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arXiv 2022年

作者： Kaya, Yaren Bilge Mantell, Sophia Lee Maass, Kayse Konrad, Renata Trapp, Andrew C. Dimas, Geri L. Dank, Meredith Mechanical and Industrial Engineering Northeastern University 360 Huntington Ave BostonMA02115 United States School of Business Worcester Polytechnic Institute 100 Institute Rd WorcesterMA01609 United States Data Science Program Worcester Polytechnic Institute 100 Institute Rd WorcesterMA01609 United States Marron Institute of Urban Management New York University 60 5th Ave 2nd floor New YorkNY10011 United States

The New York City (NYC) youth shelter system provides housing, counseling, and other support services to runaway and homeless youth and young adults (RHY). These resources reduce RHY's vulnerability to human trafficking, yet most shelters are unable to meet demand. This paper presents a Discrete Event Simulation (DES) model of a crisis-emergency and drop-in center for LGBTQ+ youth in NYC, which aims to analyze the current operations and test potential capacity expansion interventions. The model uses data from publicly available resources and interviews with service providers and key stakeholders. The simulated shelter has 66 crisis-emergency beds, offers five different support services, and serves on average 1,399 LGBTQ+ RHY per year. The capacity expansion interventions examined in this paper are adding crisis-emergency beds and psychiatric therapists. This application of DES serves as a tool to communicate with policymakers, funders, and service providers-potentially having a strong humanitarian impact. © 2022, CC BY-NC-SA.

关键词： Discrete event simulation

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An artificial intelligence method for vessel detection in images of cardiac catheterization

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Informatics in Medicine Unlocked 2023年 39卷

作者： Chien, Ting-Ying Ting, Hsien-Wei Li, Hao-Wei Chang, Hsiao-Huang Department of Computer Science and Engineering Yuan Ze University 320 Taoyuan City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University 320 Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University 320 Taoyuan City Taiwan Department of Neurosurgery Taipei Hospital Ministry of Health and Welfare 242 New Taipei City Taiwan Division of Cardiovascular Surgery Department of Surgery Taipei Veterans General Hospital Taipei 11217 Taiwan Department of Surgery School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan

Coronary artery disease (CAD) is one of the top ten leading causes of death in countries worldwide. There are several methods used by physicians to diagnose CAD. One common method is the use of X-ray angiogram (XRA) images. When employing a computer-aided automatic analysis method to locate blood vessels in XRA images, problems such as complex background noise, low contrast, and difficulty in separating blood vessels from the background are encountered, especially for blood vessels with a low contrast to the background noise. In this study, we used various image preprocessing methods to highlight blood vessels from complex backgrounds and different types of blood vessel, followed by the employment of four superpixel segmentation methods to partition an image into multiple segments, and finally the utilization of Weighted Voting to determine the best superpixel algorithm. A genetic algorithm was used to identify the best weights by which to determine the locations of blood vessels in images of cardiac catheterization. Our proposed method achieved an average F1-score of 73.4% in the analysis of five patients, which was better than the other superpixel algorithms tested. The results of this research will be helpful for future SYNTAX score analysis. © 2023

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Abnormal Scanning Patterns Based on Eye Movement Entropy in Early Psychosis

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Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 2024年

作者： Zhang, Dan Ma, Chunyan Xu, Lihua Liu, Xu Cui, Huiru Wei, Yanyan Zheng, Wensi Hong, Yawen Xie, Yuou Qian, Zhenying Hu, Yegang Tang, Yingying Li, Chunbo Liu, Zhi Chen, Tao Liu, Haichun Zhang, Tianhong Wang, Jijun Shanghai Key Laboratory of Psychotic Disorders Shanghai Mental Health Center Shanghai Jiao Tong University School of Medicine People's Republic of China Shanghai China First Clinical Medical College of Nanjing Medical University People's Republic of China Nanjing China Shanghai Institute for Advanced Communication and Data Science Shanghai University People's Republic of China Shanghai China School of Communication and Information Engineering Shanghai University People's Republic of China Shanghai China Labor and Worklife Program Harvard University Cambridge Massachusetts United States Big Data Research Laboratory University of Waterloo Waterloo ON Canada Niacin (Shanghai) Technology Co. Ltd. People's Republic of China Shanghai China Department of Automation Shanghai Jiao Tong University People's Republic of China Shanghai China Shanghai Mental Health Center Shanghai Engineering Research Center of Intelligent Psychological Evaluation and Intervention Shanghai Key Laboratory of Psychotic Disorders Shanghai Jiaotong University School of Medicine People's Republic of China Shanghai China CAS Center for Excellence in Brain Science and Intelligence Technology Chinese Academy of Sciences People's Republic of China Shanghai China Institute of Psychology and Behavioral Science Shanghai Jiao Tong University People's Republic of China Shanghai China

