fehiepsi/mimic3

research for MIMIC-III dataset

mimic3

research for MIMIC-III dataset

guide to install

• go to data folder and do wget --user YOURUSERNAME --ask-password -A csv.gz -m -p -E -k -K -np -nd https://physionet.org/works/MIMICIIIClinicalDatabase/files/ with YOURUSERNAME is the email you register for mimic3 dataset
• install postgresql sudo apt-get install postgresql libpq-dev
• install pgadmin4: download wget https://ftp.postgresql.org/pub/pgadmin3/pgadmin4/v1.3/pip/pgadmin4-1.3-py2.py3-none-any.whl and do pip install pgadmin* in your conda environment
• make your computer account a superuser for postgres: sudo su - postgres then psql postgres then CREATE USER youraccount;, ALTER USER youraccount superuser;, and CREATE DATABASE mimic3 OWNER youraccount
• fork the repo git clone --recursive https://github.com/AM2-Labs/mimic3.git
• go the the subfolder cd mimic3/mimic-code/buildmimic/postgres/
• create tables psql mimic3 -f postgres_create_tables.sql -U youraccount
• import data into tables psql mimic3 -f postgres_load_data_gz.sql -U youraccount -v mimic_data_dir='<path_to_data>'
• add indices to database psql mimic3 -f postgres_add_indexes.sql -U your account
• add password to your account psql mimic3 then ALTER USER youraccount PASSWORD 'yourpassword' then ALTER USER youraccount nosuperuser;
• run pgadmin4: go to your python source folder of pgadmin4 cd PATH/lib/python3.5/site-packages/pgadmin4, do python pgAdmin4.py, and go to the browser http://127.0.0.1:5050
• to add database to pgadmin4, right click in Servers -> Create -> Server -> fill name (any name) -> Connection -> host: localhost -> database: mimic3 -> username: youraccount -> pass: yourpassword -> Save

practice to query

• go to https://mimic.physionet.org/tutorials/intro-to-mimic-iii/ and practice

understand tables

• go to https://mimic.physionet.org/mimictables/admissions/
• more at https://mimic.physionet.org/mimicdata/metavision/
• an example: https://www.youtube.com/watch?v=S4Iyp_wONGc

papers

• https://scholar.google.co.kr/scholar?um=1&ie=UTF-8&lr&cites=4115250243685522
• base line 1: https://cs224d.stanford.edu/reports/priyanka.pdf
• base line 2: http://cs224d.stanford.edu/reports/lukelefebure.pdf
• base line 3: http://cs229.stanford.edu/proj2016/report/TanigawaPfohl-ComputationalPredictionOfClinicalOutcomeOfSepsisFromCriticalCareDatabase-report.pdf

mimic3's Issues

Jupyter notebooks?

Hello,

Right now the Jupyter Notebooks only contain a link to the paper. Is there anyway to see the actual Jupyter notebooks that were used by your team?

Thank you.