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Systems biology and bioinformatics approach to identify gene signatures, pathways and therapeutic targets of Alzheimer's disease

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Informatics in Medicine Unlocked 2020年 21卷

作者： Chowdhury, Utpala Nanda Islam, M. Babul Ahmad, Shamim Moni, Mohammad Ali Department of Computer Science and Engineering University of Rajshahi Rajshahi Bangladesh Department of Electrical and Electronic Engineering University of Rajshahi Bangladesh Department of Computer Science and Engineering Pabna University of Science and Technology Pabna Bangladesh WHO Collaborating Centre on eHealth School of Public Health and Community Medicine Faculty of Medicine University of New South Wales Sydney Australia

Alzheimer's disease (AD) develops relentlessly in affected individuals and its occurrence is increasing. A clinical test to diagnose early-stage AD could be an important means of enabling interventions to slow its progression. However, available neuroimaging and cerebrospinal fluid-based diagnoses are very costly. Therefore, detecting AD from blood transcripts that mirror the expression of brain transcripts in the AD could improve the diagnosis. To achieve this goal, we employed a transcriptional analysis of affected tissues and integrated them with cis-eQTL data. In this study, we analyzed microarray gene expression data of brain and blood cells from AD patients and control individuals. Differentially expressed genes (DEGs) common to both brain tissue and blood cells were identified. Potential common genes and molecular pathways were identified using overlapping DEGs through the pathway and gene ontology enrichment analysis. We identified 18 significantly dysregulated genes shared by both brain and blood cells in AD affected individuals. We validated these candidates as disease-associated genes using gold-standard benchmarking databases (gene SNP-disease linkage). Significant molecular pathway and gene ontology indicating AD progression were identified. This study also identified regulatory factors, including transcription factors (TFs), microRNAs and candidate drugs. In sum, we identified new putative links between pathological processes in brain tissue and blood cells in AD that may allow assessment of AD status using blood samples. Thus, our formulated methodologies demonstrate the power of gene and gene expression analysis for brain-related pathologies transcriptomics, cis-eQTL, and epigenetics data from brain and blood cells. © 2020 The Author(s)

关键词： Alzheimer's disease (AD) Blood Brain cis-eQTL GWAS

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The Need for Ethical, Responsible, and Trustworthy Artificial Intelligence for Environmental Sciences

arXiv

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arXiv 2021年

作者： McGovern, Amy Ebert-Uphoff, Imme Gagne, David John Bostrom, Ann School of Computer Science and School of Meteorology University of Oklahoma NormanOK73019 United States Electrical and Computer Engineering Colorado State University Fort CollinsCO80523 United States Cooperative Institute for Research in the Atmosphere Colorado State University Fort CollinsCO80523 United States Computational and Information Systems Laboratory National Center for Atmospheric Research BoulderCO80301 United States Evans School of Public Policy & Governance University of Washington SeattleWA98195 United States

Given the growing use of Artificial Intelligence (AI) and machine learning (ML) methods across all aspects of environmental sciences, it is imperative that we initiate a discussion about the ethical and responsible use of AI. In fact, much can be learned from other domains where AI was introduced, often with the best of intentions, yet often led to unintended societal consequences, such as hard coding racial bias in the criminal justice system or increasing economic inequality through the financial system. A common misconception is that the environmental sciences are immune to such unintended consequences when AI is being used, as most data come from observations, and AI algorithms are based on mathematical formulas, which are often seen as objective. In this article, we argue the opposite can be the case. Using specific examples, we demonstrate many ways in which the use of AI can introduce similar consequences in the environmental sciences. This article will stimulate discussion and research efforts in this direction. As a community, we should avoid repeating any foreseeable mistakes made in other domains through the introduction of AI. In fact, with proper precautions, AI can be a great tool to help reduce climate and environmental injustice. We primarily focus on weather and climate examples but the conclusions apply broadly across the environmental sciences. © 2021, CC BY-SA.

