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41st International Conference on Machine Learning, ICML 2024

作者： Peng, Bo Ling, Xinyi Chen, Ziru Sun, Huan Ning, Xia Department of Computer Science and Engineering The Ohio State University United States Translational Data Analytics Institute The Ohio State University United States Department of Biomedical Informatics The Ohio State University United States

With tremendous efforts in developing effective e-commerce models, conventional e-commerce models show limited success in generalist e-commerce modeling, and suffer from unsatisfactory performance on new users and new products - a typical out-of-domain generalization challenge. Meanwhile, large language models (LLMs) demonstrate outstanding performance in generalist modeling and out-of-domain generalizability in many fields. Toward fully unleashing their power for e-commerce, in this paper, we construct ECInstruct, the first open-sourced, large-scale, and high-quality benchmark instruction dataset for e-commerce. Leveraging ECInstruct, we develop eCeLLM, a series of e-commerce LLMs, by instruction-tuning general-purpose LLMs. Our comprehensive experiments and evaluation demonstrate that eCeLLM models substantially outperform baseline models, including the most advanced GPT-4, and the state-of-the-art task-specific models in in-domain evaluation. Moreover, eCeLLM exhibits excellent generalizability to out-of-domain settings, including unseen products and unseen instructions, highlighting its superiority as a generalist e-commerce model. Both the ECInstruct dataset and the eCeLLM models show great potential in empowering versatile and effective LLMs for e-commerce. ECInstruct and eCeLLM models are publicly accessible through https://***/eCeLLM/. Copyright 2024 by the author(s)

关键词： Marketplaces

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R2V-PPI: Enhancing Prediction of Protein-Protein Interactions Using Word2Vec Embeddings and Deep Neural Networks 4

R2V-PPI: Enhancing Prediction of Protein-Protein Interaction...

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4th International Conference on Advances in Electrical, Computing, Communication and Sustainable Technologies, ICAECT 2024

作者： Oviya, I.R. Sravya N, Shanmukha Raja, Kalpana Amrita Vishwa Vidyapeetham Amrita School of Computing Department of Computer Science Engineering Chennai601103 India Yale University Section for Biomedical Informatics and Data Science School of Medicine New HavenCT United States

ISBN: (纸本)9798350343670

Proteins play a crucial role in living organisms, and understanding protein-protein interactions is vital for comprehending their functions and aiding drug discovery. In recent years, advanced deep learning models have been developed to predict protein-protein interactions from sequences. However, these large-scale approaches often suffer from deficiencies, resulting in both false positive and false negative predictions. Traditional encoding methods struggle to effectively represent the semantic meaning of individual residues in protein sequences and their impact on neighbouring residues. To overcome these deficiencies, we propose a novel method named R2V-PPI (Residue-to-Vector embeddings based Protein-Protein Interaction Framework) that effectively represents protein sequences and predicts protein-protein interactions. Inspired by Word2Vec, R2V-PPI learns informative representations of individual amino acid residues, capturing the context and relationships between them in raw protein sequences. These representations provide valuable input features for a downstream deep learning model. Our methodology offers a robust and versatile approach for predicting protein-protein interactions, especially when structural information is limited or unavailable. Evaluation on the S. cerevisiae dataset demonstrates that R2V-PPI outperforms existing state-of-the-art machine learning models. © 2024 IEEE.

关键词： Deep Learning Machine Learning Protein Feature Encoding Protein Protein interaction Protein sequence

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Health Information Exchange: Contributions from 2023

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Yearbook of Medical informatics 2025年第1期33卷 191-194页

作者： Bloomrosen, Meryl Feldman, Sue S. American Medical Association Chicago IL United States Graduate Programs in Health Informatics Department of Health Services Administration University of Alabama at Birmingham Birmingham AL United States Department of Biomedical Informatics and Data Science Heersink School of Medicine University of Alabama at Birmingham Birmingham AL United States

OBJECTIVES: To summarize the recent literature and research and present a selection of the best papers published online and in print in 2023 related to health information exchange (HIE). METHODS: Using Covidence as a screening and analysis tool, a systematic review of the literature was independently conducted by the two section editors. Seven studies emerged as suitable for final IMIA Yearbook consideration. RESULTS: Among the papers reviewed, three major themes emerged: clinical services utilization, continuity of care, and public and population health. These themes represent an increased breadth and depth of HIE application. CONCLUSIONS: Review of the literature suggested more studies with the use of data from HIEs, perhaps suggesting increased trust in data accuracy, adequacy, and completeness. The section editors noted the increase in papers from diverse countries describing applications of HIEs suggesting more widespread implementation of HIEs worldwide. As health data standards are developed and adopted globally, this could set the stage for increased international health data exchange. The larger corpus of 2023 literature reviewed resulted in conversations by the section editors on the changing landscape of the expanding, maturing, and innovative use cases for HIEs and HIE data. This landscape bears continued watching in 2024. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://***/licenses/by/4.0/).

