MIMIC Code Repository: Code shared by the research community for the MIMIC-III database

Overview

MIMIC Code Repository Build Status DOI

The MIMIC Code Repository is intended to be a central hub for sharing, refining, and reusing code used for analysis of the MIMIC critical care database. To find out more about MIMIC, please see: https://mimic.mit.edu. Source code for the website is in the mimic-website GitHub repository.

You can read more about the code repository in the following open access paper: The MIMIC Code Repository: enabling reproducibility in critical care research.

Cloud access to datasets

The various MIMIC databases are available on Google Cloud Platform (GCP) and Amazon Web Services (AWS). To access the data on the cloud, simply add the relevant cloud identifier to your PhysioNet profile. Then request access to the dataset for the particular cloud platform via the PhysioNet project page. Further instructions are available on the MIMIC website.

Navigating this repository

This repository contains code for five databases on PhysioNet:

  • MIMIC-III - critical care data for patients admitted to ICUs at the BIDMC between 2001 - 2012
  • MIMIC-IV - hospital and critical care data for patients admitted to the ED or ICU between 2008 - 2019
  • MIMIC-IV-ED - emergency department data for individuals attending the ED between 2011 - 2019
  • MIMIC-IV Waveforms (TBD) - this dataset has yet to be published.
  • MIMIC-CXR - chest x-ray imaging and deidentified free-text radiology reports for patients admitted to the ED from 2012 - 2016

The repository contains one top-level folder containing community developed code for each datasets:

  • mimic-iii - build scripts for MIMIC-III, derived concepts which are available on the physionet-data.mimiciii_derived dataset on BigQuery, and tutorials.
  • mimic-iv - build scripts for MIMIC-IV, derived concepts which are available on the physionet-data.mimic_derived dataset on BigQuery, and tutorials.
  • mimic-iv-cxr - code for loading and analyzing both dicom (mimic-iv-cxr/dcm) and text (mimic-iv-cxr/txt) data. In order to clearly indicate that MIMIC-CXR can be linked with MIMIC-IV, we have named this folder mimic-iv-cxr, and any references to MIMIC-CXR / MIMIC-IV-CXR are interchangeable.
  • mimic-iv-ed - build scripts for MIMIC-IV-ED.
  • mimic-iv-waveforms - TBD

Each subfolder has a README with further detail regarding its content.

Launch MIMIC-III in AWS

MIMIC-III is available on AWS (and MIMIC-IV will be available in the future). Use the below Launch Stack button to deploy access to the MIMIC-III dataset into your AWS account. This will give you real-time access to the MIMIC-III data in your AWS account without having to download a copy of the MIMIC-III dataset. It will also deploy a Jupyter Notebook with access to the content of this GitHub repository in your AWS account. Prior to launching this, please login to the MIMIC PhysioNet website, input your AWS account number, and request access to the MIMIC-III Clinical Database on AWS.

To start this deployment, click the Launch Stack button. On the first screen, the template link has already been specified, so just click next. On the second screen, provide a Stack name (letters and numbers) and click next, on the third screen, just click next. On the forth screen, at the bottom, there is a box that says I acknowledge that AWS CloudFormation might create IAM resources.. Check that box, and then click Create. Once the Stack has complete deploying, look at the Outputs tab of the AWS CloudFormation console for links to your Juypter Notebooks instance.

cloudformation-launch-stack

Other useful tools

  • Bloatectomy (paper) - A python based package for removing duplicate text in clinical notes
  • Medication categories - Python script for extracting medications from free-text notes
  • MIMIC Extract (paper) - A python based package for transforming MIMIC-III data into a machine learning friendly format
  • FIDDLE (paper) - A python based package for a FlexIble Data-Driven pipeLinE (FIDDLE), transforming structured EHR data into a machine learning friendly format

Acknowledgement

If you use code or concepts available in this repository, we would be grateful if you would:

@article{johnson2018mimic,
  title={The MIMIC Code Repository: enabling reproducibility in critical care research},
  author={Johnson, Alistair E W and Stone, David J and Celi, Leo A and Pollard, Tom J},
  journal={Journal of the American Medical Informatics Association},
  volume={25},
  number={1},
  pages={32--39},
  year={2018},
  publisher={Oxford University Press}
}

Contributing

Our team has worked hard to create and share the MIMIC dataset. We encourage you to share the code that you use for data processing and analysis. Sharing code helps to make studies reproducible and promotes collaborative research. To contribute, please:

We encourage users to share concepts they have extracted by writing code which generates a materialized view. These materialized views can then be used by researchers around the world to speed up data extraction. For example, ventilation durations can be acquired by creating the ventdurations view in concepts/durations/ventilation_durations.sql.

