projects:workgroups:nlp-wg
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projects:workgroups:nlp-wg [2021/08/26 22:10] vipina [OHDSI NLP WG Monthly Meeting] |
projects:workgroups:nlp-wg [2023/05/10 01:37] (current) vipina [Ongoing Projects] |
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| The primary goal of the NLP working group is to promote the use of textual information from Electronic Health Records (EHRs) for observational studies under the OHDSI umbrella. To facilitate this objective, the group will develop methods and software that can be implemented to utilize clinical text for studies by the OHDSI community. | The primary goal of the NLP working group is to promote the use of textual information from Electronic Health Records (EHRs) for observational studies under the OHDSI umbrella. To facilitate this objective, the group will develop methods and software that can be implemented to utilize clinical text for studies by the OHDSI community. | ||
| - | ==== Project Lead ==== | + | ==== Workgroup Lead ==== |
| - | Hua Xu [[https://www.ohdsi.org/who-we-are/collaborators/hua-xu/|OHDSI Collaborator Bio]]\\ | + | [[https://www.ohdsi.org/who-we-are/collaborators/hua-xu/|Hua Xu]]\\ |
| Line 13: | Line 13: | ||
| ==== Project Coordinator ==== | ==== Project Coordinator ==== | ||
| - | Vipina K Keloth | + | [[vipina.kuttichikeloth@yale.edu | Vipina K. Keloth ]] |
| ==== OHDSI NLP WG Monthly Meeting ==== | ==== OHDSI NLP WG Monthly Meeting ==== | ||
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| **Where:** [[https://teams.microsoft.com/dl/launcher/launcher.html?url=%2F_%23%2Fl%2Fmeetup-join%2F19%3Acd9841fec6df4f3d8eb6a6bf49ea305f%40thread.tacv2%2F1610663053273%3Fcontext%3D%257b%2522Tid%2522%253a%2522a30f0094-9120-4aab-ba4c-e5509023b2d5%2522%252c%2522Oid%2522%253a%252200626e72-b11c-482a-9dc4-d8eff51c5e5f%2522%257d%26anon%3Dtrue&type=meetup-join&deeplinkId=42431bac-788d-4a7b-8531-5eb2612224a6&directDl=true&msLaunch=true&enableMobilePage=true&suppressPrompt=true|Click here to join the meeting]] | **Where:** [[https://teams.microsoft.com/dl/launcher/launcher.html?url=%2F_%23%2Fl%2Fmeetup-join%2F19%3Acd9841fec6df4f3d8eb6a6bf49ea305f%40thread.tacv2%2F1610663053273%3Fcontext%3D%257b%2522Tid%2522%253a%2522a30f0094-9120-4aab-ba4c-e5509023b2d5%2522%252c%2522Oid%2522%253a%252200626e72-b11c-482a-9dc4-d8eff51c5e5f%2522%257d%26anon%3Dtrue&type=meetup-join&deeplinkId=42431bac-788d-4a7b-8531-5eb2612224a6&directDl=true&msLaunch=true&enableMobilePage=true&suppressPrompt=true|Click here to join the meeting]] | ||
| - | **Monthly Research Webinar:** Upcoming - September 8, 2021 (as part of the WG meeting) | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
| - | **Title: Natural Language Processing for Clinical Excellence: The State of Practices, Opportunities, and Challenges**\\ | + | **Agenda** |
| - | **Abstract:** Rapid growth in adoption of electronic health records (EHRs) has led to an unprecedented expansion in the availability of large longitudinal datasets. Large initiatives such as the Electronic Medical Records and Genomics (eMERGE) Network, the Patient-Centered Outcomes Research Network (PCORNet), and the Observational Health Data Science and Informatics (OHDSI) consortium, have been established and have reported successful applications of secondary use of EHRs in clinical research and practice. In these applications, natural language processing (NLP) technologies have played a crucial role as much of detailed patient information in EHRs is embedded in narrative clinical documents. Meanwhile, a number of clinical NLP systems, such as MedLEE, MetaMap/MetaMap Lite, cTAKES, MedTagger, and i2b2 have been developed and utilized to extract useful information from diverse types of clinical text, such as clinical notes, radiology reports, and pathology reports. This talk will walk through some successful applications of NLP techniques in the clinical domain with potential opportunities and challenges. | + | |
