IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics最新文献

{"title":"Designing Software for Genomics Medicine Service Leaders to Engage Stakeholders.","authors":"Juandalyn Coffen-Burke, Kai-Wen K Yang, Zoljargal Lkhagvajav, Yuzhi L Lu, Tamisha Dzifa Segbefia, Natalie Wang, James Michael Stevenson, Casey Overby Taylor","doi":"10.1109/ichi57859.2023.00059","DOIUrl":"10.1109/ichi57859.2023.00059","url":null,"abstract":"<p><strong>Background: </strong>Stakeholder engagement can be challenging yet is critically important for the success of a new genomic medicine service or genetic test offering. Services may include ordering, analysis, interpretation, and counseling associated with using a patient's genetic information to make decisions about medical choices.</p><p><strong>Objective: </strong>The aim of this study was to use a human-centered design (HCD) approach to design software for genomic medicine service leaders seeking to engage stakeholders. Of particular interest were stakeholders that could be partners to champion a new genetic test offering.</p><p><strong>Methods: </strong>Our HCD process was driven by a modified design sprint methodology involving participatory design sessions and semi-structured interviews with experts. Subsequently, we created a low-fidelity prototype aiming to facilitate early engagement with potential genomic medicine service partners. The prototype was used to test the design with current genomic medicine service leaders. To guide our evaluation, we developed a set of design considerations for the software application that reflected common strategies used by programs successfully implementing genetic test offerings in diverse settings.</p><p><strong>Results: </strong>We analyzed notes collected from interview sessions with seven genomic medicine service leaders. We identified ten sub-themes, synthesized corresponding notes, and focused our interpretations around three design considerations: #1-identify potential genomic medicine service partners to champion a new genetic test offering; #2-train and educate stakeholders; and #3-obtain and use genomic medicine partner feedback. The top three ranked sub-themes were: 1 - add new information, 2 - general approval, and 3 - add/change functionality.</p><p><strong>Conclusion: </strong>Our findings suggest that genomic medicine service leaders approve of our software design and process to facilitate key stakeholders' review and endorsement of a new genetic test offering. We also demonstrated an evaluation strategy that draws from lessons of successful genomic medicine programs to identify and prioritize areas to improve the software in future design iterations.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2023 ","pages":"398-406"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12743354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145851716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"End-to-End Models for Chemical-Protein Interaction Extraction: Better Tokenization and Span-Based Pipeline Strategies.","authors":"Xuguang Ai, Ramakanth Kavuluru","doi":"10.1109/ichi57859.2023.00108","DOIUrl":"10.1109/ichi57859.2023.00108","url":null,"abstract":"<p><p>End-to-end relation extraction (E2ERE) is an important task in information extraction, more so for biomedicine as scientific literature continues to grow exponentially. E2ERE typically involves identifying entities (or named entity recognition (NER)) and associated relations, while most RE tasks simply assume that the entities are provided upfront and end up performing relation classification. E2ERE is inherently more difficult than RE alone given the potential snowball effect of errors from NER leading to more errors in RE. A complex dataset in biomedical E2ERE is the ChemProt dataset (BioCreative VI, 2017) that identifies relations between chemical compounds and genes/proteins in scientific literature. ChemProt is included in all recent biomedical natural language processing benchmarks including BLUE, BLURB, and BigBio. However, its treatment in these benchmarks and in other separate efforts is typically not end-to-end, with few exceptions. In this effort, we employ a span-based pipeline approach to produce a new state-of-the-art E2ERE performance on the ChemProt dataset, resulting in > 4% improvement in F1-score over the prior best effort. Our results indicate that a straightforward fine-grained tokenization scheme helps span-based approaches excel in E2ERE, especially with regards to handling complex named entities. Our error analysis also identifies a few key failure modes in E2ERE for ChemProt.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2023 ","pages":"610-618"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10809256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139565432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of COVID-19 Patients' Emergency Room Revisit using Multi-Source Transfer Learning.","authors":"Yuelyu Ji, Yuhe Gao, Runxue Bao, Qi Li, Disheng Liu, Yiming Sun, Ye Ye","doi":"10.1109/ICHI57859.2023.00028","DOIUrl":"10.1109/ICHI57859.2023.00028","url":null,"abstract":"<p><p>The coronavirus disease 2019 (COVID-19) has led to a global pandemic of significant severity. In addition to its high level of contagiousness, COVID-19 can have a heterogeneous clinical course, ranging from asymptomatic carriers to severe and potentially life-threatening health complications. Many patients have to revisit the emergency room (ER) within a short time after discharge, which significantly increases the workload for medical staff. Early identification of such patients is crucial for helping physicians focus on treating life-threatening cases. In this study, we obtained Electronic Health Records (EHRs) of 3,210 encounters from 13 affiliated ERs within the University of Pittsburgh Medical Center between March 2020 and January 2021. We leveraged a Natural Language Processing technique, ScispaCy, to extract clinical concepts and used the 1001 most frequent concepts to develop 7-day revisit models for COVID-19 patients in ERs. The research data we collected were obtained from 13 ERs, which may have distributional differences that could affect the model development. To address this issue, we employed a classic deep transfer learning method