License

By committing your code to the MIMIC Code Repository you agree to release the code under the MIT License attached to the repository.

Coding style

Please refer to the style guide for guidelines on formatting your code for the repository.

Comments
  • How to determine IV start/end time? Ambiguity in dose.

    How to determine IV start/end time? Ambiguity in dose.

    Hi,

    For vancomycin inputevents_mv row_id=429 gives starttime at 8 and endtime at 8:01. How to determine actual administration duration? In row_id=462 amount is 500. What does it mean? Perhaps this came from half 1g frozen bag or 500mg vial? For row_id=429 the amount=1 dose which is quite ambiguous as well. In both cases rate=0.

    Thanks in advance for any suggestions.

    L

    mimic-iii 
    opened by lmockus 27
  • Could not stat file chartevents.csv unknown error

    Could not stat file chartevents.csv unknown error

    Prerequisites

    • [ X] Put an X between the brackets on this line if you have done all of the following:
      • Checked the online documentation: https://mimic.physionet.org/about/mimic/
      • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

    When I run Postgres_load_data script, first three table are loaded and after that I got message: could not stat file CHARTEVENTS.csv: unknown error. Is anyone has this situation and can help.

    mimic-iii 
    opened by Lejla1979 26
  • Installing MIMIC-III in a local Postgres database is slow

    Installing MIMIC-III in a local Postgres database is slow

    Hi !

    I'm trying to load the MIMIC-III data into a local postgres database by following instructions from this link: https://mimic.physionet.org/tutorials/install-mimic-locally-ubuntu/

    So far despite leaving it overnight, it consistently hangs at this stage:

    $ psql -f postgres_load_data.sql -U mimic -v mimic_data_dir='/Documents/MIMIC_III/' SET

    COPY 58976

    COPY 34499

    COPY 7567

    Here's the configuration of my machine: MacBook Air (13-inch, Early 2014) Processor: 1.7 GHz Intel Core i7 Memory: 8 GB 1600 MHz DDR3

    How long should it take to load this data on a machine with my configuration tentatively? The website states it might take several hours, but I didn't find any explicit benchmarking information.

    Should I attempt to load this local instance using a machine with more RAM available?

    I look forward to your guidance on this. Thanks!

    mimic-iii 
    opened by postgres-newbie 22
  • Postgres CHARTEVENTS partition is no longer efficient

    Postgres CHARTEVENTS partition is no longer efficient

    With the addition of text data (a fix in MIMIC-III v1.4), the partitioning of CHARTEVENTS is no longer effectively distributing the data.

    with drb_stats as (
    select 1 as bucket, 1 as itemid_min , 210 as itemid_max UNION
    select 2 as bucket, 210 as itemid_min     , 250 as itemid_max UNION
    select 3 as bucket, 250 as itemid_min     , 614 as itemid_max UNION
    select 4 as bucket, 614 as itemid_min     , 640 as itemid_max UNION
    select 5 as bucket, 640 as itemid_min     , 742 as itemid_max UNION
    select 6 as bucket, 742 as itemid_min     , 1800 as itemid_max UNION
    select 7 as bucket, 1800 as itemid_min    , 2700 as itemid_max UNION
    select 8 as bucket, 2700 as itemid_min    , 3700 as itemid_max UNION
    select 9 as bucket, 3700 as itemid_min    , 4700 as itemid_max UNION
    select 10 as bucket, 4700 as itemid_min    , 6000 as itemid_max UNION
    select 11 as bucket, 6000 as itemid_min    , 7000 as itemid_max UNION
    select 12 as bucket, 7000 as itemid_min    , 8000 as itemid_max UNION
    select 13 as bucket, 8000 as itemid_min    , 220074 as itemid_max UNION
    select 14 as bucket, 220074 as itemid_min  , 323769 as itemid_max
    ),
    histogram as (
    select bucket, itemid_min, itemid_max, count(*) as freq
    from drb_stats drb
    left join chartevents ce
    on ce.itemid >= drb.itemid_min and ce.itemid < drb.itemid_max
    group by bucket, itemid_min, itemid_max
    order by bucket, itemid_min, itemid_max
    )
    select bucket, itemid_min, itemid_max,
    repeat('*', (freq::float / max(freq) over() * 50)::int) as bar
    from histogram;
    
