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Retrieval augmented scientific claim verification. 检索增强科学索赔验证。
IF 2.5
JAMIA Open Pub Date : 2024-02-21 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae021
Hao Liu, Ali Soroush, Jordan G Nestor, Elizabeth Park, Betina Idnay, Yilu Fang, Jane Pan, Stan Liao, Marguerite Bernard, Yifan Peng, Chunhua Weng
{"title":"Retrieval augmented scientific claim verification.","authors":"Hao Liu, Ali Soroush, Jordan G Nestor, Elizabeth Park, Betina Idnay, Yilu Fang, Jane Pan, Stan Liao, Marguerite Bernard, Yifan Peng, Chunhua Weng","doi":"10.1093/jamiaopen/ooae021","DOIUrl":"10.1093/jamiaopen/ooae021","url":null,"abstract":"<p><strong>Objective: </strong>To automate scientific claim verification using PubMed abstracts.</p><p><strong>Materials and methods: </strong>We developed CliVER, an end-to-end scientific <b>Cl</b>a<b>i</b>m <b>VER</b>ification system that leverages retrieval-augmented techniques to automatically retrieve relevant clinical trial abstracts, extract pertinent sentences, and use the PICO framework to support or refute a scientific claim. We also created an ensemble of three state-of-the-art deep learning models to classify rationale of support, refute, and neutral. We then constructed CoVERt, a new <b>CO</b>VID <b>VER</b>ifica<b>t</b>ion dataset comprising 15 PICO-encoded drug claims accompanied by 96 manually selected and labeled clinical trial abstracts that either support or refute each claim. We used CoVERt and SciFact (a public scientific claim verification dataset) to assess CliVER's performance in predicting labels. Finally, we compared CliVER to clinicians in the verification of 19 claims from 6 disease domains, using 189 648 PubMed abstracts extracted from January 2010 to October 2021.</p><p><strong>Results: </strong>In the evaluation of label prediction accuracy on CoVERt, CliVER achieved a notable F1 score of 0.92, highlighting the efficacy of the retrieval-augmented models. The ensemble model outperforms each individual state-of-the-art model by an absolute increase from 3% to 11% in the F1 score. Moreover, when compared with four clinicians, CliVER achieved a precision of 79.0% for abstract retrieval, 67.4% for sentence selection, and 63.2% for label prediction, respectively.</p><p><strong>Conclusion: </strong>CliVER demonstrates its early potential to automate scientific claim verification using retrieval-augmented strategies to harness the wealth of clinical trial abstracts in PubMed. Future studies are warranted to further test its clinical utility.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae021"},"PeriodicalIF":2.5,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10919922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060751","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}
引用次数: 0
Medicare meets the cloud: the development of a secure platform for the storage and analysis of claims data. 医疗保险与云计算的结合:开发一个用于存储和分析报销数据的安全平台。
IF 2.5
JAMIA Open Pub Date : 2024-02-09 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae007
Roy L Simpson, Joseph A Lee, Yin Li, Yu Jin Kang, Circe Tsui, Jeannie P Cimiotti
{"title":"Medicare meets the cloud: the development of a secure platform for the storage and analysis of claims data.","authors":"Roy L Simpson, Joseph A Lee, Yin Li, Yu Jin Kang, Circe Tsui, Jeannie P Cimiotti","doi":"10.1093/jamiaopen/ooae007","DOIUrl":"10.1093/jamiaopen/ooae007","url":null,"abstract":"<p><strong>Introduction: </strong>Cloud-based solutions are a modern-day necessity for data intense computing. This case report describes in detail the development and implementation of Amazon Web Services (AWS) at Emory-a secure, reliable, and scalable platform to store and analyze identifiable research data from the Centers for Medicare and Medicaid Services (CMS).</p><p><strong>Materials and methods: </strong>Interdisciplinary teams from CMS, MBL Technologies, and Emory University collaborated to ensure compliance with CMS policy that consolidates laws, regulations, and other drivers of information security and privacy.</p><p><strong>Results: </strong>A dedicated team of individuals ensured successful transition from a physical storage server to a cloud-based environment. This included implementing access controls, vulnerability scanning, and audit logs that are reviewed regularly with a remediation plan. User adaptation required specific training to overcome the challenges of cloud computing.</p><p><strong>Conclusion: </strong>Challenges created opportunities for lessons learned through the creation of an end-product accepted by CMS and shared across disciplines university-wide.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae007"},"PeriodicalIF":2.5,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10856805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724334","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}