Background: Restricted scan path mode is hypothesized to explain abnormal scanning patterns in patients with schizophrenia. Here, we calculated entropy scores (drawing on gaze data to measure the statistical randomness of eye movements) to quantify how strategical and random participants were when processing image stimuli. Methods: Eighty-six patients with first-episode schizophrenia (FES), 124 individuals at clinical high risk (CHR) for psychosis, and 115 healthy control participants (HCs) completed an eye-tracking examination while freely viewing 35 static images (each presented for 10 seconds) and cognitive assessments. We compared group differences in the overall entropy score, as well as entropy scores under various conditions. We also investigated the correlations between entropy scores and symptoms and cognitive function. Results: Increased overall entropy scores were noted in the FES and CHR groups compared with the HC group, and these differences were already apparent within 0 to 2.5 seconds. In addition, the CHR group exhibited higher entropy than the HC group when viewing low-meaning images. Moreover, the entropy within 0 to 2.5 seconds showed significant correlations with negative symptoms in the FES group, attention/vigilance scores in the CHR group, and speed of processing and attention/vigilance scores across all 3 groups. Conclusions: The results indicate that individuals with FES and those at CHR scanned pictures more randomly and less strategically than HCs. These patterns also correlated with clinical symptoms and neurocognition. The current study highlights the potential of the eye movement entropy measure as a neurophysiological marker for early psychosis. © 2024 Society of Biological Psychiatry

关键词： Biomarker Clinical high risk for psychosis Cognitive impairments Early psychosis Eye movement Schizophrenia

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MedRep: Medical Concept Representation for General Electronic Health Record Foundation Models

arXiv

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arXiv 2025年

作者： Kim, Junmo Lee, Namkyeong Kim, Jiwon Kim, Kwangsoo Interdisciplinary Program in Bioengineering Seoul National University Korea Republic of Dept. of Industrial and Systems Engineering KAIST Korea Republic of Interdisciplinary Program of Medical Informatics Seoul National University Korea Republic of Dept. of Transdisciplinary Medicine ICMIT Seoul National University Hospital Korea Republic of Center for Data Science Healthcare AI Research Institute Seoul National University Hospital Korea Republic of Dept. of Medicine College of Medicine Seoul National University Korea Republic of

Electronic health record (EHR) foundation models have been an area ripe for exploration with their improved performance in various medical tasks. Despite the rapid advances, there exists a fundamental limitation: Processing unseen medical codes out of the vocabulary. This problem limits the generality of EHR foundation models and the integration of models trained with different vocabularies. To deal with this problem, we propose MedRep for EHR foundation models based on the observational medical outcome partnership (OMOP) common data model (CDM), providing the integrated medical concept representations and the basic data augmentation strategy for patient trajectories. For concept representation learning, we enrich the information of each concept with a minimal definition through large language model (LLM) prompts and enhance the text-based representations through graph ontology of OMOP vocabulary. Trajectory augmentation randomly replaces selected concepts with other similar concepts that have closely related representations to let the model practice with the concepts out-of-vocabulary. Finally, we demonstrate that EHR foundation models trained with MedRep better maintain the prediction performance in external datasets. Our code implementation is publicly available at https://***/kicarussays/MedRep. Copyright © 2025, The Authors. All rights reserved.

