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7th International Conference on Medical and Health informatics, ICMHI 2023

作者： Li, Ai-Hsien Adams Nguyen, Duc-Khanh Lai, Yen-Jun Chien, Ting-Ying Chiu, Yen-Ling Chan, Chien-Lung Yang, Pan-Chyr Division of Cardiology Far Eastern Memorial Hospital Taipei220 Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Department of Information Management Yuan Ze University Taoyuan320 Taiwan Department of Radiology Far Eastern Memorial Hospital Taipei220 Taiwan Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan Graduate Institute of Medicine and Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Department of Medical Research Far Eastern Memorial Hospital Taipei Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan320 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei106 Taiwan Department of Internal Medicine College of Medicine National Taiwan University Taipei100 Taiwan Center of Genomic Medicine National Taiwan University Taipei100 Taiwan

ISBN: (纸本)9798400700712

Lung cancer remains a significant global public health concern, being the leading cause of cancer-related deaths worldwide. Despite recent medical advancements, the disease still has a high mortality rate, making early detection and treatment critical for improving patient outcomes. Accurate prediction of nodule growth is key to early lung cancer treatment, but current assessments offer unclear indications of future growth, leading physicians to recommend costly and anxiety-provoking follow-up appointments every 3 to 12 months. To address this need, this study develops an ensemble deep learning approach that combines demographic data with existing CT images to predict whether lung nodules will grow, potentially reducing unnecessary examinations and easing the burden on patients. Our study, conducted on 862 patients with 1004 nodules, produced promising preliminary results with Accuracy, Sensitivity, Precision, F1 Score, and AUC of 0.66, 0.66, 0.67, 0.66, and 0.71, respectively. The proposed method provides a promising support system to empower patients to make informed decisions about seeking medical attention and helps physicians facilitate early treatment regimens, leading to improved patient outcomes and potentially saving lives. © 2023 ACM.

关键词： Forecasting

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Heightened COVID-19 Mortality in People With Severe Mental Illness Persists After Vaccination: A Cohort Study of Greater Manchester Residents (vol 49, pg 275, 2023)

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SCHIZOPHRENIA BULLETIN 2023年第5期49卷 1399-1403页

作者： Hassan, Lamiece Sawyer, Chelsea Peek, Niels Lovell, Karina Carvalho, Andre F. Solmi, Marco Tilston, George Sperrin, Matthew Firth, Joseph Division of Psychology and Mental Health The University of Manchester Manchester Academic Health Science Centre Manchester M13 9PL UK Centre for Health Informatics Division of Informatics Imaging and Data Sciences The University of Manchester M13 9PL UK NIHR Greater Manchester Patient Safety Translational Research Centre The University of Manchester Manchester UK Manchester Academic Health Science Centre National Institute for Health Research Manchester Biomedical Research Centre The University of Manchester Manchester M13 9PL UK Division of Nursing Midwifery and Social Work University of Manchester Manchester Academic Health Science Centre Manchester M13 9PL UK IMPACT (Innovation in Mental and Physical Health and Clinical Treatment) Strategic Research Centre School of Medicine Barwon Health Deakin University Geelong Victoria Australia Psychiatry Department University of Ottawa Ottawa ON Canada The Ottawa Hospital University of Ottawa Ottawa ON Canada Clinical Epidemiology Program Ottawa Hospital Research Institute (OHRI) University of Ottawa Ottawa ON Canada Greater Manchester Mental Health NHS Foundation Trust Manchester Academic Health Science Centre Manchester M13 9PL UK

Background and hypothesis Previous studies show that people with severe mental illness (SMI) are at higher risk of COVID-19 mortality, however limited evidence exists regarding risk post-vaccination. We investigated COVID-19 mortality among people with schizophrenia and other SMIs before, during and after the UK vaccine roll-out. Study Design Using the Greater Manchester (GM) Care Record to access routinely collected health data linked with death records, we plotted COVID-19 mortality rates over time in GM residents with schizophrenia/psychosis, bipolar disorder (BD) and/or recurrent major depressive disorder (MDD) from February 2020 to September 2021. Multivariable logistic regression was used to compare mortality risk (risk ratios;RRs) between people with SMI (N=190,188) and age-sex matched controls (N=760,752), adjusted for sociodemographic factors, pre-existing comorbidities and vaccination *** Results Mortality risks were significantly higher among people with SMI compared with matched controls, particularly among people with schizophrenia/psychosis (RR 3.14, CI 2.66-3.71) and/or BD (RR 3.17, CI 2.15-4.67). In adjusted models, the relative risk of COVID-19 mortality decreased, though remained significantly higher than matched controls for people with schizophrenia (RR 1.53, CI 1.24-1.88) and BD (RR 2.28, CI 1.49-3.49), but not recurrent MDD (RR 0.92, CI 0.78-1.09). People with SMI continued to show higher mortality rate ratios relative to controls throughout 2021, during vaccination roll-out. Conclusions People with SMI, notably schizophrenia and bipolar disorder, were at greater risk of COVID-19 mortality compared to matched controls. Despite population vaccination efforts that have prioritised people with SMI, disparities still remain in COVID-19 mortality for people with SMI.