关键词： Artificial intelligence

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Automatic standard plane and diagnostic usability classification in obstetric ultrasounds

WFUMB Ultrasound Open

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WFUMB Ultrasound Open 2024年第2期2卷 100050-100050页

作者： Lim, Adam Abdalla, Mohamed Abolhassani, Farbod Law, Wyanne Fine, Benjamin Sussman, Dafna Department of Electrical Computer and Biomedical Engineering Toronto Metropolitan University Faculty of Engineering and Architectural Sciences Toronto Ontario Canada Institute for Biomedical Engineering Science and Technology (iBEST) Toronto Metropolitan University and St. Michael's Hospital Toronto Ontario Canada Institute for Better Health Mississauga Ontario Canada Dalla Lana School of Public Health University of Toronto Toronto Ontario Canada Department of Radiology Memorial Sloan Kettering Cancer Center New York NY United States Department of Medical Imaging University of Toronto Toronto Ontario Canada Department of Obstetrics and Gynecology Faculty of Medicine University of Toronto Toronto Ontario Canada

AbstractObjectiveThis study introduces an innovative end-to-end deep learning pipeline designed to automatically classify and order fetal ultrasound standard planes in alignment with the guidelines of the Canadian Association of Radiologists, while also assessing the diagnostic usability of each view. The primary objective is to address the manual and cumbersome challenges that interpreting radiologists encounter in the existing obstetric ultrasound workflow. MethodsWe compiled a diverse dataset, comprising 33,561 de-identified two-dimensional obstetrical ultrasound images acquired from January 1, 2010, to June 1, 2020. This dataset was categorized into 19 distinct classes associated with standard planes and further partitioned into training, validation, and testing subsets via a 60:20:20 stratified split. The standard plane and diagnostic usability networks are founded on a convolutional neural network framework and employ the benefits of transfer learning. ResultsThe standard plane classification network demonstrated promising results by achieving 99.4 % and 98.7 % for accuracy and F1 score, respectively. Subsequently, the diagnostic usability network demonstrated strong performance, registering 80 % accuracy and an 82 % F1 score. Notably, this study is the first to investigate whether deep learning methods can surpass sonographers in the standard plane labeling task, with some instances revealing the algorithm's capacity to rectify sonographer mislabeled planes. ConclusionThe results highlight the algorithm's potential to be integrated into a clinical setting by serving as a reliable assistive tool, alleviating the cognitive workload faced by radiologists and enhancing efficiency and diagnostic outcomes in the current obstetric ultrasound process.

关键词： Deep learning Obstetric ultrasound Convolutional neural network Image classification

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AI recognition of patient race in medical imaging: a modelling study

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The Lancet Digital Health 2022年第6期4卷 e406-e414页

作者： Gichoya, Judy Wawira Banerjee, Imon Bhimireddy, Ananth Reddy Burns, John L Celi, Leo Anthony Chen, Li-Ching Correa, Ramon Dullerud, Natalie Ghassemi, Marzyeh Huang, Shih-Cheng Kuo, Po-Chih Lungren, Matthew P Palmer, Lyle J Price, Brandon J Purkayastha, Saptarshi Pyrros, Ayis T Oakden-Rayner, Lauren Okechukwu, Chima Seyyed-Kalantari, Laleh Trivedi, Hari Wang, Ryan Zaiman, Zachary Zhang, Haoran Department of Radiology Emory University Atlanta GA United States Department of Computer Science Emory University Atlanta GA United States School of Computing Informatics and Decision Systems Engineering Arizona State University Tempe AZ United States School of Informatics and Computing Indiana University–Purdue University Indianapolis IN United States Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Department of Medicine Beth Israel Deaconess Medical Center Boston MA United States Department of Computer Science National Tsing Hua University Hsinchu Taiwan Department of Computer Science University of Toronto Toronto ON Canada Stanford University School of Medicine Palo Alto CA United States Australian Institute for Machine Learning University of Adelaide Adelaide SA Australia School of Public Health University of Adelaide Adelaide SA Australia Florida State University College of Medicine Tallahassee FL United States Dupage Medical Group Hinsdale IL United States Department of Computer Science Georgia Institute of Technology Atlanta GA United States Lunenfeld-Tanenbaum Research Institute Sinai Health Toronto ON Canada Vector Institute for Artificial Intelligence Toronto ON Canada

