diff --git a/GSoC.md b/GSoC.md new file mode 100644 index 0000000..d631352 --- /dev/null +++ b/GSoC.md @@ -0,0 +1,45 @@ +@def title = "JuliaHealth - Google Summer of Code" + +This page lists our [Google Summer of Code (GSoC)](https://summerofcode.withgoogle.com) fellows and their experiences working across the JuliaHealth ecosystem. +Students interested in being a GSoC fellow should review these past projects to get a sense for what we look for in building projects that contribute to the JuliaHealth ecosystem. + +\toc + +# GSoC 2023 + +## JuliaHealth's Tools for Patient-Level Predictions: Strengthening Capacity and Innovation + +**Student:** Fareeda Abdelazeez + +**Mentor:** Jacob Zelko + +[Project Proposal](https://docs.google.com/document/d/18-p6VG6MwvzFdyA45MvXyqxOLVEByFP6D_gff9-E1XE/edit#heading=h.zgq6k5hzq0t) ##add the pdf + +**Summary:** Working with the OMOP CDM (Observational Medical Outcomes Partnership Common Data Model) involves handling large datasets that require a set of tools for extracting necessary data efficiently for various analyses. +The first part of the project focused on improving JuliaHealth's infrastructure by increasing the range of tools available to users. +This involved enabling connections to various databases and working with building understanding on how to robustly work with observational health data. +The second goal was to leverage the capacity built in the previous phase to develop a comprehensive framework for patient-level prediction. +This framework explored how to predict patient cohort outcomes with given treatments and was tested on the [MIMIC III dataset](https://physionet.org/content/mimiciii/1.4/) that was converted to the OMOP CDM. + + + +**Fellowship core accomplishments:** + +The [PR](https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl/pull/54) for OMOPCDMCohortCreator added new features: + +- Enriched OMOPCDMCohortCreator tools +- Intensive tests for new functions +- Updated the documentation + +The [PR](https://github.com/JuliaDatabases/DBConnector.jl/pull/13) +for DBConnector + +- Created a documentation +- Rewired tools used to connect to SQLite,postgresql, MySQL +- Created test unit + +This Jupyter notebook shows the flow of creating a prediction model from OMOP CDM using developed packages through the program. +You can find it on juliahealth website - the tutorial section. +For more details, this [blogpost] (https://medium.com/@fareedaabdelazeez/google-summer-of-code-2023-strengthening-healthcare-with-juliahealth-7b8fde5af9ec) wraps up the details of GSoC program achievements. Check Acknowledgments too! + +- Poster presentation at [JuliaCon 2023, _JuliaHealth's Tools for Patient-Level Predictions: Strengthening Capacity and Innovation_](/assets/JuliaCon-gsoc.pdf) diff --git a/_assets/JuliaCon-gsoc.pdf b/_assets/JuliaCon-gsoc.pdf new file mode 100644 index 0000000..ff8835d Binary files /dev/null and b/_assets/JuliaCon-gsoc.pdf differ diff --git a/_assets/JuliaHealth-Patient-level-prediction.html b/_assets/JuliaHealth-Patient-level-prediction.html new file mode 100644 index 0000000..5ad673a --- /dev/null +++ b/_assets/JuliaHealth-Patient-level-prediction.html @@ -0,0 +1,16901 @@ + + + + + +JuliaHealth-Patient-level-prediction + + + + + + + + + + + + + + + + + + + + +
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  • GitHub
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  • Tutorials
    • diff --git a/_rss/head.xml b/_rss/head.xml new file mode 100644 index 0000000..4c9f62b --- /dev/null +++ b/_rss/head.xml @@ -0,0 +1,37 @@ + + + + + + + <![CDATA[ {{fd2rss website_title}} ]]> + + {{website_url}} + + + + + diff --git a/_rss/item.xml b/_rss/item.xml new file mode 100644 index 0000000..07f6506 --- /dev/null +++ b/_rss/item.xml @@ -0,0 +1,60 @@ + + + + <![CDATA[ {{fd2rss rss_title}} ]]> + + {{fd_full_url}} + {{fd_full_url}} + + + + + + {{if rss_full_content}} + + + + {{end}} + + + {{RFC822 rss_pubdate}} + + + {{isnotempty rss_author}} + {{rss_author}} + {{end}} + {{isnotempty author}} + + {{author}} + + {{end}} + + {{isnotempty rss_category}} + {{rss_category}} + {{end}} + + {{isnotempty rss_comments}} + {{rss_comments}} + {{end}} + + {{isnotempty rss_enclosure}} + {{rss_enclosure}} + {{end}} + diff --git a/tutorials.md b/tutorials.md new file mode 100644 index 0000000..a145326 --- /dev/null +++ b/tutorials.md @@ -0,0 +1,12 @@ +@def title = "JuliaHealth - Tutorials" + +** How to create a patient-Level prediction model using JuliaHealth ** + +This notebook uses the packages: +* [MLJ](https://alan-turing-institute.github.io/MLJ.jl/) for machine learning tasks, including data +* [OMOPCDMCohortCreator](https://github.com/JuliaHealth/OMOPCDMCohortCreator.jl) for dealing with OMOP Databases +* [LibPQ](https://github.com/chris-b1/LibPQ.jl#dbinterface) to connect to the database on the server (hidden for the server security) + +[The notebook](/assets/JuliaHealth-Patient-level-prediction.html) + +The model predicts patients of AFib that got stroke and produces accuracy of 86%