be implemented as a low-rank Matrix Completion (MC) problem. MC methods are currently used to solve challenging real-world problems, such as image inpainting and recommender systems, and we leverage extent efficient optimization techniques that use a nuclear norm convex relaxation as a surrogate for non-convex and discontinuous rank minimization. Our proposed method provides several advantages over current nonlinear dimensionality reduction techniques, with the two most important being theoretical guarantees on the detection of low-dimensional embeddings and robustness to non-uniformity in the sampling of the manifold. We validate the performance of this approach using both a theoretical analysis as well as synthetic and real-world benchmark *** Codes 68T05 Copyright © 2019, The Authors. All rights reserved.

关键词： Relaxation processes

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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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Transfer Learning from Chest X-Ray Pre-trained Convolutional Neural Network for Learning Mammogram data

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Procedia computer science 2018年 135卷 400-407页

作者： Bens Pardamean Tjeng Wawan Cenggoro Reza Rahutomo Arif Budiarto Ettikan Kandasamy Karuppiah Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 NVIDIA Corporation

Breast cancer is one of the deadliest cancer for female nowadays. Despite of the rapid advancement in medical image analysis with the rise of deep learning, development of breast cancer detection system is limited due to relatively small size of the publicly available mammogram dataset. In this paper, we discover an effective configuration for transfer learning from Chest X-Ray pre-trained Convolutional Neural Network to overcome the small-size mammogram dataset problem. We found that the best configuration achieve 90.38% validation accuracy for modified.

关键词： Transfer learning Convolutional neural network Medical image analysis Chest X-ray Mammogram

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Enhancing Suicide Risk Prediction With Polygenic Scores in Psychiatric Emergency Settings: Prospective Study

JMIR Bioinformatics and Biotechnology

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JMIR Bioinformatics and Biotechnology 2024年第1期5卷 e58357页

作者： Lee, Younga Heather Zhang, Yingzhe Kennedy, Chris J. Mallard, Travis T. Liu, Zhaowen Vu, Phuong Linh Feng, Yen-Chen Anne Ge, Tian Petukhova, Maria V. Kessler, Ronald C. Nock, Matthew K. Smoller, Jordan W. Psychiatric & Neurodevelopmental Genetics Unit Center for Genomic Medicine Massachusetts General Hospital Boston MA United States Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA United States Department of Psychiatry Harvard Medical School Boston MA United States Department of Epidemiology Harvard T. H. Chan School of Public Health Boston MA United States Center for Precision Psychiatry Massachusetts General Hospital Boston MA United States School of Computer Science Northwestern Polytechnical University Xi’an China Harvard College Harvard University Cambridge MA United States Institute of Health Data Analytics and Statistics College of Public Health National Taiwan University Taipei Taiwan Department of Health Care Policy Harvard Medical School Boston MA United States Department of Psychology Harvard University Cambridge MA United States Mental Health Research Program Franciscan Children’s Brighton MA United States Department of Psychiatry Massachusetts General Hospital Boston MA United States

Background: Despite growing interest in the clinical translation of polygenic risk scores (PRSs), it remains uncertain to what extent genomic information can enhance the prediction of psychiatric outcomes beyond the data collected during clinical visits alone. Objective: This study aimed to assess the clinical utility of incorporating PRSs into a suicide risk prediction model trained on electronic health records (EHRs) and patient-reported surveys among patients admitted to the emergency department. Methods: Study participants were recruited from the psychiatric emergency department at Massachusetts General Hospital. There were 333 adult patients of European ancestry who had high-quality genotype data available through their participation in the Mass General Brigham Biobank. Multiple neuropsychiatric PRSs were added to a previously validated suicide prediction model in a prospective cohort enrolled between February 4, 2015, and March 13, 2017. data analysis was performed from July 11, 2022, to August 31, 2023. Suicide attempt was defined using diagnostic codes from longitudinal EHRs combined with 6-month follow-up surveys. The clinical risk score for suicide attempt was calculated from an ensemble model trained using an EHR-based suicide risk score and a brief survey, and it was subsequently used to define the baseline model. We generated PRSs for depression, bipolar disorder, schizophrenia, suicide attempt, and externalizing traits using a Bayesian polygenic scoring method for European ancestry participants. Model performance was evaluated using area under the receiver operator curve (AUC), area under the precision-recall curve, and positive predictive values. Results: Of the 333 patients (n=178, 53.5% male;mean age 36.8, SD 13.6 years;n=333, 100% non-Hispanic and n=324, 97.3% self-reported White), 28 (8.4%) had a suicide attempt within 6 months. Adding either the schizophrenia PRS or all PRSs to the baseline model resulted in the numerically highest discrimination

