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arXiv 2023年

作者： Sivarajkumar, Sonish Tandale, Pratyush Bhardwaj, Ankit Johnson, Kipp W. Titus, Anoop Glicksberg, Benjamin S. Khader, Shameer Yadav, Kamlesh K. Subramanian, Lakshminarayanan Molecular Robotics Kerala India School of Computing and Information University of Pittsburgh Pennsylvania PA United States Health Informatics & Data Science Georgetown University WashingtonDC United States Department of Computer Science Courant Institute of Mathematical Sciences New York University New YorkNY United States Institute for Next Generation Healthcare Mount Sinai Health System New YorkNY United States Department of Preventive Cardiology DeBakey Heart & Vascular Center Houston Methodist HoustonTX United States Hasso Plattner Institute for Digital Health Icahn School of Medicine at Mount Sinai New YorkNY United States Faculty of Medicine Imperial College London London United Kingdom School of Engineering Medicine Texas A&M University HoustonTX United States Department of Translational Medical Sciences Center for Genomic and Precision Medicine Texas A&M University HoustonTX United States

Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using data extracted from the STRING database. A TF cascade is a sequence of TFs that regulate each other, forming a directed path in the TF network. We constructed a knowledge graph of 81,488 unique TF cascades, with the longest cascade consisting of 62 TFs. Our results highlight the complex and intricate nature of TF interactions, where multiple TFs work together to regulate gene expression. We also identified 10 TFs with the highest regulatory influence based on centrality measurements, providing valuable information for researchers interested in studying specific TFs. Furthermore, our pathway enrichment analysis revealed significant enrichment of various pathways and functional categories, including those involved in cancer and other diseases, as well as those involved in development, differentiation, and cell signaling. The enriched pathways identified in this study may have potential as targets for therapeutic intervention in diseases associated with dysregulation of transcription factors. We have released the dataset, knowledge graph, and graphML methods for the TF cascades, and created a website to display the results, which can be accessed by researchers interested in using this dataset. Our study provides a valuable resource for understanding the complex network of interactions between TFs and their regulatory roles in cellular processes. Copyright © 2023, The Authors. All rights reserved.

关键词： Transcription factors

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Reflections from the Workshop on AI-Assisted Decision Making for Conservation

arXiv

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arXiv 2023年

作者： Xu, Lily Rolf, Esther Beery, Sara Bennett, Joseph R. Berger-Wolf, Tanya Birch, Tanya Bondi-Kelly, Elizabeth Brashares, Justin Chapman, Melissa Corso, Anthony Davies, Andrew Garg, Nikhil Gaylard, Angela Heilmayr, Robert Kerner, Hannah Klemmer, Konstantin Kumar, Vipin MacKey, Lester Monteleoni, Claire Moorcroft, Paul Palmer, Jonathan Perrault, Andrew Thau, David Tambe, Milind School of Engineering and Applied Sciences Harvard University United States Harvard University United States United States Department of Computer Science University of Colorado Boulder United States Electrical Engineering and Computer Science Massachusetts Institute of Technology United States Department of Biology Carleton University Canada Department of Computer Science and Engineering The Ohio State University United States Department of Electrical and Computer Engineering The Ohio State University United States Department of Evolution Ecology and Organismal Biology The Ohio State University United States Translational Data Analytics Institute The Ohio State University United States Google United States Electrical Engineering and Computer Science University of Michigan United States Department of Environmental Science Policy and Management University of California Berkeley United States Department of Aeronautics and Astronautics Stanford University United States Department of Organismic and Evolutionary Biology Harvard University United States Operations Research and Information Engineering Cornell Tech United States African Parks South Africa Bren School of Environmental Science and Management University of California Santa Barbara United States School of Computing and Augmented Intelligence Arizona State University United States Microsoft Research United States Department of Computer Science and Engineering University of Minnesota United States Inria Paris France United States Wwf Global Science United States

In this white paper, we synthesize key points made during presentations and discussions from the AI-Assisted Decision Making for Conservation workshop, hosted by the Center for Research on Computation and Society at Harvard University on October 20-21, 2022. We identify key open research questions in resource allocation, planning, and interventions for biodiversity conservation, highlighting conservation challenges that not only require AI solutions, but also require novel methodological advances. In addition to providing a summary of the workshop talks and discussions, we hope this document serves as a call-to-action to orient the expansion of algorithmic decision-making approaches to prioritize real-world conservation challenges, through collaborative efforts of ecologists, conservation decision-makers, and AI researchers. Copyright © 2023, The Authors. All rights reserved.