Background: Previous studies in medical imaging have shown disparate abilities of artificial intelligence (AI) to detect a person's race, yet there is no known correlation for race on medical imaging that would be obvious to human experts when interpreting the images. We aimed to conduct a comprehensive evaluation of the ability of AI to recognise a patient's racial identity from medical images. Methods: Using private (Emory CXR, Emory Chest CT, Emory Cervical Spine, and Emory Mammogram) and public (MIMIC-CXR, CheXpert, National Lung Cancer Screening Trial, RSNA Pulmonary Embolism CT, and Digital Hand Atlas) datasets, we evaluated, first, performance quantification of deep learning models in detecting race from medical images, including the ability of these models to generalise to external environments and across multiple imaging modalities. Second, we assessed possible confounding of anatomic and phenotypic population features by assessing the ability of these hypothesised confounders to detect race in isolation using regression models, and by re-evaluating the deep learning models by testing them on datasets stratified by these hypothesised confounding variables. Last, by exploring the effect of image corruptions on model performance, we investigated the underlying mechanism by which AI models can recognise race. Findings: In our study, we show that standard AI deep learning models can be trained to predict race from medical images with high performance across multiple imaging modalities, which was sustained under external validation conditions (x-ray imaging [area under the receiver operating characteristics curve (AUC) range 0·91–0·99], CT chest imaging [0·87–0·96], and mammography [0·81]). We also showed that this detection is not due to proxies or imaging-related surrogate covariates for race (eg, performance of possible confounders: body-mass index [AUC 0·55], disease distribution [0·61], and breast density [0·61]). Finally, we provide evidence to show that t

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Late fusion of machine learning models using passively captured interpersonal social interactions and motion from smartphones predicts decompensation in heart failure

arXiv

引用

arXiv 2021年

作者： Cakmak, Ayse S. Densen, Samuel Najarro, Gabriel Rout, Pratik Rozell, Christopher J. Inan, Omer T. Shah, Amit J. Clifford, Gari D. Department of Electrical and Computer Engineering Georgia Institute of Technology AtlantaGA30332 United States Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology AtlantaGA30332 United States Department of Biomedical Informatics School of Medicine Emory University AtlantaGA30322 United States Department of Epidemiology Rollins School of Public Health Emory University AtlantaGA30322 United States School of Medicine Emory University AtlantaGA30322 United States Emory Healthcare Emory University AtlantaGA30322 United States

Objective: Worldwide, heart failure (HF) is a major cause of morbidity and mortality and one of the leading causes of hospitalization. Early detection of HF symptoms and pro-active management may reduce adverse events. Approach: Twenty-eight participants were monitored using a smartphone app after discharge from hospitals, and each clinical event during the enrollment (N=110 clinical events) was recorded. Motion, social, location, and clinical survey data collected via the smartphone-based monitoring system were used to develop and validate an algorithm for predicting or classifying HF decompensation events (hospitalizations or clinic visit) versus clinic monitoring visits in which they were determined to be compensated or stable. Models based on single modality as well as early and late fusion approaches combining patient-reported outcomes and passive smartphone data were evaluated. Results: The highest AUCPr for classifying decompensation with a late fusion approach was 0.80 using leave one subject out cross-validation. Significance: Passively collected data from smartphones, especially when combined with weekly patient-reported outcomes, may reflect behavioral and physiological changes due to HF and thus could enable prediction of HF decompensation. Copyright © 2021, The Authors. All rights reserved.

关键词： Smartphones

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Improving confidence in the estimation of values and norms

arXiv

引用

arXiv 2020年

作者： Siebert, Luciano Cavalcante Mercuur, Rijk Dignum, Virginia van den Hoven, Jeroen Jonker, Catholijn Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Netherlands Faculty of Technology Policy and Management Delft University of Technology Netherlands Department of Computing Sciences Ume University Sweden Leiden Institute of Advance Computer Science Leiden University Netherlands

Autonomous agents (AA) will increasingly be interacting with us in our daily lives. While we want the benefits attached to AAs, it is essential that their behavior is aligned with our values and norms. Hence, an AA will need to estimate the values and norms of the humans it interacts with, which is not a straightforward task when solely observing an agent's behavior. This paper analyses to what extent an AA is able to estimate the values and norms of a simulated human agent (SHA) based on its actions in the ultimatum game. We present two methods to reduce ambiguity in profiling the SHAs: one based on search space exploration and another based on counterfactual analysis. We found that both methods are able to increase the confidence in estimating human values and norms, but differ in their applicability, the latter being more efficient when the number of interactions with the agent is to be minimized. These insights are useful to improve the alignment of AAs with human values and norms. Copyright © 2020, The Authors. All rights reserved.