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Scalable Numerical Embeddings for Multivariate Time Series: Enhancing Healthcare data Representation Learning

arXiv

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arXiv 2024年

作者： Huang, Chun-Kai Hsieh, Yi-Hsien Chien, Ta-Jung Chien, Li-Cheng Sun, Shao-Hua Su, Tung-Hung Kao, Jia-Horng Lin, Che Taiwan Data Science Degree Program NTU Taiwan Department of Electrical Engineering NTU Taiwan Division of Gastroenterology and Hepatology NTU Hospital Taiwan Hepatitis Research Center NTU Hospital Taiwan Graduate Institute of Clinical Medicine College of Medicine NTU Taiwan Center for Advanced Computing and Imaging in Biomedicine NTU Taiwan Smart Medicine and Health Informatics Program NTU Taiwan

Multivariate time series (MTS) data, when sampled irregularly and asynchronously, often present extensive missing values. Conventional methodologies for MTS analysis tend to rely on temporal embeddings based on timestamps that necessitate subsequent imputations, yet these imputed values frequently deviate substantially from their actual counterparts, thereby compromising prediction accuracy. Furthermore, these methods typically fail to provide robust initial embeddings for values infrequently observed or even absent within the training set, posing significant challenges to model generalizability. In response to these challenges, we propose SCAlable Numerical Embedding (SCANE), a novel framework that treats each feature value as an independent token, effectively bypassing the need for imputation. SCANE regularizes the traits of distinct feature embeddings and enhances representational learning through a scalable embedding mechanism. Coupling SCANE with the Transformer Encoder architecture, we develop the Scalable nUMerical eMbeddIng Transformer (SUMMIT), which is engineered to deliver precise predictive outputs for MTS characterized by prevalent missing entries. Our experimental validation, conducted across three disparate electronic health record (EHR) datasets marked by elevated missing value frequencies, confirms the superior performance of SUMMIT over contemporary state-of-the-art approaches addressing similar challenges. These results substantiate the efficacy of SCANE and SUMMIT, underscoring their potential applicability across a broad spectrum of MTS data analytical tasks. Copyright © 2024, The Authors. All rights reserved.

关键词： Embeddings

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Employing texture features of chest x-ray images and machine learning in covid-19 detection and classification

Mendel

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Mendel 2021年第1期27卷 9-17页

作者： Alquran, Hiam Alsleti, Mohammad Alsharif, Roaa Qasmieh, Isam Abu Alqudah, Ali Mohammad Harun, Nor Hazlyna Binti Department of Biomedical Systems and Informatics Engineering Yarmouk University Irbid21163 Jordan The Institute of Biomedical Technology King Hussein Medical Center Royal Jordanian Medical Service Amman11855 Jordan College of applied medical Sciences Radiological Science Program King Saud University Jeddah21435 Saudi Arabia Data Science Research Lab School of Computing Universiti Utara Malaysia Sintok Kedah06010 Malaysia