called the Domain Adversarial Neural Network (DANN) and evaluated different modeling strategies, including the Multi-DANN algorithm (which considers the source differences), the Single-DANN algorithm (which doesn't consider the source differences), and three baseline methods: using only source data, using only target data, and using a mixture of source and target data. Results showed that the Multi-DANN models outperformed the Single-DANN models and baseline models in predicting revisits of COVID-19 patients to the ER within 7 days after discharge (median AUROC = 0.8 vs. 0.5). Notably, the Multi-DANN strategy effectively addressed the heterogeneity among multiple source domains and improved the adaptation of source data to the target domain. Moreover, the high performance of Multi-DANN models indicates that EHRs are informative for developing a prediction model to identify COVID-19 patients who are very likely to revisit an ER within 7 days after discharge.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2023 ","pages":"138-144"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140133379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Effect of Eligibility Criteria on AD Severity and Severe Adverse Event in Eligible Patients.","authors":"Aokun Chen, Qian Li, Elizabeth Shenkman, Yonghui Wu, Yi Guo, Jiang Bian","doi":"10.1109/ichi57859.2023.00139","DOIUrl":"10.1109/ichi57859.2023.00139","url":null,"abstract":"<p><p>Clinical trials were vital tools to prove the effectiveness and safety of medications. To maximize generalizability, the study sample should represent the sample population and the target population. However, the clinical trial design tends to favor the evaluation of drug safety and procedure (i.e., internal validity) without clear knowledge of its penalty on trial generalizability (i.e., external validity). Alzheimer's Disease (AD) trials are known to have generalizability issues. Thus, in this study, we explore the effect of eligibility criteria on the AD severity patients and the severe adverse event (SAE) among the eligible patients.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2023 ","pages":"756-759"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11273173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141790216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Offensive Language in Social Media Using Prompt Learning.","authors":"Leilei Su, Yifan Peng, Zezheng Wang, Cong Sun","doi":"10.1109/ichi57859.2023.00122","DOIUrl":"10.1109/ichi57859.2023.00122","url":null,"abstract":"<p><p>Offensive language refers to the use of language in a manner that may offend or harm others who are within earshot or view in a public place. Given the importance of identifying such language in social media for promoting emotional well-being, we propose a prompt learning method and compare its performance with fine-tuning on two widely used datasets, HatEval and OffensEval. Experimental results demonstrate that prompt learning can achieve a performance improvement over fine-tuning in a fully supervised setting.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2023 ","pages":"690-691"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Named Entity Recognition and Normalization for Alzheimer's Disease Eligibility Criteria.","authors":"Zenan Sun, Cui Tao","doi":"10.1109/ichi57859.2023.00100","DOIUrl":"10.1109/ichi57859.2023.00100","url":null,"abstract":"<p><p>Alzheimer's Disease (AD) is a complex neurodegenerative disorder that affects millions of people worldwide. Finding effective treatments for this disease is crucial. Clinical trials play an essential role in developing and testing new treatments for AD. However, identifying eligible participants can be challenging, time-consuming, and costly. In recent years, the development of natural language processing (NLP) techniques, specifically named entity recognition (NER) and named entity normalization (NEN), have helped to automate the identification and extraction of relevant information from the eligibility criteria (EC) more efficiently, in order to facilitate semi-automatic patient recruitment and enable data FAIRness for clinical trial data. Nevertheless, most current biomedical NER models only provide annotations for a restricted set of entity types that may not be applicable to the clinical trial data. Additionally, accurately performing NEN on entities that are negated using a negative prefix currently lacks established techniques. In this paper, we introduce a pipeline designed for information extraction from AD clinical trial EC, which involves preprocessing of the EC data, clinical NER, and biomedical NEN to Unified Medical Language System (UMLS). Our NER model can identify named entities in seven pre-defined categories, while our NEN model employs a combination of exact match and partial match search strategies, as well as customized rules to accurately normalize entities with negative prefixes. To evaluate the performance of our pipeline, we measured the precision, recall, and F1 score for the NER component, and we manually reviewed the top five mapping results produced by the NEN component. Our evaluation of the pipeline's performance revealed that it can successfully normalize named entities in clinical trial ECs with optimal accuracies. The NER component achieved a overall F1 of 0.816, demonstrating its ability to accurately identify seven types of named entities in clinical text. The NEN component of the pipeline also demonstrated impressive performance, with customized rules and a combination of exact and partial match strategies leading to an accuracy of 0.940 for normalized entities.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2023 ","pages":"558-564"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10815931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitigating Membership Inference in Deep Learning Applications with High Dimensional Genomic Data.","authors":"Chonghao Zhang,&nbsp;Luca Bonomi","doi":"10.1109/ichi54592.2022.00101","DOIUrl":"https://doi.org/10.1109/ichi54592.2022.00101","url":null,"abstract":"<p><p>The use of deep learning techniques in medical applications holds great promises for advancing health care. However, there are growing privacy concerns regarding what information about individual data contributors (i.e., patients in the training set) these deep models may reveal when shared with external users. In this work, we first investigate the membership privacy risks in sharing deep learning models for cancer genomics tasks, and then study the applicability of privacy-protecting strategies for mitigating these privacy risks.