     bucket | itemid_min | itemid_max |                        bar                         
    --------+------------+------------+----------------------------------------------------
          1 |          1 |        210 | *******************
          2 |        210 |        250 | *******
          3 |        250 |        614 | *******************
          4 |        614 |        640 | *****
          5 |        640 |        742 | *********
          6 |        742 |       1800 | **************
          7 |       1800 |       2700 | 
          8 |       2700 |       3700 | *****************
          9 |       3700 |       4700 | *
         10 |       4700 |       6000 | *****
         11 |       6000 |       7000 | 
         12 |       7000 |       8000 | 
         13 |       8000 |     220074 | ********************
         14 |     220074 |     323769 | **************************************************
    

    Essentially, the addition of the text data added ~100 million rows to ITEMIDs > 220000. I've noticed queries are going slower and I'm sure users will start to notice this too. Perhaps we should take this opportunity move to a smarter partitioning strategy - one based on the type of data stored with the ITEMID (e.g. the Metavision text data goes into a few partitions of its own, vital sign data goes into its own partition, etc). I'd welcome thoughts from anyone who has any - @parisni @tompollard

    mimic-iii 
    opened by alistairewj 18
  • MIMIC-IV Database Demo

    MIMIC-IV Database Demo

    First of all: thanks for the great project !

    Is there a plan to release a database demo for the MIMIC-IV as well? There is already one for the MIMIC-III.

    Thanks !

    mimic-iv 
    opened by hannesUlrich 16
  • MIMIC III Waveform Data

    MIMIC III Waveform Data

    Apologies if this is not the right place to ask this question.

    The MIMIC III Documentation points to "A separate, complementary resource named the “MIMIC-III Waveform Database” contains high resolution waveforms and numerics..." https://mimic.physionet.org/mimicdata/waveforms/

    I have been able to find the MIMIC II, version 3 waveform DB. https://www.physionet.org/physiobank/database/mimic2wdb/

    After searching extensively for a MIMIC III waveform database, I am not having any luck. Does anyone know if this exists yet? Or is the most recent publicly accessible version of waveform data the MIMIC II, version 3 waveform DB?

    Thank you!

    mimic-iii 
    opened by jgenk 16
  • Buliding MIMIC-III Waveform Database

    Buliding MIMIC-III Waveform Database

    Hi, I have downloaded and build the MIMIC-III clinical database. I am just wondering how to build the MIMIC-III waveform database as there is no information available on the website. Is there a way I can build it just like the way clinical database is being set up. ?

    Thanks

    mimic-iii 
    opened by waqaraziz123 15
  • Patients Urine Output - questions

    Patients Urine Output - questions

    Dear all, I have some doubts regarding the codes that should be used to analyse the urine output of the patient. I am interested in study patients with kidney injuries and I need to verify the level of the urine output volume. I need in the mL/kg/hr units. Can I use 51108/51109 from LABEVENTS or should be use another code from IOEVENTS? Another question, what is the difference between the codes 51108 and 51109? They seem equal, in the value, date and units. If we have to use the LABEVENTS code, how can we have the urine output in mL/kg/hr? To have in mL/kg it is just needed to divide by the weight of the patient, but what is the sample time rate of the measurements from 51108 and 51109? Thank you! Sincerely, Vanessa Cunha

    mimic-iii 
    opened by vanessacunha 15
  • ERROR loading the postgres_load_data_pg10.sql

    ERROR loading the postgres_load_data_pg10.sql

    I got an error loading postgres_load_data_pg10.sql.