The novel coronavirus (nCoV-19) was first detected in December 2019. It had spread worldwide and was declared coronavirus disease (COVID-19) pandemic by March 2020. Patients presented with a wide range of symptoms affecting multiple organ systems predominantly the lungs. Severe cases required intensive care unit (ICU) admissions while there were asymptomatic cases as well. Although early detection of the COVID-19 virus by Real-time reverse transcription-polymerase chain reaction (RT-PCR) is effective, it is not efficient;as there can be false negatives, it is time consuming and expensive. To increase the accuracy of in-vivo detection, radiological image-based methods like a simple chest X-ray (CXR) can be utilized. This reduces the false negatives as compared to solely using the RT-PCR technique. This paper employs various image processing techniques besides extracted texture features from the radiological images and feeds them to different artificial intelligence (AI) scenarios to distinguish between normal, pneumonia, and COVID-19 cases. The best scenario is then adopted to build an automated system that can segment the chest region from the acquired image, enhance the segmented region then extract the texture features, and finally, classify it into one of the three classes. The best overall accuracy achieved is 93.1% by exploiting Ensemble classifier. Utilizing radiological data to conform to a machine learning format reduces the detection time and increase the chances of survival. © 2021, Brno University of Technology. All rights reserved.

关键词： COVID-19

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Machine Learning in Chemoinformatics and Medicinal Chemistry

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Biomedical data science 1000年第1期5卷 43-65页

作者： Raquel Rodríguez-Pérez Filip Miljković Jürgen Bajorath 2Current affiliation: Novartis Institutes for Biomedical Research Novartis Campus Basel Switzerland 1Department of Life Science Informatics B-IT (Bonn-Aachen International Center for Information Technology) Chemical Biology and Medicinal Chemistry Program Unit LIMES (Life and Medical Sciences Institute) Rheinische Friedrich-Wilhelms-Universität Bonn Germany email: bajorath@bit.uni-bonn.de 3Current affiliation: Data Science and AI Imaging and Data Analytics Clinical Pharmacology and Safety Sciences R&D AstraZeneca Gothenburg Sweden

In chemoinformatics and medicinal chemistry, machine learning has evolved into an important approach. In recent years, increasing computational resources and new deep learning algorithms have put machine learning onto a new level, addressing previously unmet challenges in pharmaceutical research. In silico approaches for compound activity predictions, de novo design, and reaction modeling have been further advanced by new algorithmic developments and the emergence of big data in the field. Herein, novel applications of machine learning and deep learning in chemoinformatics and medicinal chemistry are reviewed. Opportunities and challenges for new methods and applications are discussed, placing emphasis on proper baseline comparisons, robust validation methodologies, and new applicability domains.

关键词： machine learning deep learning chemoinformatics medicinal chemistry data structures learning strategies

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graph-GPA 2.0: A Graphical Model for Multi-disease Analysis of GWAS Results with Integration of Functional Annotation data

arXiv

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arXiv 2022年

作者： Deng, Qiaolan Nam, Jin Hyun Yilmaz, Ayse Selen Chang, Won Pietrzak, Maciej Li, Lang Kim, Hang J. Chung, Dongjun The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Division of Big Data Science Korea University Sejong Campus Sejong Korea Republic of Department of Biomedical Informatics The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH United States

Motivation: Genome-wide association studies (GWAS) have successfully identified a large number of genetic variants associated with traits and diseases. However, it still remains challenging to fully understand functional mechanisms underlying many associated variants. This is especially the case when we are interested in variants shared across multiple phenotypes. To address this challenge, we propose graph-GPA 2.0 (GGPA 2.0), a novel statistical framework to integrate GWAS datasets for multiple phenotypes and incorporate functional annotations within a unified framework. Results: First, we conducted simulation studies to evaluate GGPA 2.0. The results indicate that incorporating functional annotation data using GGPA 2.0 does not only improve detection of disease-associated variants, but also allows to identify more accurate relationships among diseases. Second, we analyzed five autoimmune diseases and five psychiatric disorders with the functional annotations derived from GenoSkyline and GenoSkyline-Plus and the prior disease graph generated by biomedical literature mining. For autoimmune diseases, GGPA 2.0 identified enrichment for blood, especially B cells and regulatory T cells across multiple diseases. Psychiatric disorders were enriched for brain, especially prefrontal cortex and inferior temporal lobe for bipolar disorder (BIP) and schizophrenia (SCZ), respectively. Finally, GGPA 2.0 successfully identified the pleiotropy between BIP and SCZ. These results demonstrate that GGPA 2.0 can be a powerful tool to identify associated variants associated with each phenotype or those shared across multiple phenotypes, while also promoting understanding of functional mechanisms underlying the associated variants. Availability: R package ‘GGPA2’ is available at https://***/GGPA2/. © 2022, CC BY.

