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projects:workgroups:nlp-wg [2021/11/09 04:41] vipina [OHDSI NLP WG Monthly Meeting] |
projects:workgroups:nlp-wg [2023/05/10 01:35] vipina [Upcoming Meeting Dates (2023)] |
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==== Project Lead ==== | ==== Project 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]]\\ |
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==== 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 Meeting:** Upcoming - November 10, 2021 | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
- | + | ||
- | **Agenda**\\ | + | |
- | + | ||
- | * Overview of the Post-acute sequelae of SARS-CoV-2 infection (PASC) study | + | |
- | * Inviting participation for a project on Clinical Abbreviations [[https://ohdsiorg.sharepoint.com/:v:/r/sites/Workgroup-NLPNaturalLanguageProcessing/Shared%20Documents/General/Monthly%20Meeting%20Recordings/OHDSI_NLP_WG/OHDSI%20NLP%20WG%20Monthly%20Meeting-20210714_180313-Meeting%20Recording.mp4?csf=1&web=1&e=Nwy75h|Link to the meeting describing the project]] | + | |
- | * Discussion on the OMOP CDM Note_NLP paper draft and author guidelines. | + | |
- | * New project suggestions from the working group members. | + | |
+ | **Agenda** | ||
+ | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ | ||
+ | **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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==== 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) ==== | + | |
- | * November 10 | + | ==== Upcoming Meeting Dates (2023) ==== |
- | * December 8 | + | |
+ | * June 14 | ||
+ | * July 12 | ||
+ | * August 9 | ||
+ | * September 13 | ||
+ | * October 11 | ||
+ | * 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**\\ | ||
+ | -[[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_oct_13_2021]] | ||
-[[WG_meeting_sep_08_2021]] | -[[WG_meeting_sep_08_2021]] |