关键词： Conservation

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229TiP A phase II trial of a neural network-based treatment decision support tool in patients (pts) with refractory solid organ malignancies

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Annals of Oncology 2024年 35卷 S307-S308页

作者： R.J. Walsh A. Jayagopal T.Z. Tan J. Pitt R. Sundar S.C. Lee B-C. Goh V. Rajan D.S. Tan A.D. Jeyasekharan Department of Haematology-Oncology National University Cancer Institute Singapore Singapore Department of Information Systems and Analytics School of Computing NUS - National University of Singapore Singapore Genomics and Data Analytics Cancer Science Institute (CSI) - National University of Singapore (NUS) Singapore National University Singapore Cancer Science Institute (CSI) - National University of Singapore (NUS) Singapore Medical Oncology Department NUHS - National University Health System Singapore

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The EMPOWER blended digital intervention for relapse prevention in schizophrenia: a feasibility cluster randomised controlled trial in Scotland and Australia

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The Lancet Psychiatry 2022年第6期9卷 477-486页

作者： Gumley, Andrew I Bradstreet, Simon Ainsworth, John Allan, Stephanie Alvarez-Jimenez, Mario Aucott, Lorna Birchwood, Maximillian Briggs, Andrew Bucci, Sandra Cotton, Sue M Engel, Lidia French, Paul Lederman, Reeva Lewis, Shôn Machin, Matthew MacLennan, Graeme McLeod, Hamish McMeekin, Nicola Mihalopoulos, Cathy Morton, Emma Norrie, John Schwannauer, Matthias Singh, Swaran P Sundram, Suresh Thompson, Andrew Williams, Chris Yung, Alison R Farhall, John Gleeson, John Glasgow Institute of Health and Wellbeing University of Glasgow Glasgow United Kingdom Division of Psychology and Mental Health School of Health Sciences Faculty of Biology Medicine and Health Manchester Academic Health Science Centre University of Manchester Manchester United Kingdom Division of Informatics Imaging and Data Sciences School of Health Sciences Faculty of Biology Medicine and Health Manchester Academic Health Science Centre University of Manchester Manchester United Kingdom Orygen Melbourne Melbourne VIC Australia Centre for Youth Mental Health University of Melbourne Melbourne VIC Australia School of Computing and Information Systems Faculty of Engineering and Information Technology University of Melbourne Melbourne VIC Australia Centre for Healthcare Randomised Trials (CHaRT) University of Aberdeen Aberdeen United Kingdom Centre for Mental Health and Wellbeing Research Warwick Medical School University of Warwick Warwick United Kingdom Department of Health Services Research and Policy London School of Hygiene & Tropical Medicine London United Kingdom Greater Manchester Mental Health NHS Foundation Trust Manchester United Kingdom School of Public Health and Preventive Medicine Monash University Melbourne VIC Australia Department of Psychiatry School of Clinical Sciences Monash University Melbourne VIC Australia School of Medicine Deakin University Melbourne VIC Australia Department of Psychiatry Manchester Metropolitan University Manchester United Kingdom Department of Psychiatry University of British Columbia Vancouver BC Canada The Usher Institute University of Edinburgh Edinburgh United Kingdom School for Health in Social Sciences University of Edinburgh Edinburgh United Kingdom Mental Health Program Monash Health Melbourne VIC Australia Department of Psychology and Counselling La Trobe University Melbourne VIC Australia NorthWestern Mental Health The Royal Melbourne Hospital Epping VIC Australia Healthy Brain and Mi