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2022 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9473339/pdf/nihms-1815588.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10181248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mining Social Media Data to Predict COVID-19 Case Counts.","authors":"Maksims Kazijevs,&nbsp;Furkan A Akyelken,&nbsp;Manar D Samad","doi":"10.1109/ichi54592.2022.00027","DOIUrl":"https://doi.org/10.1109/ichi54592.2022.00027","url":null,"abstract":"<p><p>The unpredictability and unknowns surrounding the ongoing coronavirus disease (COVID-19) pandemic have led to an unprecedented consequence taking a heavy toll on the lives and economies of all countries. There have been efforts to predict COVID-19 case counts (CCC) using epidemiological data and numerical tokens online, which may allow early preventive measures to slow the spread of the disease. In this paper, we use state-of-the-art natural language processing (NLP) algorithms to numerically encode COVID-19 related tweets originated from eight cities in the United States and predict city-specific CCC up to eight days in the future. A city-embedding is proposed to obtain a time series representation of daily tweets posted from a city, which is then used to predict case counts using a custom long-short term memory (LSTM) model. The universal sentence encoder yields the best normalized root mean squared error (NRMSE) 0.090 (0.039), averaged across all cities in predicting CCC six days in the future. The <i>R</i> ² scores in predicting CCC are more than 0.70 and often over 0.8, which suggests a strong correlation between the actual and our model predicted CCC values. Our analyses show that the NRMSE and <i>R</i> ² scores are consistently robust across different cities and different numbers of time steps in time series data. Results show that the LSTM model can learn the mapping between the NLP-encoded tweet semantics and the case counts, which infers that social media text can be directly mined to identify the future course of the pandemic.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":" ","pages":"104-111"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9490453/pdf/nihms-1836082.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33477762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sharing Time-to-Event Data with Privacy Protection.","authors":"Luca Bonomi, Liyue Fan","doi":"10.1109/ichi54592.2022.00014","DOIUrl":"10.1109/ichi54592.2022.00014","url":null,"abstract":"<p><p>Sharing time-to-event data is beneficial for enabling collaborative research efforts (e.g., survival studies), facilitating the design of effective interventions, and advancing patient care (e.g., early diagnosis). Despite numerous privacy solutions for sharing time-to-event data, recent research studies have shown that external information may become available (e.g., self-disclosure of study participation on social media) to an adversary, posing new privacy concerns. In this work, we formulate a cohort inference attack for time-to-event data sharing, in which an informed adversary aims at inferring the membership of a target individual in a specific cohort. Our study investigates the privacy risks associated with time-to-event data and evaluates the empirical privacy protection offered by popular privacy-protecting solutions (e.g., binning, differential privacy). Furthermore, we propose a novel approach to privately release individual level time-to-event data with high utility, while providing indistinguishability guarantees for the input value. Our method TE-Sanitizer is shown to provide effective mitigation against the inference attacks and high usefulness in survival analysis. The results and discussion provide domain experts with insights on the privacy and the usefulness of the studied methods.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2022 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9473343/pdf/nihms-1815589.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10181249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of Dementia Signals from Longitudinal Clinical Visits Using One-Class Classification.","authors":"Omar A Ibrahim, Sunyang Fu, Maria Vassilaki, Michelle M Mielke, Jennifer St Sauver, Ronald C Petersen, Sunghwan Sohn","doi":"10.1109/ichi54592.2022.00040","DOIUrl":"10.1109/ichi54592.2022.00040","url":null,"abstract":"<p><p>Dementia is one of the major health challenges in aging populations, with 50 million people diagnosed worldwide. However, dementia is often underdiagnosed or delayed resulting in missed opportunities for appropriate care plans. Identifying early signs of dementia is essential for better life quality of aging populations. Monitoring early signs of individual health changes could help clinicians diagnose dementia in its early stages with more effective treatment plans. However, rare data for dementia cases compared to the normal (i.e., imbalance class distribution) make it challenging to develop robust supervised learning models. In order to alleviate this issue, we investigated one-class classification (OCC) techniques, which use only majority class (i.e., normal cases) in model development to detect dementia signals from older adult clinical visits. The OCC models identify abnormality of older adults' longitudinal health conditions to predict incident dementia. The predictive performance of the OCC was compared with a recent streaming clustering-based technique and demonstrated higher predictive power. Our analysis showed that OCC has a promising potential to increase power in predicting dementia.</p>","PeriodicalId":73284,"journal":{"name":"IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics","volume":"2022 ","pages":"211-216"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9728104/pdf/nihms-1852693.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9328507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}