引用次数: 0
smdi: an R package to perform structural missing data investigations on partially observed confounders in real-world evidence studies. smdi:一个 R 软件包,用于对真实世界证据研究中部分观察到的混杂因素进行结构性缺失数据调查。
IF 2.5
JAMIA Open Pub Date : 2024-01-31 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae008
Janick Weberpals, Sudha R Raman, Pamela A Shaw, Hana Lee, Bradley G Hammill, Sengwee Toh, John G Connolly, Kimberly J Dandreo, Fang Tian, Wei Liu, Jie Li, José J Hernández-Muñoz, Robert J Glynn, Rishi J Desai
{"title":"smdi: an R package to perform structural missing data investigations on partially observed confounders in real-world evidence studies.","authors":"Janick Weberpals, Sudha R Raman, Pamela A Shaw, Hana Lee, Bradley G Hammill, Sengwee Toh, John G Connolly, Kimberly J Dandreo, Fang Tian, Wei Liu, Jie Li, José J Hernández-Muñoz, Robert J Glynn, Rishi J Desai","doi":"10.1093/jamiaopen/ooae008","DOIUrl":"10.1093/jamiaopen/ooae008","url":null,"abstract":"<p><strong>Objectives: </strong>Partially observed confounder data pose a major challenge in statistical analyses aimed to inform causal inference using electronic health records (EHRs). While analytic approaches such as imputation are available, assumptions on underlying missingness patterns and mechanisms must be verified. We aimed to develop a toolkit to streamline missing data diagnostics to guide choice of analytic approaches based on meeting necessary assumptions.</p><p><strong>Materials and methods: </strong>We developed the smdi (structural missing data investigations) R package based on results of a previous simulation study which considered structural assumptions of common missing data mechanisms in EHR.</p><p><strong>Results: </strong>smdi enables users to run principled missing data investigations on partially observed confounders and implement functions to visualize, describe, and infer potential missingness patterns and mechanisms based on observed data.</p><p><strong>Conclusions: </strong>The smdi R package is freely available on CRAN and can provide valuable insights into underlying missingness patterns and mechanisms and thereby help improve the robustness of real-world evidence studies.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae008"},"PeriodicalIF":2.5,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139673099","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}
引用次数: 0
Assessing the use of HL7 FHIR for implementing the FAIR guiding principles: a case study of the MIMIC-IV Emergency Department module. 评估使用 HL7 FHIR 实施 FAIR 指导原则的情况:MIMIC-IV 急诊科模块案例研究。
IF 2.5
JAMIA Open Pub Date : 2024-01-27 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae002
Philip van Damme, Matthias Löbe, Nirupama Benis, Nicolette F de Keizer, Ronald Cornet
{"title":"Assessing the use of HL7 FHIR for implementing the FAIR guiding principles: a case study of the MIMIC-IV Emergency Department module.","authors":"Philip van Damme, Matthias Löbe, Nirupama Benis, Nicolette F de Keizer, Ronald Cornet","doi":"10.1093/jamiaopen/ooae002","DOIUrl":"10.1093/jamiaopen/ooae002","url":null,"abstract":"<p><strong>Objectives: </strong>To provide a real-world example on how and to what extent Health Level Seven Fast Healthcare Interoperability Resources (FHIR) implements the Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles for scientific data. Additionally, presents a list of FAIR implementation choices for supporting future FAIR implementations that use FHIR.</p><p><strong>Materials and methods: </strong>A case study was conducted on the Medical Information Mart for Intensive Care-IV Emergency Department (MIMIC-ED) dataset, a deidentified clinical dataset converted into FHIR. The FAIRness of this dataset was assessed using a set of common FAIR assessment indicators.</p><p><strong>Results: </strong>The FHIR distribution of MIMIC-ED, comprising an implementation guide and demo data, was more FAIR compared to the non-FHIR distribution. The FAIRness score increased from 60 to 82 out of 95 points, a relative improvement of 37%. The most notable improvements were observed in interoperability, with a score increase from 5 to 19 out of 19 points, and reusability, with a score increase from 8 to 14 out of 24 points. A total of 14 FAIR implementation choices were identified.