projects:workgroups:nlp-wg
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projects:workgroups:nlp-wg [2021/08/08 19:06] vipina [Start Date] |
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]]\\ | ||
| - | Hua Xu | ||
| ==== 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 - August 11, 2021 (as part of the WG meeting) | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
| - | **Title: Leveraging longitudinal and multi-modal EHR in Survival Analysis** | + | **Agenda** |
| - | **Abstract:** Survival analysis is a fundamental statistical tool that predicts the time of an event. It has multiple healthcare applications in areas, such as hospitalization and patient mortality. Clinicians predict patient outcomes by heterogeneous modalities (e.g., text, images, and lab values). Such data poses significant challenges for traditional survival analysis techniques. In this talk, we present our effort to expand the survival analysis using multimodal, longitudinal EHR data. Our results indicate that extracted high-dimensional features from text and image provide complementary information in addition to structured EHR, and incorporating longitudinal data is useful in time-to-event prediction. | + | 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.\\ | ||
| - | **Presenter:** Dr. Yifan Peng | + | 2) Updates on the progress of ongoing studies |
| - | + | - SDoH | |
| - | Dr. Peng is an assistant professor at the Department of Population Health Sciences at Weill Cornell Medicine. His main research interests include BioNLP and medical image analysis, such as named entity recognition, information extraction, and eye disease diagnosis and prognosis. Before joining Cornell Medicine, Dr. Peng was a research fellow at the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH). He obtained his Ph.D. degree from the University of Delaware. During his doctoral training, he investigated applications of machine learning in biomedical relation extraction, with a focus on deep analysis of the linguistic structures of biomedical texts. | + | - Psychiatry |
| + | - Oncology | ||
| + | 3) NLP book chapter | ||
| ==== Ongoing Projects ==== | ==== Ongoing Projects ==== | ||
| - | TBD | + | * Note type normalization |
| + | * 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 ==== | ||
| - | TBD | + | * Note_NLP table |
| + | * COVID-19 testing normalization (TestNorm) | ||
| + | * Note type | ||
| + | * NLP tools: NLP Wrappers; THEIA; Ananke | ||
| ==== 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) ==== | + | |
| - | * August 11 | + | ==== Upcoming Meeting Dates (2023) ==== |
| - | * September 8 | + | |
| - | * October 13 | + | * June 14 |
| - | * November 10 | + | * July 12 |
| - | * December 8 | + | * August 9 |
| + | * September 13 | ||
| + | * October 11 | ||
| + | * November 8 | ||
| + | * December 13 | ||
| ==== Repository ==== | ==== Repository ==== | ||
| Line 80: | Line 73: | ||
| ==== Past WG meetings (Agenda/Minutes/Recordings) ==== | ==== Past WG meetings (Agenda/Minutes/Recordings) ==== | ||
| - | **2019** | + | **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**\\ | ||
| + | -[[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]] | ||
| + | |||
| + | **2019**\\ | ||
| -[[WG_meeting_10092019]] | -[[WG_meeting_10092019]] | ||
| -[[WG_meeting_09112019]] | -[[WG_meeting_09112019]] | ||
| Line 91: | Line 109: | ||
| -[[WG_meeting_02132019]] | -[[WG_meeting_02132019]] | ||
| -[[WG_meeting_01092019]] | -[[WG_meeting_01092019]] | ||
| - | + | **2018**\\ | |
| - | **2018** | + | |
| -[[WG_meeting_11142018]] | -[[WG_meeting_11142018]] | ||
| -[[WG_meeting_09122018]] | -[[WG_meeting_09122018]] | ||
| Line 102: | Line 119: | ||
| -[[WG_meeting_01102018]] | -[[WG_meeting_01102018]] | ||
| - | **2017** | + | **2017**\\ |
| -[[WG_meeting_12122017]] | -[[WG_meeting_12122017]] | ||
| -[[WG_meeting_10112017]] | -[[WG_meeting_10112017]] | ||
| Line 110: | Line 126: | ||
| -[[WG_meeting_06142017]] | -[[WG_meeting_06142017]] | ||
| - | **2016** | + | **2016**\\ |
| -[[WG_meeting_04202016]] | -[[WG_meeting_04202016]] | ||
| -[[WG_meeting_04132016]] | -[[WG_meeting_04132016]] | ||
| Line 117: | Line 133: | ||
| -[[WG_meeting_01062016]] | -[[WG_meeting_01062016]] | ||
| - | **2015** | + | **2015**\\ |
| -[[WG_meeting_11042015]] | -[[WG_meeting_11042015]] | ||
| -[[projects:workgroups:minutes|WG_meeting_10072015]] | -[[projects:workgroups:minutes|WG_meeting_10072015]] | ||
projects/workgroups/nlp-wg.1628449617.txt.gz · Last modified: 2021/08/08 19:06 by vipina
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