    I got COPY 58976 COPY 34499 COPY 7567 COPY 1048575 COPY 573146 COPY 1048575 COPY 651047 COPY 125557 COPY 134

    then

    ERROR: duplicate key value violates unique constraint "d_icd_diag_code_unique" DETAIL: Key (icd9_code) = (844) already exists. CONTEXT: COPY d_icd_diagnoses,line 307

    ERROR loading postgres_load_data_pg10.sql.docx image

    How can I fix it please?

    mimic-iii 
    opened by OluOrojo 14
  • Difficulty Building Database Using PostgreSQL

    Difficulty Building Database Using PostgreSQL

    I'm not terribly experienced in building databases. I'm running on mac os X 10.10.5 I attempted to download the files using make mimic-download but got the following error:


    -- Downloading MIMIC-III from PhysioNet --

    wget --user --ask-password -P -A csv.gz -m -p -E -k -K -np -nd "https://physionet.org/works/MIMICIIIClinicalDatabase/files/" --2017-07-19 13:32:39-- http://csv.gz/ Resolving csv.gz (csv.gz)... failed: nodename nor servname provided, or not known. wget: unable to resolve host address ‘csv.gz’ --2017-07-19 13:32:39-- https://physionet.org/works/MIMICIIIClinicalDatabase/files/ Resolving physionet.org (physionet.org)... 128.30.30.88 Connecting to physionet.org (physionet.org)|128.30.30.88|:443... connected. ERROR: cannot verify physionet.org's certificate, issued by ‘CN=Let's Encrypt Authority X3,O=Let's Encrypt,C=US’: Unable to locally verify the issuer's authority. To connect to physionet.org insecurely, use `--no-check-certificate'. Converted links in 0 files in 0 seconds. make[1]: *** [mimic-download] Error 4 make: *** [mimic-download] Error 2

    I then manually downloaded the data files and decompressed them. I then downloaded and installed PostgreSQL. I then tried to run: make mimic datadir=/path to data/

    from the command line and had issues with the mimic/postgres password. I modified the Makefile script to change the user to postgres so that I could use the password I specified on install. I re-ran: make mimic datadir=/path to data/

    and am now getting the following error:

    psql "dbname=mimic user=postgres options=--search_path=mimiciii" -f postgres_create_tables.sql psql: FATAL: database "mimic" does not exist make[1]: *** [mimic-build] Error 2 make: *** [mimic-build] Error 2

    I'd love some help with this. Thanks,

    mimic-iii 
    opened by RJBeetel3 14
  • Eliminating

    Eliminating "_DATA_TABLE" from names of .csv files

    The current naming convention of calling the .csv files things like ADMISSIONS_DATA_TABLE.csv seems redundant, and also causes extra work to edit the output of my heuristic structure finder (https://github.com/mitmedg/csv2mysql), which thus generates scripts like CREATE TABLE ADMISSIONS_DATA_TABLE ...

    Why not just change them all by eliminating _DATA_TABLE from the name of the file?

    mimic-iii 
    opened by pszolovits 14
  • What is the specific TESTs of glucose? What is the control level of the glucose?

    What is the specific TESTs of glucose? What is the control level of the glucose?

    The measure

    • [X] Put an X between the brackets on this line if you have done all of the following:
      • Checked the online documentation: https://mimic.mit.edu/
      • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

    Description

    This is a clinical knowledge. I am doing analysis on MIMIC-IV(2.0) dataset. What I have done is that

    SELECT * FROM mimiciv_hosp.d_labitems where label like '%lucose%' and fluid='Blood'
    

    The result is

    50809	"Glucose"	"Blood"	"Blood Gas"
    50931	"Glucose"	"Blood"	"Chemistry"
    52027	"Glucose, Whole Blood"	"Blood"	"Blood Gas"
    52569	"Glucose"	"Blood"	"Chemistry"
    

    Then, I run

    SELECT * FROM mimiciv_hosp.labevents WHERE ITEMID=50809 LIMIT 1000
    

    I got the glucose value successfully. Now, here is a question. How do you GROUPING the glucose value? There are several way to do blood glucose test(e.g. A1C Test, Fasting Blood Sugar Test, Glucose Tolerance Test, Random Blood Sugar Test ). For different tests, we can see whether the patients get diabetes according to the following tabe. | Result* | A1C Test | Fasting Blood Sugar Test | Glucose Tolerance Test | Random Blood Sugar Test | | :--- | :--- | :--- | :--- | :--- | | Diabetes | 6.5% or above | 126mg//dL or above | 200mg//dL or above | 200mg//dL or above | | Prediabetes | 5.7-6.4% | 100-125mg//dL | 140-199mg//dL | N//A | | Normal | Below 5.7% | 99mg//dL or below | 140mg//dL or below | N//A |