Background: Early warning signs monitoring by service users with schizophrenia has shown promise in preventing relapse but the quality of evidence is low. We aimed to establish the feasibility of undertaking a definitive randomised controlled trial to determine the effectiveness of a blended digital intervention for relapse prevention in schizophrenia. Methods: This multicentre, feasibility, cluster randomised controlled trial aimed to compare Early signs Monitoring to Prevent relapse in psychosis and prOmote Well-being, Engagement, and Recovery (EMPOWER) with treatment as usual in community mental health services (CMHS) in Glasgow and Melbourne. CMHS were the unit of randomisation, selected on the basis of those that probably had five or more care coordinators willing to participate. Participants were eligible if they were older than 16 years, had a schizophrenia or related diagnosis confirmed via case records, were able to provide informed consent, had contact with CMHS, and had had a relapse within the previous 2 years. Participants were randomised within stratified clusters to EMPOWER or to continue their usual approach to care. EMPOWER blended a smartphone for active monitoring of early warning signs with peer support to promote self-management and clinical triage to promote access to relapse prevention. Main outcomes were feasibility, acceptability, usability, and safety, which was assessed through face-to-face interviews. App usage was assessed via the smartphone and self-report. Primary end point was 12 months. Participants, research assistants and other team members involved in delivering the intervention were not masked to treatment conditions. Assessment of relapse was done by an independent adjudication panel masked to randomisation group. The study is registered at ISRCTN (99559262). Findings: We identified and randomised eight CMHS (six in Glasgow and two in Melbourne) comprising 47 care coordinators. We recruited 86 service users between Jan 19 and Au

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Machine learning clustering technique applied to powder X-ray diffraction patterns to distinguish alloy substitutions

arXiv

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arXiv 2018年

作者： Utimula, Keishu Hunkao, Rutchapon Yano, Masao Kimoto, Hiroyuki Hongo, Kenta Kawaguchi, Shogo Suwanna, Sujin Maezono, Ryo School of Materials Science JAIST Asahidai 1-1 Nomi Ishikawa923-1292 Japan Optical and Quantum Physics Laboratory Department of Physics faculty of Science Mahidol University Bangkok10400 Thailand Advanced Material Engineering Div. Toyota Motor Corporation Toyota-cho 1 Toyota Aichi471-8572 Japan Research Center for Advanced Computing Infrastructure JAIST Asahidai 1-1 Nomi Ishikawa923-1292 Japan Center for Materials Research by Information Integration Research and Services Division of Materials Data and Integrated System National Institute for Materials Science Tsukuba305-0047 Japan PRESTO JST Kawaguchi Saitama332-0012 Japan Sayo-gun Hyogo679-5148 Japan Asahidai 1-1 Nomi Ishikawa923-1292 Japan Computational Engineering Applications Unit RIKEN 2-1 Hirosawa Wako Saitama351-0198 Japan

We applied the clustering technique using DTW (dynamic time wrapping) analysis to XRD (X-ray diffraction) spectrum patterns in order to identify the microscopic structures of substituents introduced in the main phase of magnetic alloys. The clustering is found to perform well to identify the concentrations of the substituents with successful rates (∼90%). The sufficient performance is attributed to the nature of DTW processing to filter out irrelevant informations such as the peak intensities (due to the incontrollability of diffraction conditions in polycrystalline samples) and the uniform shift of peak positions (due to the thermal expansions of lattices). The established framework is applicable not limited to the system treated in this work but widely to the systems to be tuned their properties by atomic substitutions within a phase. The framework has larger potential to predict wider properties from observed XRD patterns in a way that it can provide such properties evaluated from predicted microscopic local structure, such as magnetic moments, optical spectrum etc.). Copyright © 2018, The Authors. All rights reserved.