| - | **Presenter: Dr. Yanshan Wang**\\ | + | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ |
| - | Yanshan Wang, PhD, FAMIA is vice chair of Research and assistant professor within the Department of Health Information Management at the University of Pittsburgh. His research interests focus on artificial intelligence (AI), natural language processing (NLP) and machine/deep learning methodologies and applications in health care. His research goal is to leverage different dimensions of data and data-driven computational approaches to meet the needs of clinicians, researchers, patients and customers. Prior to joining Pitt, Dr. Wang was assistant professor in the Department of AI & Informatics at Mayo Clinic. Yanshan has extensive collaborative research experience with physicians, epidemiology researchers, statisticians, NLP researchers, and IT technicians. He has served as investigators for multiple extramural NIH-funded projects and intramural operational projects. He has published over 50 peer-reviewed articles in high-impact medical informatics journals (e.g., JBI, JAMIA), and conferences (e.g., AMIA Annual Symposium, AMIA summit, IEEE BIBM). Dr. Wang is also active in organizing conference workshops and shared tasks in the medical informatics community, including the international Health NLP workshops and the national NLP clinical challenge (n2c2). | + | **Title:** LeafAI: query generator for clinical cohort discovery rivaling a human programmer\\ |
| + | **Abstract:** Identifying study-eligible patients within clinical databases is a critical step in clinical research. However, accurate query design typically requires extensive technical and biomedical expertise. We sought to create a system capable of generating data model-agnostic queries while also providing novel logical reasoning capabilities for complex clinical trial eligibility criteria. We incorporated hybrid deep learning and rule-based modules for these, as well as a knowledge base of the Unified Medical Language System (UMLS) and linked ontologies. To enable data-model agnostic query creation, we introduce a novel method for tagging database schema elements using UMLS concepts. To evaluate our system, called LeafAI, we compared the capability of LeafAI to a human database programmer to identify patients who had been enrolled in 8 clinical trials conducted at our institution. We measured performance by the number of actual enrolled patients matched by generated queries. LeafAI matched a mean 43% of enrolled patients with 27,225 eligible across 8 clinical trials, compared to 27% matched and 14,587 eligible in queries by a human database programmer. The human programmer spent 26 total hours crafting queries compared to several minutes by LeafAI. Finally, we introduce a novel multimodal user interface for interaction with LeafAI.\\ | ||
| + | |||
| + | 2) Updates on the progress of ongoing studies | ||
| + | - SDoH | ||
| + | - Psychiatry | ||
| + | - Oncology | ||
| + | 3) NLP book chapter | ||
| ==== Ongoing Projects ==== | ==== Ongoing Projects ==== | ||
| - | * Clinical Abbreviations | ||
| - | * Post-acute sequelae of SARS-CoV-2 infection (PASC) study | ||
| - | * Extraction, Transformation, and Load Process (ETL) | ||
| * Note type normalization | * Note type normalization | ||