关键词： Electronic health record

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Biases in inverse Ising estimates of near-critical behavior

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Physical Review E 2023年第1期108卷 014109-014109页

作者： Maximilian B. Kloucek Thomas Machon Shogo Kajimura C. Patrick Royall Naoki Masuda Francesco Turci School of Physics HH Wills Physics Laboratory University of Bristol Tyndall Avenue Bristol BS8 1TL United Kingdom Bristol Centre for Functional Nanomaterials HH Wills Physics Laboratory University of Bristol Tyndall Avenue Bristol BS8 1TL United Kingdom Faculty of Information and Human Sciences Kyoto Institute of Technology Kyoto 606-8585 Japan Gulliver UMR CNRS 7083 ESPCI Paris Université PSL 75005 Paris France Department of Mathematics State University of New York at Buffalo Buffalo New York 14260-2900 USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo New York 14260-5030 USA

Inverse Ising inference allows pairwise interactions of complex binary systems to be reconstructed from empirical correlations. Typical estimators used for this inference, such as pseudo-likelihood maximization (PLM), are biased. Using the Sherrington-Kirkpatrick model as a benchmark, we show that these biases are large in critical regimes close to phase boundaries, and they may alter the qualitative interpretation of the inferred model. In particular, we show that the small-sample bias causes models inferred through PLM to appear closer to criticality than one would expect from the data. data-driven methods to correct this bias are explored and applied to a functional magnetic resonance imaging data set from neuroscience. Our results indicate that additional care should be taken when attributing criticality to real-world data sets.

关键词： Critical phenomena Cortical networks Spin glasses Functional magnetic resonance imaging Ising model

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Smart IoT CPO Storage Tank

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： Rengga Arnalis Renjani Hermantoro Prima Okta Adi Nugraha Kartika Purwandari Teddy Suparyanto Bens Pardamean Department of Agricultural Engineering Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Indonesia's crude palm oil (CPO) production from year to year continues to increase, at the end of 2020 it reached 17.35 million tons, up 3.6% from the previous year. Increasing production will result in more CPO stock and require good storage. The storage process that occurs is to maintain the temperature of the CPO so that the quality is not damaged. This temperature regulation is still done manually and raises the risk of work accidents. The purpose of this research is to create a temperature control system and automatic volume measurement that can be monitored from a smartphone. The manufacture of a control system used ESP8266 NodeMCu microcontroller, temperature sensor, proximity sensor, and 1000-Watt heater. programming used the Arduino IDE and C++. The result of this study was an IoT CPO Storage Tank design equipped with sensors and microcontrollers. The temperature was measured with the DS18B20 sensor had a data accuracy of 99.19% while the volume measured with the HC-SR04 sensor had an accuracy of 99.78%. data obtained from the sensor could be seen through the Thingspeak application from a computer or smartphone.

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Real-time Weed Identification Using Machine Learning and Image Processing in Oil Palm Plantations

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： Erick Firmansyah Teddy Suparyanto Alam Ahmad Hidayat Bens Pardamean Agricultural Engineering Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The effectiveness and efficiency of the operation of oil palm plantations are considered to be the most crucial factor to develop the productivity and profitability of the palm oil business. One of the major obstacles for the plants to optimally produce crops based on their capacity is caused by the presence of noxious weeds in the plantation area. However, weed control via chemical processes may potentially harm the surrounding environment if it is not properly managed. Therefore, an automatic system to assist the farmers to identify and control the weeds is required to minimize harmful impacts on the environment. Machine Learning (ML) and Artificial Intelligence (AI)-based systems provide powerful tools to perform such tasks. In this work, we aim for an ML-based system design to perform an automatic weed recognition task. The methodology can provide an effort for environmental sustainability in oil palm plantations. The weed identification involves the description, the local names, and tolerance class of the weeds as well as suggestions to control them. The flow of this work consists of weed and herbicide data acquisition, data labeling, model configurations, and data training. Further, the proposed system can be adopted as an android-based application in mobile devices that can deploy the trained model to predict weed category in both real-time and non-real-time tasks.