关键词： Autonomous agents

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基于大语言模型的糖尿病管理:潜力与展望

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Science Bulletin 2024年第5期69卷 583-588页

作者：盛斌管洲榆 Lee-Ling Lim 江泽铧 Nestoras Mathioudakis 李佳佳刘茹涵包玉倩 Yong Mong Bee 王亚星郑颖丰 Gavin Siew Wei Tan 纪宏伟 Josip Car 王海波 David C.Klonoff 李华婷覃宇宗黄天荫贾伟平 Shanghai International Joint Laboratory of Intelligent Prevention and Treatment for Metabolic Diseases Department of Computer Science and EngineeringSchool of ElectronicInformationand Electrical EngineeringShanghai Jiao Tong UniversityDepartment of Endocrinology and MetabolismShanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai Diabetes InstituteShanghai Clinical Center for DiabetesShanghai 200240China MOE Key Laboratory of Artificial Intelligence Artificial Intelligence InstituteShanghai Jiao Tong UniversityShanghai 200240China Department of Medicine Faculty of MedicineUniversity of MalayaKuala Lumpur 50603Malaysia Department of Medicine and Therapeutics The Chinese University of Hong KongHong KongChina Asia Diabetes Foundation Hong KongChina Tsinghua Medicine of Tsinghua University Beijing 100084China School of Clinical Medicine Beijing Tsinghua Changgung HospitalBeijing 102218China Division of Endocrinology Diabetes&MetabolismJohns Hopkins University School of MedicineBaltimoreMD 21211USA Department of Endocrinology Singapore General HospitalSingapore 169608Singapore Beijing Institute of Ophthalmology Beijing Tongren HospitalCapital University of Medical ScienceBeijing Ophthalmology and Visual Sciences Key LaboratoryBeijing 100730China State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangzhou 510060China Singapore Eye Research Institute Singapore National Eye CentreSingapore 168751Singapore Department of Cardiology the Affiliated Hospital of Qingdao UniversityQingdao 266011China Centre for Population Health Sciences Lee Kong Chian School of MedicineNanyang Technological University SingaporeSingapore 639798Singapore Department of Primary Care and Public Health School of Public HealthImperial College LondonLondon SW72BUUK Clinical Trial Unit Research Centre of Big Data and Artificial Intelligence in Medicine

The increasing prevalence of diabetes has become a global public health concern in the 21st *** 2021,it was estimated that 537 million people had diabetes,and this number is projected to reach 643 million by 2030,and 783 million by 2045[1].Such a huge burden of diabetes brings great challenges in its prevention and management,including early diagnosis,timely interventions,and regular monitoring of risk factor control and complications *** self-care support and patient empowerment can enhance clinical and psychobehavioural outcomes[2],although these require additional resources including manpower,infrastructure(hard and technology),and *** emergence of digital health technologies(DHTs),especially artificial intelligence(AI),may help address these obstacles and alleviate the burden of diabetes[3].Large language models(LLMs),a generative AI that can accept image and text inputs and produce text outputs,have shown promise in various aspects of medical care.

关键词： prevention diagnosis finance

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Detecting Influenza Outbreaks Based on Spatiotemporal Information from Urban Systems

Detecting Influenza Outbreaks Based on Spatiotemporal Inform...

引用

GeoInformation for Disaster Management Conference, Gi4DM 2018

作者： Grottenberg, Lars Ole Njå, Ove Tøssebro, Erlend Braut, Geir Sverre Bragstad, Karoline Grøneng, Gry Marysol Department of Safety Economics and Planning University of Stavanger Stavanger Norway Department of Electrical Engineering and Computer Science University of Stavanger Stavanger Norway Stavanger University Hospital Stavanger Norway Department of Influenza Norwegian Institute of Public Health Oslo Norway Department of Infectious Diseases Epidemiology and Modelling Norwegian Institute of Public Health Oslo Norway

ISBN: (纸本)9783030053291

This paper explores the application of real-time spatial information from urban transport systems to understand the outbreak, severity and spread of seasonal and pandemic influenza outbreaks from a spatiotemporal perspective. We believe that combining travel data with epidemiological data is the first step to develop a tool to predict future epidemics and better understand the effects that these outbreaks have on societal functions over time. Real-time data-streams provide a powerful, yet underutilised tool when it comes to monitoring and detecting changes to the daily behaviour of inhabitants. Historical datasets from public transport and road traffic serves as an initial indication of whether changes in daily transport patterns corresponds to seasonal influenza data. It is expected that changes in daily transportation habits corresponds to swings in daily and weekly influenza activity and that these differences can be measured through geostatistical analysis. Conceptually one could be able to monitor changes in human behaviour and activity in nearly true time by using indicators derived from outside the clinical health services. This type of more up-to-date and geographically precise information could contribute to earlier detection of influenza outbreaks and serve as background for implementing tailor-made emergency response measures over the course of the outbreaks. © 2019, Springer Nature Switzerland AG.