    Of course, we can obtain information from the Diagnoses related forms (ICD-9, ICD-10). I am now concerned about Glucose, and I hope to understand the test method and grouping method of this indicator (as shown in the table). For GLUCOSE, what interval is normal, what interval is prediabetes, and what interval is diabetes. This test method and grouping method for my research, look forward to your reply.

    opened by ljz756245026 0
  • add crrt to kdigo concept

    add crrt to kdigo concept

    Dear MIMIC-Community,

    I noticed that the presence of CRRT is missing as a parameter for KDIGO stage calculation. KDIGO states that "presence of CRRT" automatically classifies the patient as AKI stage 3.

    I allowed myself to quickly write up a query which I believe would fix the problem.

    I am so grateful to be able to contribute to this amazing project and I am looking forward to your input.

    Kind regards Christian

    opened by aegis301 0
  • How to determine if a patient has NIV or Invasive ventilation when ventilator is not a Hamilton

    How to determine if a patient has NIV or Invasive ventilation when ventilator is not a Hamilton

    Prerequisites

    • [x] Put an X between the brackets on this line if you have done all of the following:
      • Checked the online documentation: https://mimic.mit.edu/
      • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q= Hi, I find it hard to determine wether someone has non invasive ventilation (NIV) or it that patient has invasive ventilation through an endotracheal tube. Looking at ventilation.sql in mimiciv-derived gives some hints about that, but it still seems fuzzy to me.

    Ventilation.sql after defining thracheostomy ventilation mode, defines ventilation_status as InvasiveVent

    WHEN o2_delivery_device_1 IN
    (
        'Endotracheal tube'
    )
    OR ventilator_mode IN
    (
        '(S) CMV',
        'APRV',
        'APRV/Biphasic+ApnPress',
        'APRV/Biphasic+ApnVol',
        'APV (cmv)',
        'Ambient',
        'Apnea Ventilation',
        'CMV',
        'CMV/ASSIST',
        'CMV/ASSIST/AutoFlow',
        'CMV/AutoFlow',
        'CPAP/PPS',
        'CPAP/PSV+Apn TCPL',
        'CPAP/PSV+ApnPres',
        'CPAP/PSV+ApnVol',
        'MMV',
        'MMV/AutoFlow',
        'MMV/PSV',
        'MMV/PSV/AutoFlow',
        'P-CMV',
        'PCV+',
        'PCV+/PSV',
        'PCV+Assist',
        'PRES/AC',
        'PRVC/AC',
        'PRVC/SIMV',
        'PSV/SBT',
        'SIMV',
        'SIMV/AutoFlow',
        'SIMV/PRES',
        'SIMV/PSV',
        'SIMV/PSV/AutoFlow',
        'SIMV/VOL',
        'SYNCHRON MASTER',
        'SYNCHRON SLAVE',
        'VOL/AC'
    )
    OR ventilator_mode_hamilton IN
    (
        'APRV',
        'APV (cmv)',
        'Ambient',
        '(S) CMV',
        'P-CMV',
        'SIMV',
        'APV (simv)',
        'P-SIMV',
        'VS',
        'ASV'
    )
    

    and NonInvasiveVent by:

    WHEN o2_delivery_device_1 IN
    (
        'Bipap mask ', -- 8997 observations
        'CPAP mask ' -- 5568 observations
    )
    OR ventilator_mode_hamilton IN
    (
        'DuoPaP',
        'NIV',
        'NIV-ST'
    )
        THEN 'NonInvasiveVent'
    

    In oxygen_delivery table, there are oxygen_delivery_device_1, o2_delivery_device_2, o2_delivery_device_3, o2_delivery_device_4 that are filled by alphabetical order with o2 delivery device names if there are more than once at the same time. In case of several simultaneous oxygen delivery devices connected, as Bipap mask, or CPAP mask may not be the first to appear in the alphabetical order, I would say that Non Invasive ventilation detection could be missed just focusing on o2_delivery_device_1 without considering o2_delivery_device_2, o2_delivery_device_3 and o2_delivery_device_4.