关键词： electronic health record genomics genotypes machine learning polygenic risk score predictive algorithms suicide attempt suicide risk prediction

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The science of Precision Prevention: Research Opportunities and Clinical Applications to Reduce Cardiovascular Health Disparities

JACC: Advances

引用

JACC: Advances 2024年第1期3卷 100759-100759页

作者： Pearson, Thomas A. Vitalis, Debbie Pratt, Charlotte Campo, Rebecca Armoundas, Antonis A. Au, David Beech, Bettina Brazhnik, Olga Chute, Christopher G. Davidson, Karina W. Diez-Roux, Ana V. Fine, Lawrence J. Gabriel, Davera Groenveld, Peter Hall, Jaclyn Hamilton, Alison B. Hu, Hui Ji, Heng Kind, Amy Kraus, William E. Krumholz, Harlan Mensah, George A. Merchant, Raina M. Mozaffarian, Dariush Murray, David M. Neumark-Sztainer, Dianne Petersen, Maya Goff, David College of Medicine and College of Public Health and Health Professions University of Florida Health Science Center Gainesville FL United States Division of Cardiovascular Sciences National Heart Lung and Blood Institute National Institutes of Health Bethesda MD United States Cardiovascular Research Center Massachusetts General Hospital and Broad Institute Massachusetts Institute of Technology Cambridge MA United States Center of Innovation for Veteran-Centered and Value-Driven Care University of Washington Seattle WA United States UH Population Health University of Houston Houston TX United States Johns Hopkins Medicine Institute for Clinical and Translational Research Baltimore MD United States Institute of Health System Science Feinstein Institutes for Medical Research Northwell Health New Hyde Park NY United States Feinstein Institutes for Medical Research Northwell Health Manhasset NY United States Urban Health Collaborative Drexel Dornsife School of Public Health Philadelphia PA United States Biomedical Informatics and Data Science Section Johns Hopkins University School of Medicine Baltimore MD United States Center for Health Care Transformation and Innovation University of Pennsylvania Perelman School of Medicine Philadelphia PA United States Department of Health Outcomes and Biomedical Informatics Institute for Child Health Policy College of Medicine University of Florida Gainesville FL United States Center for the Study of Healthcare Innovation Implementation & Policy VA Greater Los Angeles Healthcare System Los Angeles CA United States Channing Division of Network Medicine Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA United States Department of Computer Science University of Illinois Urbana-Champaign Champaign IL United States Center for Health Disparities Research (CHDR) University of Wisconsin School of Medicine and Public Health Madison WI United States Duke Molecular Physiology Insti

Precision prevention embraces personalized prevention but includes broader factors such as social determinants of health to improve cardiovascular health. The quality, quantity, precision, and diversity of data relatable to individuals and communities continue to expand. New analytical methods can be applied to these data to create tools to attribute risk, which may allow a better understanding of cardiovascular health disparities. Interventions using these analytic tools should be evaluated to establish feasibility and efficacy for addressing cardiovascular disease disparities in diverse individuals and communities. Training in these approaches is important to create the next generation of scientists and practitioners in precision prevention. This state-of-the-art review is based on a workshop convened to identify current gaps in knowledge and methods used in precision prevention intervention research, discuss opportunities to expand trials of implementation science to close the health equity gaps, and expand the education and training of a diverse precision prevention workforce. © 2023 The Authors

关键词： data science health equity health promotion implementation science personalized medicine precision analytics

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An Improved Version of Texture-based Foreground Segmentation: Block-based Adaptive Segmenter

引用

Procedia computer science 2018年 135卷 579-586页

作者： Kahlil Muchtar Faris Rahman Tjeng Wawan Cenggoro Arif Budiarto Bens Pardamean Nodeflux Inc. Jakarta Indonesia Syiah Kuala University Aceh Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Foreground segmentation is one of moving object detection techniques of computer vision applications. To date, modern moving object detection methods require complex background modeling and thresholds tuning to confront illumination changes. This paper proposes an adaptive approach based on non-overlapping block texture representation. It aims to design a computationally light and efficient solution to improve the robustness of detection. We evaluate our proposed method on internal and public sequences and provide the quantitative and qualitative measurements. Experimental results show that the proposed method can improve the results of previous method and suitable for real-time challenges.