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Pan-cancer integrative histology-genomic analysis via interpretable multimodal deep learning

arXiv

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arXiv 2021年

作者： Chen, Richard J. Lu, Ming Y. Williamson, Drew F.K. Chen, Tiffany Y. Lipkova, Jana Shaban, Muhammad Shady, Maha Williams, Mane Joo, Bumjin Noor, Zahra Mahmood, Faisal Department of Pathology Brigham and Women's Hospital Harvard Medical School BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard MIT CambridgeMA United States Cancer Data Science Program Dana-Farber Cancer Institute BostonMA United States Department of Computer Science Harvard University CambridgeMA United States

The rapidly emerging field of deep learning-based computational pathology has demonstrated promise in developing objective prognostic models from histology whole slide images. However, most prognostic models are either based on histology or genomics alone and do not address how histology and genomics can be integrated to develop joint image-omic prognostic models. Additionally identifying explainable morphological and molecular descriptors from these models that govern such prognosis is of interest. We used multimodal deep learning to integrate gigapixel whole slide pathology images, RNA-seq abundance, copy number variation, and mutation data from 5,720 patients across 14 major cancer types. Our interpretable, weakly-supervised, multimodal deep learning algorithm is able to fuse these heterogeneous modalities for predicting outcomes and discover prognostic features from these modalities that corroborate with poor and favorable outcomes via multimodal interpretability. We compared our model with unimodal deep learning models trained on histology slides and molecular profiles alone, and demonstrate performance increase in risk stratification on 9 out of 14 cancers. In addition, we analyze morphologic and molecular markers responsible for prognostic predictions across all cancer types. All analyzed data, including morphological and molecular correlates of patient prognosis across the 14 cancer types at a disease and patient level are presented in an interactive open-access database (http://***) to allow for further exploration and prognostic biomarker discovery. To validate that these model explanations are prognostic, we further analyzed high attention morphological regions in WSIs, which indicates that tumor-infiltrating lymphocyte presence corroborates with favorable cancer prognosis on 9 out of 14 cancer types studied. Copyright © 2021, The Authors. All rights reserved.

关键词： Diseases

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A semi-supervised machine learning approach to detecting recurrent metastatic breast cancer cases using linked cancer registry and electronic medical record data

arXiv

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arXiv 2019年

作者： Ling, Albee Y. Kurian, Allison W. Caswell-Jin, Jennifer L. Sledge, George W. Shah, Nigam H. Tamang, Suzanne R. Stanford University Biomedical Informatics Training Program United States Stanford University School of Medicine Department of Medicine United States Stanford University School of Medicine Department of Health Research and Policy United States Stanford University Department of Biomedical Data Science United States Stanford University Center for Biomedical Informatics Research United States Stanford University Center for Population Health Sciences United States

Purpose: Most cancer data sources lack information on an important outcome: metastatic recurrence. Electronic medical records (EMRs) and population-based cancer registries contain complementary information on cancer outcomes and treatment, yet are rarely used synergistically. To enable detection of metastatic breast cancer (MBC) recurrence, we applied a semi-supervised machine learning framework to linked EMR-California Cancer Registry (CCR) data. Patients and Methods: We studied 11,459 female patients who received an incident breast cancer diagnosis from 2000-2014 and were treated at Stanford Health Care. The dataset consisted of structured data and unstructured free-text clinical notes from each patient’s EMR, linked to the population-based CCR, a component of the Surveillance, Epidemiology and End Results (SEER) database. We extracted information on metastatic disease from patient notes to infer a class label and then trained a logistic regression model with regularization for metastatic recurrence classification. We evaluated model performance on an oncologist-labeled set of 146 patients. Results: Among 11,459 patients studied, 495 (4.3%) had de novo stage IV MBC. Of the remaining 10,964 patients with Stage 0-III disease, 1,374 (12.5%) were classified as having recurrent MBC and 9,590 (87.5%) were classified as not having MBC. The median follow-up time is 96.3 months (mean 97.8, standard deviation 46.7). The best-performing model incorporated natural language processing of EMR-derived features with CCR-derived features and had an area under the receiver-operating characteristic curve=0.925 [95% confidence interval: 0.880-0.969], sensitivity=0.861, specificity=0.878 and overall accuracy=0.870. Conclusion: A framework for MBC case detection combining EMR and SEER registry data achieved good sensitivity, specificity and discrimination without requiring expert-labeled examples. This approach enables population-based research on how patients die from cancer and may i