</p><p><strong>Discussion: </strong>Our work examined how and to what extent the FHIR standard contributes to FAIR data. Challenges arose from interpreting the FAIR assessment indicators. This study stands out for providing a real-world example of a dataset that was made more FAIR using FHIR.</p><p><strong>Conclusion: </strong>To the best of our knowledge, this is the first study that formally assessed the conformance of a FHIR dataset to the FAIR principles. FHIR improved the accessibility, interoperability, and reusability of MIMIC-ED. Future research should focus on implementing FHIR in research data infrastructures.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae002"},"PeriodicalIF":2.5,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10822118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571801","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}
引用次数: 0
Design and evaluation of an electronic prospective medication order review system for medication orders in the inpatient setting. 针对住院病人用药医嘱的电子前瞻性用药医嘱审查系统的设计与评估。
IF 2.1
JAMIA Open Pub Date : 2024-01-27 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae003
Pooja Ojha, Benjamin J Anderson, Evan W Draper, Susan M Flaker, Mark H Siska, Kristin C Mara, Brian D Kennedy, Diana J Schreier
{"title":"Design and evaluation of an electronic prospective medication order review system for medication orders in the inpatient setting.","authors":"Pooja Ojha, Benjamin J Anderson, Evan W Draper, Susan M Flaker, Mark H Siska, Kristin C Mara, Brian D Kennedy, Diana J Schreier","doi":"10.1093/jamiaopen/ooae003","DOIUrl":"10.1093/jamiaopen/ooae003","url":null,"abstract":"<p><strong>Objectives: </strong>Since the 1970s, a plethora of tools have been introduced to support the medication use process. However, automation initiatives to assist pharmacists in prospectively reviewing medication orders are lacking. The review of many medications may be protocolized and implemented in an algorithmic fashion utilizing discrete data from the electronic health record (EHR). This research serves as a proof of concept to evaluate the capability and effectiveness of an electronic prospective medication order review (EPMOR) system compared to pharmacists' review.</p><p><strong>Materials and methods: </strong>A subset of the most frequently verified medication orders were identified for inclusion. A team of clinical pharmacist experts developed best-practice EPMOR criteria. The established criteria were incorporated into conditional logic built within the EHR. Verification outcomes from the pharmacist (human) and EPMOR (automation) were compared.</p><p><strong>Results: </strong>Overall, 13 404 medication orders were included. Of those orders, 13 133 passed pharmacist review, 7388 of which passed EPMOR. A total of 271 medication orders failed pharmacist review due to order modification or discontinuation, 105 of which passed EPMOR. Of the 105 orders, 19 were duplicate orders correctly caught by both EPMOR and pharmacists, but the opposite duplicate order was rejected, 51 orders failed due to scheduling changes.</p><p><strong>Discussion: </strong>This simulation was capable of effectively discriminating and triaging orders. Protocolization and automation of the prospective medication order review process in the EHR appear possible using clinically driven algorithms.</p><p><strong>Conclusion: </strong>Further research is necessary to refine such algorithms to maximize value, improve efficiency, and minimize safety risks in preparation for the implementation of fully automated systems.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae003"},"PeriodicalIF":2.1,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10822119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571803","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}
引用次数: 0
Feasibility of cross-vendor linkage of ophthalmic images with electronic health record data: an analysis from the IRIS Registry®. 眼科图像与电子健康记录数据跨供应商链接的可行性:IRIS Registry® 分析。
IF 2.5
JAMIA Open Pub Date : 2024-01-25 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae005
Michael Mbagwu, Zhongdi Chu, Durga Borkar, Alex Koshta, Nisarg Shah, Aracelis Torres, Hylton Kalvaria, Flora Lum, Theodore Leng