关键词： Real time systems

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BRIDGE: Benchmarking Large Language Models for Understanding Real-world Clinical Practice Text

arXiv

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arXiv 2025年

作者： Wu, Jiageng Gu, Bowen Zhou, Ren Xie, Kevin Snyder, Doug Jiang, Yixing Carducci, Valentina Wyss, Richard Desai, Rishi J. Alsentzer, Emily Celi, Leo Anthony Rodman, Adam Schneeweiss, Sebastian Chen, Jonathan H. Romero-Brufau, Santiago Lin, Kueiyu Joshua Yang, Jie Division of Pharmacoepidemiology and Pharmacoeconomics Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Siebel School of Computing and Data Science The Grainger College of Engineering University of Illinois Urbana-Champaign UrbanaIL United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Department of Otorhinolaryngology – Head & Neck Surgery Mayo Clinic RochesterMN United States Department of Biostatistics Harvard T.H. Chan School of Public Health Harvard University BostonMA United States Department of Biomedical Data Science Stanford University Palo AltoCA United States Laboratory for Computational Physiology Massachusetts Institute of Technology CambridgeMA United States Division of Pulmonary Critical Care and Sleep Medicine Beth Israel Deaconess Medical Center BostonMA United States Division of General Internal Medicine Department of Medicine Beth Israel Deaconess Medical Center BostonMA United States Stanford Center for Biomedical Informatics Research Stanford University StanfordCA United States Division of Hospital Medicine Stanford University StanfordCA United States Stanford Clinical Excellence Research Center Stanford University StanfordCA United States Kempner Institute for the Study of Natural and Artificial Intelligence Harvard University MA United States Broad Institute of MIT and Harvard CambridgeMA United States Harvard Data Science Initiative Harvard University CambridgeMA United States

Large language models (LLMs) hold great promise for medical applications and are evolving rapidly, with new models being released at an accelerated pace. However, current evaluations of LLMs in clinical contexts remain limited. Most existing benchmarks rely on medical exam-style questions or PubMed-derived text, failing to capture the complexity of real-world electronic health record (EHR) data. Others focus narrowly on specific application scenarios, limiting their generalizability across broader clinical use. To address this gap, we present BRIDGE, a comprehensive multilingual benchmark comprising 87 tasks sourced from real-world clinical data sources across nine languages. We systematically evaluated 52 state-of-the-art LLMs (including DeepSeek-R1, GPT-4o, Gemini, and Llama 4) under various inference strategies. With a total of 13,572 experiments, our results reveal substantial performance variation across model sizes, languages, natural language processing tasks, and clinical specialties. Notably, we demonstrate that open-source LLMs can achieve performance comparable to proprietary models, while medically fine-tuned LLMs based on older architectures often underperform versus updated general-purpose models. The BRIDGE and its corresponding leaderboard serve as a foundational resource and a unique reference for the development and evaluation of new LLMs in real-world clinical text understanding. © 2025, CC BY-NC-SA.

关键词： Electronic health record

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A robotic dating coaching system leveraging online communities posts

arXiv

引用

arXiv 2020年

作者： Jo, Sihyeon Joung, Eun Gyo So, Minseob Jung, Donghwi Nespoli, Giulia Seo, Seung-Woo Kim, Keonwoo Yoo, Seungryong Kim, Seong-Woo Department of Electrical and Computer Engineering Seoul National University Seoul Korea Republic of Technology Management Economics and Policy Program Seoul National University Seoul Korea Republic of Department of Industrial Engineering Seoul National University Seoul Korea Republic of Department of Civil and Environmental Engineering Seoul National University Seoul Korea Republic of Department of Industrial Design Seoul National University Seoul Korea Republic of Graduate School of Engineering Practice Seoul National University Seoul Korea Republic of

Can a robot be a personal dating coach? Even with the increasing amount of conversational data on the internet, the implementation of conversational robots remains a challenge. In particular, a detailed and professional counseling log is expensive and not publicly accessible. In this paper, we develop a robot dating coaching system leveraging corpus from online communities. We examine people’s perceptions of the dating coaching robot with a dialogue module. 97 participants joined to have a conversation with the robot, and 30 of them evaluated the robot. The results indicate that participants thought the robot could become a dating coach while considering the robot is entertaining rather than helpful. © 2020, CC-BY.

关键词： Social networking (online)

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