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projects:workgroups:nlp-wg [2022/06/07 14:46] vipina [OHDSI NLP WG Monthly Meeting] |
projects:workgroups:nlp-wg [2023/05/10 01:34] vipina [OHDSI NLP WG Monthly Meeting] |
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==== 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 ==== | ||
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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 Meeting:** Upcoming - June 8, 2022 | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
**Agenda** | **Agenda** | ||
- | - Presentation on “Note type normalization” followed by a discussion. | + | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ |
- | - Brainstorm ideas for a chapter on NLP in the Book of OHDSI | + | **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.\\ | ||
- | ==== Invited talk ==== | + | 2) Updates on the progress of ongoing studies |
- | **Title: Cancer-Focused Natural Language Processing for EHR Data** | + | - SDoH |
+ | - Psychiatry | ||
+ | - Oncology | ||
+ | 3) NLP book chapter | ||
- | **Presenter:** Dr. Kirk Roberts\\ | ||
- | 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. | ||
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==== 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 | ||
==== 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) ==== |
- | * April 13 | + | * March 8 |
- | * May 11 | + | * April 12 |
- | * June 8 | + | * May 10 |
- | * July 13 | + | * June 14 |
- | * August 10 | + | * July 12 |
- | * September 14 | + | * August 9 |
- | * October 12 | + | * September 13 |
- | * November 9 | + | * October 11 |
- | * December 14 | + | * November 8 |
+ | * December 13 | ||
==== Repository ==== | ==== Repository ==== | ||
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==== 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_apr_13_2022]] | ||
-[[WG_meeting_mar_09_2022]] | -[[WG_meeting_mar_09_2022]] |