{"title":"Feasibility of cross-vendor linkage of ophthalmic images with electronic health record data: an analysis from the IRIS Registry<sup>®</sup>.","authors":"Michael Mbagwu, Zhongdi Chu, Durga Borkar, Alex Koshta, Nisarg Shah, Aracelis Torres, Hylton Kalvaria, Flora Lum, Theodore Leng","doi":"10.1093/jamiaopen/ooae005","DOIUrl":"10.1093/jamiaopen/ooae005","url":null,"abstract":"<p><strong>Purpose: </strong>To link compliant, universal Digital Imaging and Communications in Medicine (DICOM) ophthalmic imaging data at the individual patient level with the American Academy of Ophthalmology IRIS<sup>®</sup> Registry (Intelligent Research in Sight).</p><p><strong>Design: </strong>A retrospective study using de-identified EHR registry data.</p><p><strong>Subjects participants controls: </strong>IRIS Registry records.</p><p><strong>Materials and methods: </strong>DICOM files of several imaging modalities were acquired from two large retina ophthalmology practices. Metadata tags were extracted and harmonized to facilitate linkage to the IRIS Registry using a proprietary, heuristic patient-matching algorithm, adhering to HITRUST guidelines. Linked patients and images were assessed by image type and clinical diagnosis. Reasons for failed linkage were assessed by examining patients' records.</p><p><strong>Main outcome measures: </strong>Success rate of linking clinicoimaging and EHR data at the patient level.</p><p><strong>Results: </strong>A total of 2 287 839 DICOM files from 54 896 unique patients were available. Of these, 1 937 864 images from 46 196 unique patients were successfully linked to existing patients in the registry. After removing records with abnormal patient names and invalid birthdates, the success linkage rate was 93.3% for images. 88.2% of all patients at the participating practices were linked to at least one image.</p><p><strong>Conclusions and relevance: </strong>Using identifiers from DICOM metadata, we created an automated pipeline to connect longitudinal real-world clinical data comprehensively and accurately to various imaging modalities from multiple manufacturers at the patient and visit levels. The process has produced an enriched and multimodal IRIS Registry, bridging the gap between basic research and clinical care by enabling future applications in artificial intelligence algorithmic development requiring large linked clinicoimaging datasets.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae005"},"PeriodicalIF":2.5,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10811449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571868","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}
引用次数: 0
Incorporation of emergent symptoms and genetic covariates improves prediction of aromatase inhibitor therapy discontinuation. 纳入突发症状和遗传协变量可提高对芳香化酶抑制剂停药的预测。
IF 2.1
JAMIA Open Pub Date : 2024-01-19 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae006
Ilia Rattsev, Vered Stearns, Amanda L Blackford, Daniel L Hertz, Karen L Smith, James M Rae, Casey Overby Taylor
{"title":"Incorporation of emergent symptoms and genetic covariates improves prediction of aromatase inhibitor therapy discontinuation.","authors":"Ilia Rattsev, Vered Stearns, Amanda L Blackford, Daniel L Hertz, Karen L Smith, James M Rae, Casey Overby Taylor","doi":"10.1093/jamiaopen/ooae006","DOIUrl":"10.1093/jamiaopen/ooae006","url":null,"abstract":"<p><strong>Objectives: </strong>Early discontinuation is common among breast cancer patients taking aromatase inhibitors (AIs). Although several predictors have been identified, it is unclear how to simultaneously consider multiple risk factors for an individual. We sought to develop a tool for prediction of AI discontinuation and to explore how predictive value of risk factors changes with time.</p><p><strong>Materials and methods: </strong>Survival machine learning was used to predict time-to-discontinuation of AIs in 181 women who enrolled in a prospective cohort. Models were evaluated via time-dependent area under the curve (AUC), c-index, and integrated Brier score. Feature importance was analysis was conducted via Shapley Additive Explanations (SHAP) and time-dependence of their predictive value was analyzed by time-dependent AUC. Personalized survival curves were constructed for risk communication.</p><p><strong>Results: </strong>The best-performing model incorporated genetic risk factors and changes in patient-reported outcomes, achieving mean time-dependent AUC of 0.66, and AUC of 0.72 and 0.67 at 6- and 12-month cutoffs, respectively. The most significant features included variants in <i>ESR1</i> and emergent symptoms. Predictive value of genetic risk factors was highest in the first year of treatment. Decrease in physical function was the strongest independent predictor at follow-up.</p><p><strong>Discussion and conclusion: </strong>Incorporation of genomic and 3-month follow-up data improved the ability of the models to identify the individuals at risk of AI discontinuation. Genetic risk factors were particularly important for predicting early discontinuers. This study provides insight into the complex nature of AI discontinuation and highlights the importance of incorporating genetic risk factors and emergent symptoms into prediction models.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae006"},"PeriodicalIF":2.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10799747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139514103","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}
