projects:workgroups:nlp-wg
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projects:workgroups:nlp-wg [2022/04/08 19:09] 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 ==== |
| [[https://www.ohdsi.org/who-we-are/collaborators/hua-xu/|Hua Xu]]\\ | [[https://www.ohdsi.org/who-we-are/collaborators/hua-xu/|Hua Xu]]\\ | ||
| Line 13: | Line 13: | ||
| ==== Project Coordinator ==== | ==== Project Coordinator ==== | ||
| - | [[Vipina.KuttichiKeloth@uth.tmc.edu | Vipina K Keloth ]] | + | [[vipina.kuttichikeloth@yale.edu | Vipina K. Keloth ]] |
| ==== OHDSI NLP WG Monthly Meeting ==== | ==== OHDSI NLP WG Monthly Meeting ==== | ||
| Line 20: | Line 20: | ||
| **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 Meeting:** Upcoming - March 09, 2022 | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
| **Agenda** | **Agenda** | ||
| - | - Invited Talk | + | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ |
| - | Title “Cancer-Focused Natural Language Processing for EHR Data” by Dr. Kirk Roberts. | + | **Title:** LeafAI: query generator for clinical cohort discovery rivaling a human programmer\\ |
| - | Kirk Roberts, Ph.D., is an Associate Professor at the UTHealth School of Biomedical Informatics. He has previously conducted research in natural language processing (NLP) in academia, government, and industry. His research work includes using NLP to both extract structured information from unstructured free text and create interactive natural language applications, such as question answering systems and search engines. He actively performs research in clinical information extraction, spatial information extraction, question answering, and information retrieval. His research draws inspiration from fields as diverse as medicine, linguistics, data science, and machine learning. Roberts is also the primary organizer of several TREC biomedical IR tracks and a recipient of numerous federal grants, including an NLM Pathway to Independence Award and an NIBIB Trailblazer Award. | + | **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.\\ |
| - | - Updates on Note_NLP proposal, NLP paper and PASC study. | + | |
| + | 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 ==== | ||
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| A noncomprehensive list of participants: [[ Click here ]] | A noncomprehensive list of participants: [[ Click here ]] | ||
| - | ==== Upcoming Meeting Dates (2022) ==== | + | ==== Upcoming Meeting Dates (2023) ==== |
| - | * March 9 | + | * June 14 |
| - | * April 13 | + | * July 12 |
| - | * May 11 | + | * August 9 |
| - | * June 8 | + | * September 13 |
| - | * July 13 | + | * October 11 |
| - | * August 10 | + | * November 8 |
| - | * September 14 | + | * December 13 |
| - | * October 12 | + | |
| - | * November 9 | + | |
| - | * December 14 | + | |
| ==== Repository ==== | ==== Repository ==== | ||
| Line 71: | 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**\\ | **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_mar_09_2022]] | ||
| -[[WG_meeting_feb_09_2022]] | -[[WG_meeting_feb_09_2022]] | ||
projects/workgroups/nlp-wg.1649444953.txt.gz · Last modified: 2022/04/08 19:09 by vipina
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