关键词： change detection foreground segmentation texture features

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AI-Based Ripeness Grading for Oil Palm Fresh Fruit Bunch in Smart Crane Grabber

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IOP Conference Series: Earth and Environmental science 2020年第1期426卷

作者： Harsawardana Reza Rahutomo Bharuno Mahesworo Tjeng Wawan Cenggoro Arif Budiarto Teddy Suparyanto Don Bosco Surya Atmaja Bayu Samoedro Bens Pardamean Artificial Intelligence Research and Innovation Center for Agroindustry (AIRICA) Institut Pertanian STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Mechatronics and AI Research & Development Center Biotechnic Innovation Yogyakarta Indonesia 55281 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Indonesia is one of the biggest palm oil exporters in the world. For Indonesia to stay competitive in thepalm oil industry, the harvesting and evacuating process in its oil palm plantation need to be optimized. This research introduces machinerycalled as Smart Crane Grabber. This machinery can be used for automatic harvesting and evacuation process of oil palm fresh fruit bunch. To enable automation, Smart Crane Grabber is equipped with an Artificial Intelligencesystem for automatic ripeness sorting. TheArtificial Intelligence system developed for Smart Crane Grabber achieves 71.34% accuracy by using only 400 images as preliminary training data.

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Navigating the challenges in creating complex data systems: a development philosophy

arXiv

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arXiv 2022年

作者： Dittmer, Sören Roberts, Michael Gilbey, Julian Biguri, Ander Preller, Jacobus Rudd, James H.F. Aston, John A.D. Schönlieb, Carola-Bibiane Selby, Ian Breger, Anna Thorpe, Matthew Weir-McCall, Jonathan R. Gkrania-Klotsas, Effrossyni Korhonen, Anna Jefferson, Emily Langs, Georg Yang, Guang Prosch, Helmut Stanczuk, Jan Tang, Jing Babar, Judith Sánchez, Lorena Escudero Teare, Philip Patel, Mishal Wassin, Marcel Holzer, Markus Walton, Nicholas Lió, Pietro Shadbahr, Tolou Sala, Evis Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom Addenbrooke’s Hospital Cambridge University Hospitals NHS Trust Cambridge United Kingdom Department of Medicine University of Cambridge Cambridge United Kingdom Department of Pure Mathematics and Mathematical Statistics University of Cambridge Cambridge United Kingdom ZeTeM University of Bremen Bremen Germany Department of Radiology University of Cambridge Cambridge United Kingdom Faculty of Mathematics University of Vienna Austria Department of Mathematics University of Manchester Manchester United Kingdom Royal Papworth Hospital Cambridge Royal Papworth Hospital NHS Foundation Trust Cambridge United Kingdom Language Technology Laboratory University of Cambridge Cambridge United Kingdom Population Health and Genomics School of Medicine University of Dundee Dundee United Kingdom Department of Biomedical Imaging and Image-guided Therapy Computational Imaging Research Lab Medical University of Vienna Vienna Austria National Heart and Lung Institute Imperial College London London United Kingdom Research Program in Systems Oncology Faculty of Medicine University of Helsinki Helsinki Finland Data Science & Artificial Intelligence AstraZeneca Cambridge United Kingdom Clinical Pharmacology & Safety Sciences AstraZeneca Cambridge United Kingdom Contextflow GmbH Vienna Austria Institute of Astronomy University of Cambridge Cambridge United Kingdom Department of Computer Science and Technology University of Cambridge Cambridge United Kingdom

In this perspective, we argue that despite the democratization of powerful tools for data science and machine learning over the last decade, developing the code for a trustworthy and effective data science system (DSS) is getting harder. Perverse incentives and a lack of widespread software engineering (SE) skills are among many root causes we identify that naturally give rise to the current systemic crisis in reproducibility of DSSs. We analyze why SE and building large complex systems is, in general, hard. Based on these insights, we identify how SE addresses those difficulties and how we can apply and generalize SE methods to construct DSSs that are fit for purpose. We advocate two key development philosophies, namely that one should incrementally grow – not biphasically plan and build – DSSs, and one should always employ two types of feedback loops during development: one which tests the code’s correctness and another that evaluates the code’s efficacy. Copyright © 2022, The Authors. All rights reserved.

关键词： Software engineering

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

引用

database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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