关键词： data Sharing Electronic Health Records Health Information Health Information Exchange Health Information Technology International Medical informatics Association Yearbook Interoperability

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Analyzing Llama 3-based Approach for Axiom Translation from Ontologies 2

Analyzing Llama 3-based Approach for Axiom Translation from ...

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Joint of the 2nd Workshop on Knowledge Base Construction from Pre-Trained Language Models and the 3rd Challenge on Language Models for Knowledge Base Construction, KBC-LM-LM-KBC 2024

作者： Hao, Xubing Cui, Licong Tao, Cui Roberts, Kirk Amith, Muhammad McWilliams School of Biomedical Informatics The University of Texas Health Science Center Houston United States Department of Artificial Intelligence and Informatics Mayo Clinic United States Department of Biostatistics and Data Science University of Texas Medical Branch United States Department of Internal Medicine University of Texas Medical Branch United States

Ontology development involves a top-down approach where ontology engineers and domain experts collaboratively define and evaluate ontological elements and axioms. Translating ontology axioms into natural language can significantly aid in ontology evaluation by making the content more understandable to subject matter experts who may lack a background in knowledge engineering. In this preliminary study, we investigate the potential of large language models (LLMs) in axiom translation from ontologies to facilitate ontology evaluation. We utilize Llama 3 to translate 1,192 ontology axioms across 19 distinct axiom types from five published ontologies. Results show that 163 (13.67%) of the Llama 3 translation of the axiom are accurately represented, 268 (22.48%) are not accurately represented, and 761 (63.84%) are partially accurate. Our manual evaluation of the Llama 3 translation indicates some competency in producing hierarchical natural language equivalents while revealing some limitations when translating complex axioms. Nonetheless, there are opportunities to improve the results with few-shot training or using LLMs to provide support in knowledge engineering for ontologies. © 2024 Copyright for this paper by its authors.

关键词： Knowledge engineering

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Short-Term Effects of Ambient Air Pollutants on Outpatient Visits for Childhood Allergic Diseases in Shanghai,China

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Journal of Shanghai Jiaotong university(science) 2024年第6期29卷 979-994页

作者： HU Yi GU Jianlei WU Dan WANG Xiaolei LU Hui YU Guangjun Center for Biomedical Informatics Shanghai Children’s HospitalShanghai Jiao Tong University School of MedicineShanghai 200040China SJTU-Yale Joint Center for Biostatistics and Data Science Department of Bioinformatics and BiostatisticsShanghai Jiao Tong UniversityShanghai 200240China Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine Shanghai 200040China

This study aims to investigate the short-term effects of ambient air pollutants on outpatient visits for childhood allergic *** data on ambient air pollutants(NO2,SO2,CO and PM2.5)and outpatient visits for childhood allergic diseases(asthma,atopic dermatitis and allergic rhinitis)were obtained in Shanghai,China from 2013 to *** effects of ambient air pollutants were estimated for total outpatient visits for childhood allergic diseases,gender and age stratification and disease classification by using distributed lag non-linear model(DLNM).We found positive associations between short-term exposure to air pollutants and childhood allergic *** and children aged 7 years old were more likely to be sensitive to ambient air ***2 and SO2 showed stronger effects on asthma and atopic dermatitis,*** study provides evidence that short-term exposure to ambient air pollutants can increase the risk of childhood allergic diseases.

关键词： childhood allergic diseases ambient air pollutant nitrogen dioxide(NO2) sulfur dioxide(SO2) particulate matter<2.5μm in diameter(PM2.5)

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Towards Enhanced Topic Discovery on Semantic Maps for biomedical Literature Exploration

Towards Enhanced Topic Discovery on Semantic Maps for Biomed...

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IEEE Workshop on Visual Analytics in Healthcare (VAHC)

作者： Bin Choi Brian Ondov Huan He Hua Xu Yale-NUS College Department of Biomedical Informatics and Data Science Yale University

ISBN: (数字)9798331522162

ISBN: (纸本)9798331522179

The rapid growth of biomedical research has led to an overwhelming volume of literature, making it challenging for researchers to efficiently explore and analyze. While existing tools provide an overview of semantic maps and publication distributions, further refinement is needed to reveal fine-grained nuances and hierarchical topics. To address this, we propose a novel method for hierarchical topic modeling and label generation on 2D semantic maps. Our approach consists of three steps. First, we apply density-based hierarchical clustering using HDBSCAN to construct a topic tree. Second, we employ a novel tree-based TF-IDF method to refine topic representation using MeSH terms, capturing both general and local topic distinctions. Finally, we optimize label positioning using a centroid-based method to enhance visualization.