关键词： Cluster analysis

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RETRACTED: Activation-based recurrent learning method for wearable sensor data processing in human activity recognition

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Transactions on Emerging Telecommunications Technologies 2022年第10期35卷

作者： Ching-Hsien Hsu Hao Wu Weiwei Lin Anna Kobusinska Feng Xia School of Mathematics and Big Data Foshan University Foshan China Department of Computer Science and Information Engineering Asia University Taiwan Department of Medical Research China Medical University Hospital China Medical University Taiwan School of Information Science and Engineering Yunnan University Kunming China School of Computer Science and Engineering South China University of Technology Guangzhou China Institute of Computing Science Poznań University of Technology Poznań Poland School of Engineering IT and Physical Sciences Federation University Australia Ballarat Victoria Australia

Human activity recognition using wearable sensors is a universal application for providing additional real-time support in AAL and medical healthcare systems. Input signals and sensor data are analyzed for the features, followed by correlation analysis to achieve better recognition accuracy. In this article, activation-based recurrent learning for human activity detection is introduced. This method is based on recurrent neural networks that pre-classifies the features and extract them for time and rate based on the input signals. Following the pre-classification, the repetitive learning estimates the features for the correlation and activities to reduce false-negative errors in processing. This recurrent process is validated using a conditional activation function and rectified linear unit for joint and concurrent layer processing. The combined processing feature of this proposed method helps to improve the accuracy by 92% and recall by 94.5% by reducing the computation time. The performance of the proposed method is analyzed for six activities, varying iterates, and at time intervals.

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SWEMniCS: a software toolbox for modeling coastal ocean circulation, storm surges, inland, and compound flooding

npj Natural Hazards

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npj Natural Hazards 2024年第1期1卷 1-17页

作者： Clint Dawson Benjamin Pachev Jennifer Proft Eirik Valseth Mark Loveland Oden Institute for Computational Engineering and Sciences The University of Texas at Austin Austin TX USA The Department of Data Science The Norwegian University of Life Science Ås Norway Department of Scientific Computing and Numerical Analysis Simula Research Laboratory Oslo Norway Information and Technology Laboratory Engineering Research and Development Center US Army Corps of Engineers Vicksburg MS USA

Flooding from storm surges, rainfall-runoff, and their interaction into compounding events are major natural hazards in coastal regions. To assess risks of damages to life and properties alike, numerical models are needed to guide emergency responses and future assessments. Numerical models, such as ADCIRC have over many decades shown their usefulness in such assessments. However, these models have a high threshold in terms of new user engagement as development and compilation is not trivial for users trained in compiled programming languages. Here, we develop a new open-source finite element solver for the numerical simulation of flooding. The numerical solution of the underlying PDEs is developed using the finite element framework FEniCSx. The goal is a framework where new methods can be rapidly tested before time-consuming development into codes like ADCIRC. We validate the framework on several test cases, including large-scale computations in the Gulf of Mexico for Hurricane Ike (2008).

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Identification of Causal Relationship between Amyloid-β Accumulation and Alzheimer’s Disease Progression via Counterfactual Inference

arXiv

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arXiv 2023年

作者： Dai, Haixing Hu, Mengxuan Li, Qing Zhang, Lu Zhao, Lin Zhu, Dajiang Diez, Ibai Sepulcre, Jorge Zhang, Fan Gao, Xingyu Liu, Manhua Li, Quanzheng Li, Sheng Liu, Tianming Li, Xiang School of Computing University of Georgia AthensGA United States State Key Lab of Cognitive Neuroscience and Learning Beijing Normal University Beijing100875 China School of Artificial Intelligence Beijing Normal University Beijing100875 China Department of Computer Science and Engineering The University of Texas at Arlington Arlington76019 United States Department of Radiology Massachusetts General Hospital Harvard Medical School Boston02114 United States Department of Radiology Brigham and Women’s Hospital Harvard Medical School Boston02115 United States School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai200240 China The MoE Key Lab of Artificial Intelligence AI Institute Shanghai Jiao Tong University Shanghai200240 China School of Data Science The University of Virginia Charlottesville22903 United States

