projects:workgroups:nlp-wg
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
projects:workgroups:nlp-wg [2023/05/10 01:30] vipina [Past WG meetings (Agenda/Minutes/Recordings)] |
projects:workgroups:nlp-wg [2023/05/10 01:37] (current) vipina [Ongoing Projects] |
||
|---|---|---|---|
| Line 5: | Line 5: | ||
| 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]]\\ | [[https://www.ohdsi.org/who-we-are/collaborators/hua-xu/|Hua Xu]]\\ | ||
| Line 20: | Line 20: | ||
| **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 - March 8, 2023 | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
| **Agenda** | **Agenda** | ||
| - | 1) Presentation - Dr. Daniel G. Smith, Emory University\\ | + | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ |
| - | **Abstract:** Implementing an NLP process into production is an often challenging task, with considerable requirements for accuracy prior to being relied upon in a clinical workflow. However, including other local members of the clinical and research community in the process at each stage of model selection and development could provide considerable advantages. At Winship Cancer Institute, we’re starting to bring NLP to our research abstractors, as well as our tumor registrars, so that they can provide critical feedback on dictionary curation, NER label verification, and final accuracy of the models in development. We seek feedback from the NLP working group regarding our model of the current process, as well as discuss your experiences in bringing clinical and research staff into the NLP process.\\ | + | **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 | 2) Updates on the progress of ongoing studies | ||
| Line 31: | Line 32: | ||
| - Psychiatry | - Psychiatry | ||
| - Oncology | - Oncology | ||
| - | 3) NLP book chapter and other OKRs | + | 3) NLP book chapter |
| Line 40: | Line 41: | ||
| * Psychiatry - NLP for capturing administration of neuropsychiatric scales and their scores | * 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 | * 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 53: | Line 55: | ||
| ==== Upcoming Meeting Dates (2023) ==== | ==== Upcoming Meeting Dates (2023) ==== | ||
| - | * March 8 | ||
| - | * April 12 | ||
| - | * May 10 | ||
| * June 14 | * June 14 | ||
| * July 12 | * July 12 | ||
projects/workgroups/nlp-wg.1683682248.txt.gz · Last modified: 2023/05/10 01:30 by vipina
Page Tools