引用次数: 0
A platform for connecting social media data to domain-specific topics using large language models: an application to student mental health. 利用大型语言模型将社交媒体数据与特定领域主题联系起来的平台:学生心理健康应用。
IF 2.5
JAMIA Open Pub Date : 2024-01-18 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooae001
Leonard Ruocco, Yuqian Zhuang, Raymond Ng, Richard J Munthali, Kristen L Hudec, Angel Y Wang, Melissa Vereschagin, Daniel V Vigo
{"title":"A platform for connecting social media data to domain-specific topics using large language models: an application to student mental health.","authors":"Leonard Ruocco, Yuqian Zhuang, Raymond Ng, Richard J Munthali, Kristen L Hudec, Angel Y Wang, Melissa Vereschagin, Daniel V Vigo","doi":"10.1093/jamiaopen/ooae001","DOIUrl":"10.1093/jamiaopen/ooae001","url":null,"abstract":"<p><strong>Objectives: </strong>To design a novel artificial intelligence-based software platform that allows users to analyze text data by identifying various coherent topics and parts of the data related to a specific research theme-of-interest (TOI).</p><p><strong>Materials and methods: </strong>Our platform uses state-of-the-art unsupervised natural language processing methods, building on top of a large language model, to analyze social media text data. At the center of the platform's functionality is BERTopic, which clusters social media posts, forming collections of words representing distinct topics. A key feature of our platform is its ability to identify whole sentences corresponding to topic words, vastly improving the platform's ability to perform downstream similarity operations with respect to a user-defined TOI.</p><p><strong>Results: </strong>Two case studies on mental health among university students are performed to demonstrate the utility of the platform, focusing on signals within social media (Reddit) data related to depression and their connection to various emergent themes within the data.</p><p><strong>Discussion and conclusion: </strong>Our platform provides researchers with a readily available and inexpensive tool to parse large quantities of unstructured, noisy data into coherent themes, as well as identifying portions of the data related to the research TOI. While the development process for the platform was focused on mental health themes, we believe it to be generalizable to other domains of research as well.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooae001"},"PeriodicalIF":2.5,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10799551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139514512","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}
引用次数: 0
Topic modeling on clinical social work notes for exploring social determinants of health factors. 以临床社会工作笔记为主题建模,探讨健康的社会决定因素。
IF 2.5
JAMIA Open Pub Date : 2024-01-14 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooad112
Shenghuan Sun, Travis Zack, Christopher Y K Williams, Madhumita Sushil, Atul J Butte
{"title":"Topic modeling on clinical social work notes for exploring social determinants of health factors.","authors":"Shenghuan Sun, Travis Zack, Christopher Y K Williams, Madhumita Sushil, Atul J Butte","doi":"10.1093/jamiaopen/ooad112","DOIUrl":"10.1093/jamiaopen/ooad112","url":null,"abstract":"<p><strong>Objective: </strong>Existing research on social determinants of health (SDoH) predominantly focuses on physician notes and structured data within electronic medical records. This study posits that social work notes are an untapped, potentially rich source for SDoH information. We hypothesize that clinical notes recorded by social workers, whose role is to ameliorate social and economic factors, might provide a complementary information source of data on SDoH compared to physician notes, which primarily concentrate on medical diagnoses and treatments. We aimed to use word frequency analysis and topic modeling to identify prevalent terms and robust topics of discussion within a large cohort of social work notes including both outpatient and in-patient consultations.