Alzheimer’s disease (AD) is a neurodegenerative disorder that is beginning with amyloidosis, followed by neuronal loss and deterioration in structure, function, and cognition. The accumulation of amyloid-β in the brain, measured through 18F-florbetapir (AV45) positron emission tomography (PET) imaging, has been widely used for early diagnosis of AD. However, the relationship between amyloid-β accumulation and AD pathophysiology remains unclear, and causal inference approaches are needed to uncover how amyloid-β levels can impact AD development. In this paper, we propose a graph varying coefficient neural network (GVCNet) for estimating the individual treatment effect with continuous treatment levels using a graph convolutional neural network. We highlight the potential of causal inference approaches, including GVCNet, for measuring the regional causal connections between amyloid-β accumulation and AD pathophysiology, which may serve as a robust tool for early diagnosis and tailored care. © 2023, CC BY.

关键词： Neurodegenerative diseases

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Stable quantum memories with limited measurement

arXiv

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arXiv 2017年

作者： Daniel Freeman, C. Sarovar, Mohan Herdman, C.M. Whaley, K.B. Berkeley Quantum Information & Computation Center University of California BerkeleyCA94720 United States Department of Physics University of California BerkeleyCA94720 United States Extreme-scale Data Science and Analytics Sandia National Laboratories LivermoreCA94550 United States Institute for Quantum Computing University of Waterloo WaterlooONN2L 3G1 Canada Department of Chemistry University of Waterloo WaterlooONN2L 3G1 Canada Department of Physics & Astronomy University of Waterloo WaterlooONN2L 3G1 Canada Department of Chemistry University of California BerkeleyCA94720 United States

We demonstrate the existence of a finite temperature threshold for a 1D stabilizer code under an error correcting protocol that requires only a fraction of the syndrome measurements. Below the threshold temperature, encoded states have exponentially long lifetimes, as demonstrated by numerical and analytical arguments. We sketch how this algorithm generalizes to higher dimensional stabilizer codes with string-like excitations, like the toric code. Copyright © 2017, The Authors. All rights reserved.

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COVID-19 mRNA Vaccine Degradation Prediction Using LR and LGBM Algorithms

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Journal of Physics: Conference Series 2021年第1期1997卷

作者： Soon Hwai Ing Azian Azamimi Abdullah Nor Hazlyna Harun Shigehiko Kanaya Faculty of Electronic Engineering Technology Universiti Malaysia Perlis (UniMAP) Perlis Malaysia. Medical Devices and Life Sciences Cluster Sport Engineering Research Centre Centre of Excellence (SERC) Universiti Malaysia Perlis (UniMAP) Perlis Malaysia. Data Science Research Lab School of Computing School of Computing Universiti Utara Malaysia Sintok Kedah. Computational Systems Biology Lab Graduate School of Information Science Nara Institute of Science and Technology Ikoma Nara Japan.

The threatening Coronavirus which was assigned as the global pandemic concussed not only the public health but society, economy and every walks of life. Some measurements are taken to stifle the spread and one of the best ways is to carry out some precautions to prevent the contagion of SARS-CoV-2 virus to uninfected populaces. Injecting prevention vaccines is one of the precaution steps under the grandiose blueprint. Among all vaccines, it is found that mRNA vaccine which shows no side effect with marvellous effectiveness is the most preferable candidates to be considered. However, degradation had become its biggest drawback to be implemented. Hereby, this study is held with desideratum to develop prediction models specifically to predict the degradation rate of mRNA vaccine for COVID-19. Two machine learning algorithms, which are, Linear Regression (LR) and Light Gradient Boosting Machine (LGBM) are proposed for models development using Python language. dataset comprises of thousands of RNA molecules that holds degradation rates at each position from Eterna platform is extracted, pre-processed and encoded with label encoding before loaded into algorithms. The results show that LGBM (0.2447) performs better than LR (0.3957) for this study when evaluated with the RMSE metric.

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