| - | * Open source Python NLP package | + | * Social Determinants of Health |
| + | * Psychiatry - NLP for capturing administration of neuropsychiatric scales and their scores | ||
| + | * Oncology - NLP for getting oncology data using Tumor Reg data as a gold standard for assessing the information obtained through the NLP algorithm | ||
| + | * Book of OHDSI NLP Chapter | ||
| ==== Past Projects ==== | ==== Past Projects ==== | ||
| Line 44: | Line 51: | ||
| ==== Participants ==== | ==== Participants ==== | ||
| - | ^ Participants ^|| | + | A noncomprehensive list of participants: [[ Click here ]] |
| - | | Hua Xu | Abraham Hartzema | Feifan Liu | | + | |
| - | | Anupama Gururaj | David Sontag | Paris Nicolas | | + | |
| - | | Nigam Shah | Arnab Bose | Mark Dredze | | + | |
| - | | Noemie Elhadad | Lian Hu | Masoud Rouhizadeh | | + | |
| - | | Jon Duke | Jan A Kors | Malcolm McRoberts | | + | |
| - | | Alexandre Yahi | J van Der Lei | Nishanth Parameshwar Pavinkurve | | + | |
| - | | Thomas Ginter | Peter R Rijnbeek | Carol Friedman | | + | |
| - | | Olga Patterson | Vivienne Zhu | Miao Chen | | + | |
| - | | George Hripsack | Bob Patterson | Jianlin Shi | | + | |
| - | | Vojtech Huser | Michael Gurley | Vassilis Koutkias | | + | |
| - | | Mark Khayter | Xiaoling Chen | Dan Schlegel | | + | |
| - | | Karthik Natarajan | Hongfang Liu | Mark V Mai | | + | |
| - | | Min Jiang | Hong Yu | Todd Lingren | | + | |
| - | | Scott DuVall | Stephane Meystre | Jose Posada | | + | |
| - | | Xiao Dong | Timothy Miller | Andrew E Williams | | + | |
| - | | Ning Shang | Wendy Chapman | Vignesh Srinivasan | | + | |
| - | | Jessie Tenenbaum | Elizabeth Marshall | Yuan Luo | | + | |
| - | | Kathleen Nogueira | Noa Palmon | Kelly Peterson | | + | |
| - | | Chris Ryan | Danielle Bitterman | Jimyung Park | | + | |
| - | | Kate Weber | Alexander Sivura | Patrick Alba | | + | |
| - | | Tarun | Xi Yang | Meliha Yetisgen | | + | |
| - | | T.M. Seinen | Jiang Bian | Xiyu Ding | | + | |
| - | | Georgina Kennedy | Yaoyun Zhang | Rui Zhang | | + | |
| - | | Paul Heider | | | | + | |
| - | ==== Upcoming Meeting Dates (2021) ==== | + | |
| - | * September 8 | + | ==== Upcoming Meeting Dates (2023) ==== |
| - | * October 13 | + | |
| - | * November 10 | + | * June 14 |
| - | * December 8 | + | * July 12 |
| + | * August 9 | ||
| + | * September 13 | ||
| + | * October 11 | ||
| + | * November 8 | ||
| + | * December 13 | ||
| ==== Repository ==== | ==== Repository ==== | ||
| Line 86: | Line 73: | ||
| ==== Past WG meetings (Agenda/Minutes/Recordings) ==== | ==== Past WG meetings (Agenda/Minutes/Recordings) ==== | ||
| + | **2023**\\ | ||
| + | -[[WG_meeting_may_10_2023]] | ||
| + | -[[WG_meeting_apr_12_2023]] | ||
| + | -[[WG_meeting_mar_08_2023]] | ||
| + | -[[WG_meeting_feb_08_2023]] | ||
| + | -[[WG_meeting_jan_11_2023]] | ||
| + | |||
| + | **2022**\\ | ||
| + | -[[WG_meeting_dec_14_2022]] | ||
| + | -[[WG_meeting_nov_09_2022]] | ||
| + | -[[WG_meeting_sep_14_2022]] | ||
| + | -[[WG_meeting_aug_10_2022]] | ||
| + | -[[WG_meeting_jun_08_2022]] | ||
| + | -[[WG_meeting_may_11_2022]] | ||
| + | -[[WG_meeting_apr_13_2022]] | ||
| + | -[[WG_meeting_mar_09_2022]] | ||
| + | -[[WG_meeting_feb_09_2022]] | ||
| + | -[[WG_meeting_jan_12_2022]] | ||
| + | |||
| **2021**\\ | **2021**\\ | ||
| + | -[[WG_meeting_dec_08_2021]] | ||
| + | -[[WG_meeting_nov_10_2021]] | ||
| + | -[[WG_meeting_oct_13_2021]] | ||
| + | -[[WG_meeting_sep_08_2021]] | ||
| -[[WG_meeting_aug_11_2021]] | -[[WG_meeting_aug_11_2021]] | ||
projects/workgroups/nlp-wg.1630015840.txt.gz · Last modified: 2021/08/26 22:10 by vipina
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