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projects:workgroups:nlp-wg [2022/06/07 14:48] vipina [Upcoming Meeting Dates (2022)] |
projects:workgroups:nlp-wg [2023/05/10 01:35] vipina [Upcoming Meeting Dates (2023)] |
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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.\\ | ||
+ | 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 | ||
==== 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) ==== |
- | * June 8 | + | * June 14 |
- | * July 13 | + | * July 12 |
- | * August 10 | + | * August 9 |
- | * September 14 | + | * September 13 |
- | * October 12 | + | * October 11 |
- | * November 9 | + | * November 8 |
- | * December 14 | + | * 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]] |