</p><p><strong>Materials and methods: </strong>We retrieved a diverse, deidentified corpus of 0.95 million clinical social work notes from 181 644 patients at the University of California, San Francisco. We conducted word frequency analysis related to ICD-10 chapters to identify prevalent terms within the notes. We then applied Latent Dirichlet Allocation (LDA) topic modeling analysis to characterize this corpus and identify potential topics of discussion, which was further stratified by note types and disease groups.</p><p><strong>Results: </strong>Word frequency analysis primarily identified medical-related terms associated with specific ICD10 chapters, though it also detected some subtle SDoH terms. In contrast, the LDA topic modeling analysis extracted 11 topics explicitly related to social determinants of health risk factors, such as financial status, abuse history, social support, risk of death, and mental health. The topic modeling approach effectively demonstrated variations between different types of social work notes and across patients with different types of diseases or conditions.</p><p><strong>Discussion: </strong>Our findings highlight LDA topic modeling's effectiveness in extracting SDoH-related themes and capturing variations in social work notes, demonstrating its potential for informing targeted interventions for at-risk populations.</p><p><strong>Conclusion: </strong>Social work notes offer a wealth of unique and valuable information on an individual's SDoH. These notes present consistent and meaningful topics of discussion that can be effectively analyzed and utilized to improve patient care and inform targeted interventions for at-risk populations.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooad112"},"PeriodicalIF":2.5,"publicationDate":"2024-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10788143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139466752","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}
引用次数: 0
An economic evaluation of the expansion of electronic case reporting in an academic healthcare setting. 在学术医疗机构推广电子病例报告的经济评估。
IF 2.5
JAMIA Open Pub Date : 2024-01-12 eCollection Date: 2024-04-01 DOI: 10.1093/jamiaopen/ooad102
Joel Hartsell, Fernando A Wilson, Kimberley Shoaf, Angela Dunn, Matthew H Samore, Catherine Janes Staes
{"title":"An economic evaluation of the expansion of electronic case reporting in an academic healthcare setting.","authors":"Joel Hartsell, Fernando A Wilson, Kimberley Shoaf, Angela Dunn, Matthew H Samore, Catherine Janes Staes","doi":"10.1093/jamiaopen/ooad102","DOIUrl":"10.1093/jamiaopen/ooad102","url":null,"abstract":"<p><strong>Objectives: </strong>Determine the economic cost or benefit of expanding electronic case reporting (eCR) for 29 reportable conditions beyond the initial eCR implementation for COVID-19 at an academic health center.</p><p><strong>Materials and methods: </strong>The return on investment (ROI) framework was used to quantify the economic impact of the expansion of eCR from the perspective of an academic health system over a 5-year time horizon. Sensitivity analyses were performed to assess key factors such as personnel cost, inflation, and number of expanded conditions.</p><p><strong>Results: </strong>The total implementation costs for the implementation year were estimated to be $5031.46. The 5-year ROI for the expansion of eCR for the 29 conditions is expected to be 142% (net present value of savings: $7166). Based on the annual ROI, estimates suggest that the savings from the expansion of eCR will cover implementation costs in approximately 4.8 years. All sensitivity analyses yielded a strong ROI for the expansion of eCR.</p><p><strong>Discussion and conclusion: </strong>Our findings suggest a strong ROI for the expansion of eCR at UHealth, with the most significant cost savings observed implementing eCR for all reportable conditions. An early effort to ensure data quality is recommended to expedite the transition from parallel reporting to production to improve the ROI for healthcare organizations. This study demonstrates a positive ROI for the expansion of eCR to additional reportable conditions beyond COVID-19 in an academic health setting, such as UHealth. While this evaluation focuses on the 5-year time horizon, the potential benefit could extend further.</p>","PeriodicalId":36278,"journal":{"name":"JAMIA Open","volume":"7 1","pages":"ooad102"},"PeriodicalIF":2.5,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10784733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139466610","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}
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