关键词： Natural language processing systems

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A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy

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Nature communications 2025年第1期16卷 5034页

作者： Barbora Salovska Wenxue Li Oliver M Bernhardt Pierre-Luc Germain Qinyue Wang Tejas Gandhi Lukas Reiter Yansheng Liu Department of Pharmacology Yale University School of Medicine New Haven CT USA. Cancer Biology Institute Yale University School of Medicine West Haven CT USA. Biognosys AG Zurich-Schlieren Switzerland. Institute for Neuroscience Department of Health Sciences and Technology ETH Zurich Zurich Switzerland. Master Program of Public Health Department of Chronic Disease Epidemiology Yale School of Public Health New Haven CT USA. Department of Pharmacology Yale University School of Medicine New Haven CT USA. yansheng.liu@yale.edu. Cancer Biology Institute Yale University School of Medicine West Haven CT USA. yansheng.liu@yale.edu. Department of Biomedical Informatics & Data Science Yale University School of Medicine New Haven CT USA. yansheng.liu@yale.edu.

Quantifying protein turnover is fundamental to understanding cellular processes and advancing drug discovery. Multiplex-DIA mass spectrometry (MS), combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC) reliably measures protein turnover and degradation kinetics. Previous multiplex-DIA-MS workflows have employed various strategies including leveraging the highest isotopic labeling channels to enhance the detection of isotopic signal pairs. Here we present a robust workflow that integrates a machine learning algorithm and channel-specific statistical filtering, enabling dynamic adaptation to channel ratio changes across multiplexed experiments and enhancing both coverage and accuracy of protein turnover profiling. We also introduce KdeggeR, a data analysis tool optimized for pSILAC-DIA experiments, which determines and visualizes peptide and protein degradation profiles. Our workflow is broadly applicable, as demonstrated on 2-channel and 3-channel DIA datasets and across two MS platforms. Applying this framework to an aneuploid cancer cell model before and after cisplatin resistance, we uncover strong proteome buffering of key protein complex subunits encoded by the aneuploid genome mediated by protein degradation. We identify resistance-associated turnover signatures, including mitochondrial metabolic adaptation via accelerated degradation of respiratory complexes I and IV. Our approach provides a powerful platform for high-throughput, quantitative analysis of proteome dynamics and stability in health and disease.

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Contour Detection from Ultrasound Kidney Images with A Coarse-to-Fine Approach

Contour Detection from Ultrasound Kidney Images with A Coars...

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2023 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2023

作者： Peng, Tao Gu, Yidong Xu, Yanqing Wang, Caishan Zhang, Lei Cai, Jing School of Future Science and Engineering Soochow University Suzhou China UT Southwestern Medical Center Department of Radiation Oncology DallasTX United States The Affiliated Suzhou Hospital of Nanjing Medical University Department of Medical Ultrasound Suzhou Municipal Hospital Jiangsu Suzhou China University of Texas Southwestern Medical Center McDermott Center for Human Growth and Development DallasTX United States The Second Affiliated Hospital of Soochow University Department of Ultrasound Suzhou China Duke Kunshan University Graduate Program of Medical Physics and Data Science Research Center Jiangsu Kunshan China The Hong Kong Polytechnic University Department of Health Technology and Informatics Hong Kong Hong Kong

ISBN: (纸本)9798350337020

Ultrasound kidney image segmentation presents significant challenges due to missing or ambiguous boundaries. In this study, we introduce a coarse-to-refinement approach incorporating four novel aspects. Firstly, we leverage the properties of a principal curve (PC) to automatically fine-tune the curve shape and employ a neural network's learning ability to reduce model error. Secondly, a deep fusion learning network is utilized for the coarse segmentation step, incorporating a parallel architecture to enhance deep-learning performance. Thirdly, addressing the limitation of standard PC-based methods in determining the number of vertices automatically, we propose an automatic searching polygon tracking method using a mean shift clustering-based approach to replace the projection and vertex extension step in standard PC-based methods. Lastly, we develop an explainable mathematical map function for the kidney contour, as denoted by the neural network output (i.e., optimized vertices), which aligns well with the ground truth contour. We conducted various experiments to evaluate our method's performance, demonstrating its effectiveness in ultrasound kidney image segmentation. © 2023 IEEE.

关键词： Artificial intelligence Explainable mathematical model Ultrasound kidney segmentation

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