关键词： Analytical models Visual analytics Conferences Biological system modeling Semantics Medical services

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Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A data-driven Perspective

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 164-176页

作者： Jianlei Gu Jiawei Dai Hui Lu Hongyu Zhao SJTU-Yale Joint Center for Biostatistics and Data Science Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Center for Biomedical Informatics Shanghai Engineering Research Center for Big Data in Pediatric Precision MedicineShanghai Children’s HospitalShanghai 200040China Department of Biostatistics Yale UniversityNew HavenCT 06511USA

Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human *** expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an *** is known that many human genes are broadly expressed across ***,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG *** this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human *** results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression *** further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.

关键词： Ubiquitous expression Housekeeping gene Disallowed gene Expression specificity Expression variability

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Comfort Shoulder (Rhomboid Major) Muscles Chair Identifier System 6

Comfort Shoulder (Rhomboid Major) Muscles Chair Identifier S...

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6th International Conference on Communications, Information System and Computer Engineering, CISCE 2024

作者： Moshayedi, Ata Jahangir Yu, Yuexin Savoji, Kimia Andani, Mehran Emadi School of Information Engineering Jiangxi University of Science and Technology Jiangxi Ganzhou China School of Computing Clemson University Biomedical Data Science and Informatics ClemsonSC United States University of Verona Department of Neurosciences Biomedicine and Movement Sciences Verona Italy

ISBN: (纸本)9798350353174

Nowadays, Sitting is one of the frequent activities of humans. particularly with the rise of office work, which is leading to an increase in the sitting periods for many individuals. Research highlights the importance of studying sitting posture to enhance seat quality, correct sitting methods, and prevent various health issues like neck and shoulder strains, etc. This article focuses on designing an IoT-based system that enables web-based data visualization without specialized software that can enable distance sampling. Through temperature sensors (DS18b20 and SHT11) and an FSR sensor, the system can identify distinct patterns in the main rhomboid muscles (the most important muscles of humans). The results show a significant relationship between individuals' body mass (BMI) and the observed muscle patterns, highlighting the importance of this correlation for researchers and industry designers alike. © 2024 IEEE.

关键词： Seats

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A Variational Autoencoder-Feed Forward Networks (VAE-FNN) Model for Classifying DNA Barcodes 1

A Variational Autoencoder-Feed Forward Networks (VAE-FNN) Mo...

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1st International Conference on Advances in Electrical, Electronics and Computational Intelligence, ICAEECI 2023

作者： Yadav, Abhivyakti Divya, S. Oviya, I.R. Raja, Kalpana Department of Computer Science and Engineering Amrita School of Computing Amrita Vishwa Vidyapeetham Chennai India School of Medicine Yale University Section for Biomedical Informatics and Data Science New HavenCT United States

ISBN: (纸本)9798350342796

DNA Barcodes, which are particular fragments derived from brief sections of DNA (such as mitochondrial, nuclear, and plastid sequences), can be used to identify organisms from the major life kingdoms. In addition to supporting conventional taxonomic techniques, DNA barcoding is a potent tool that advances our knowledge of species diversity and their ecological functions. On a variety of organisms, the use of this approach for species categorization has been successful. In this paper, we examine how DNA barcoding has been used to classify species based on DNA barcodes as well as other related research that has been done over the years on the subject. After experimenting with a number of deep learning models, we have propose a Variational Auto Encoder + Feed Forward Neural Network workflow for classifiying species using DNA barcodes. The models have been assessed on the basis of performance factors including accuracy, recall, and precision. COI, rbcL, matK, and ITS are the specific gene sections that have been identified as barcodes. For both simulated and real datasets, the model can attain an average accuracy of greater than 95 percent. This DNA barcoding approach has the ability to simplify DNA barcode-based species identification and serve as a tool for species categorization. © 2023 IEEE.

关键词： DNA

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Real-Time Visualization and Analysis Architecture for data Integration Processes at Cologne University Hospital's Medical data Integration Center

Real-Time Visualization and Analysis Architecture for Data I...

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34th Medical informatics Europe Conference, MIE 2024

作者： Kamal, Md. Mostafa Kutafina, Ekaterina Beyan, Oya Institute for Biomedical Informatics University of Cologne Faculty of Medicine University Hospital Cologne Cologne Germany University of Cologne Faculty of Medicine University Hospital Cologne Cologne Germany Department of Data Science and Artificial Intelligence Fraunhofer FIT Germany

ISBN: (纸本)9781643685335

This paper presents an implementation of an architecture based on open-source solutions using ELK Stack - Elasticsearch, Logstash, and Kibana - for real-time data analysis and visualizations in the Medical data Integration Center, University Hospital Cologne, Germany. The architecture addresses challenges in handling diverse data sources, ensuring standardized access, and facilitating seamless analysis in real-time, ultimately enhancing the precision, speed, and quality of monitoring processes within the medical informatics domain. © 2024 The Authors.

关键词： data integration

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