projects:workgroups:nlp-wg
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projects:workgroups:nlp-wg [2021/11/09 03:58] vipina [Upcoming Meeting Dates (2021)] |
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 ==== |
| - | 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]]\\ |
| Line 13: | Line 13: | ||
| ==== 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 - October 13, 2021 (as part of the WG meeting) | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
| - | **Title: Harnessing Big Data for Population Health: Advancing NLP Techniques to Extract Social-Behavioral Risk Factors from Free Text within Large Electronic Health Record Systems**\\ | + | **Agenda** |
| - | **Abstract:** Social and Behavioral Determinants of Health (SBDH) are powerful drivers of future well-being of individuals, but the clinical community rarely has access to standardized tools to systematically incorporate SBDH into clinical research and decision-making. To address this, we have been creating fundamental resources to systematically identify SBDH from within health records. We incorporate a wide range data sources such as coded clinical data (ICD codes), encoded questionnaires, and annotated texts corpora, and we apply a variety of NLP and AI methods such as heuristic-based natural language inference, conventional machine learning, and contextual neural network models. At the same time, we also focus on the dissemination of our methods and collaborating with external partners to ensure the generalizability of our models across various health systems. Results for heuristic-based, deep learning and ensemble models are promising and we have successfully validated our models on external partners sites. | + | |
| - | **Presenter: Dr. Masoud Rouhizadeh**\\ | + | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ |
| - | Masoud Rouhizadeh is an Assistant Professor in the University of Florida College of Pharmacy, Department of Pharmaceutical Outcomes, under the AI in the Health Sciences Initiative. | + | **Title:** LeafAI: query generator for clinical cohort discovery rivaling a human programmer\\ |
| - | The primary focus of Dr. Rouhizadeh’s research involves applying machine learning and natural language processing methods for identifying clinical concepts from unstructured text and converting them into structured data. Another major part of his research has been developing clinical ontologies and lexical resources, as well as computational models for identifying social and behavioral determinants of health. | + | **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.\\ |
| - | Before joining the UF, Dr. Rouhizadeh was a Faculty Instructor at Biomedical Informatics and Data Science and the Natural Language Processing lead at the Institute for Clinical and Translational Research at the Johns Hopkins University School of Medicine. Prior to JHU, he was a postdoctoral fellow at the University of Pennsylvania’s World Well-Being Project and then at the Penn Institute for Biomedical Informatics. He obtained his Master’s and Ph.D. in Computer Science and Engineering from Oregon Health and Science University and his Master’s in Human Language Technology from the University of Trento, Italy. | + | |
| + | 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 ==== | ||
| Line 47: | Line 51: | ||
| ==== 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 ==== | ||
| Line 87: | 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**\\ | ||
| + | -[[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_sep_08_2021]] | -[[WG_meeting_sep_08_2021]] | ||
| -[[WG_meeting_aug_11_2021]] | -[[WG_meeting_aug_11_2021]] | ||
projects/workgroups/nlp-wg.1636430282.txt.gz · Last modified: 2021/11/09 03:58 by vipina
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