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Correction to: Mitigation strategies against cascading failures within a project activity network

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Journal of Computational Social science 2021年第1期5卷 1097-1098页

作者： Ellinas, Christos Nicolaides, Christos Masuda, Naoki Nodes and Links Ltd Cambridge UK Department of Business and Public Administration University of Cyprus Nicosia Cyprus Initiative on the Digital Economy Massachusetts Institute of Technology Cambridge USA Department of Mathematics State University of New York at Buffalo Buffalo USA Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo Buffalo USA Faculty of Management and Economics Dalian University of Technology Dalian China

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HRnV-Calc: A software package for heart rate n-variability and heart rate variability analysis

arXiv

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arXiv 2021年

作者： Niu, Chenglin Guo, Dagang Hock Ong, Marcus Eng Koh, Zhi Xiong Wah Ho, Andrew Fu Lin, Zhiping Liu, Chengyu Clifford, Gari D. Liu, Nan Duke-NUS Medical School National University of Singapore Singapore Singapore Department of Emergency Medicine Singapore General Hospital Singapore Singapore School of Electrical and Electronic Engineering Nanyang Technological University Singapore School of Instrument Science and Engineering Southeast University Nanjing China Department of Biomedical Informatics Emory University AtlantaGA United States Department of Biomedical Engineering Georgia Institute of Technology AtlantaGA United States SingHealth AI Health Program Singapore Health Services Singapore Singapore Institute of Data Science National University of Singapore Singapore Singapore

Objective: Heart rate variability (HRV) has been proven to be an important indicator of physiological status for numerous applications. Despite the progress and active developments made in HRV metric research over the last few decades, the representation of the heartbeat sequence upon which HRV is based has received relatively little attention. The recently introduced heart rate n-variability (HRnV) offers an alternative to R-to-R peak interval representations which complements conventional HRV analysis by considering HRV behavior on varying scales. Although HRnV has been shown to improve triage in pilot studies, there is currently no open and standard software to support future research of HRnV and its broader clinical applications. We aimed to develop an open, reliable, and easy to use software package implementing HRnV for further research and improvements of HRnV. This package has been designed to facilitate collaborative investigations between clinicians and researchers to study HRnV in various contexts and applications. Approach: We developed an open-source software, HRnV-Calc, based on the PhysioNet Cardiovascular Signal Toolbox (PCST), which features comprehensive graphical user interfaces (GUIs) for HRnV and HRV analysis. Main results: While preserving the core functionalities and performance of PCST, HRnV-Calc enables step-by-step manual inspection and configuration of HRV and HRnV analysis, so that results can be debugged, easily interpreted, and integrated to downstream applications. Significance: The open-source HRnV-Calc software, an accessible and standardized HRV and HRnV analysis platform, enhances the scope of HRV assessment and is designed to assist in future improvements and applications of HRnV and related research. © 2021, CC BY.

关键词： Heart

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Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology

Research Square

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Research Square 2021年

作者： Cai, Tian Xie, Li Chen, Muge Liu, Yang He, Di Zhang, Shuo Mura, Cameron Bourne, Philip E. Xie, Lei Ph.D. Program in Computer Science The Graduate Center The City University of New York New York10016 United States Department of Computer Science Hunter College The City University of New York New York10065 United States Master Program in Computer Science Courant Institute of Mathematical Sciences New York University United States School of Data Science Department of Biomedical Engineering University of Virginia VA22903 United States Helen and Robert Appel Alzheimer’s Disease Research Institute Feil Family Brain & Mind Research Institute Weill Cornell Medicine Cornell University New York10021 United States

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning, to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) problem in statistical machine learning. Here, we have implemented Portal Learning to predict chemical-protein interactions on a genome-wide scale. Systematic studies demonstrate that Portal Learning can effectively assign ligands to unexplored gene families (unknown functions), versus existing state-of-the-art methods. Compared with AlphaFold2-based protein-ligand docking, Portal Learning significantly improved the performance by 79% in PR-AUC and 27% in ROC-AUC, respectively. The superior performance of Portal Learning allowed us to target previously "undruggable" proteins and design novel polypharmacological agents for disrupting interactions between SARS-CoV-2 and human proteins. Portal Learning is general-purpose and can be further applied to other areas of scientific inquiry. © 2021, CC BY.

关键词： Coronavirus

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