    For patients, I am interested in, no one has in oxygen_delivery table records of 'Bipap mask', some have records with 'CPAP mask'

    Looking at ventilator_setting records for these patients , I don't find any records with charttimes closely related to oxygen_delivery charttime records when oxygen_delivery_device_1 or 2 or3 or 4 is set to 'CPAP mask'. I find quite odd, not to find even a PEEP or fiO2 setting for a non Invasive ventilation with 'CPAP mask'. These patients are connected to a ventilator for NIV, but there are no ventilator settings.

    What puzzles me too is that Non Invasive ventilation is defined by the interface ('Bipap mask' or 'CPAP mask') or by ventilation_mode_hamilton set to 'DuoPaP', 'NIV', 'NIV-ST' . Thus when a ventilator ,that is not a hamilton, is used , the determination of Non Invasive ventilation doesn't rely at all on the ventilator mode, probably because they may not have a fully specific NIV mode. I guess then that the NIV modes for these non hamilton ventilator are mixed-use and can be also used in Invasive ventilation. Therefore, I am wondering if these mixed Invasive Ventilation/Non Invasive ventilation modes for non Hamilton ventilators, may be part of those defining ventilation_status as InvasiveVent as defined in ventilation.sql.

    If all that is clear to someone, thanks very much in advance for your help and explanations ! Cedric

    Description

    Description of the issue, including:

    • what you have tried
    • references to similar issues
    • queries demonstrating your question (if applicable)
    opened by snowgato 1
  • MIMIC-CXR JPG dataset resize

    MIMIC-CXR JPG dataset resize

    99% of papers use 512x512 or maximum 1024x1024 size images in chest x-ray dataset. 512x512 after resize would hardly be 6-7 GB after zipping.

    it is criminal waste of resources to have people download data of 600GB and preprocess it to 6 GB. Can you please resize and upload..

    opened by njan-creative 2
  • SAPS in MIMIC-IV

    SAPS in MIMIC-IV

    Prerequisites

    • [x] Put an X between the brackets on this line if you have done all of the following:
      • Checked the online documentation: https://mimic.mit.edu/
      • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

    Description

    Hi! I am wondering if the SAPS-II scores for ICU visits are calculated in the MIMIC-IV dataset, and which module/table are they included in? If they are not currently included, will future versions of MIMIC-IV include mortality probability scores (e.g., SAPS, APACHE, SOFA) for ICU visits? Thank you so much for the help!

    opened by VoyagerWSH 4
Releases(v2.3.0)
  • v2.3.0(Dec 15, 2022)

    This release was built using MIMIC-IV v2.1. The release of this version will update the mimiciv_derived tables to use the latest version of MIMIC-IV on BigQuery, which is currently v2.1.

    Change log

    General

    • Notebook with figures/tables for MIMIC-IV by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1364
      • This is used to generate statistics for the paper describing MIMIC-IV (to be published shortly)
    • GitHub actions refactor by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1400
      • Runs a GH action to test concept scripts on demo data in postgresql/mysql
    • Updated row validation counts for MIMIC-IV by @nragusa in https://github.com/MIT-LCP/mimic-code/pull/1425
    • Fix bug in calculation of first day GCS by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1447

    Concept mapping

    • Add rxnorm concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1312
    • Add outputevents concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1309
    • Update loinc table by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1310
    • Add procedures concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1308
    • Add chartevents concept mapping by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1307

    PostgreSQL improvements

    • Updated MIMIC-IV-ED psql build scripts to v2.0 by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1340
      • PostgreSQL build scripts now work with MIMIC-IV v2.0 and v2.1
    • mimic-iv/concepts: fix postgres-make-concepts and minor updates by @schu in https://github.com/MIT-LCP/mimic-code/pull/1363
    • Include postgres MIMIC-III concepts by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1448
      • Now the scripts which generate MIMIC-III concepts in PostgreSQL are version controlled, and tested to work.

    MySQL improvements

    • MIMIC-IV MySQL build script update by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1341
      • MySQL build scripts now work with MIMIC-IV v2.0 and v2.1.

    SQLite improvements

    • mimic-iv/buildmimic/sqlite/import.py: replace strip() by @schu in https://github.com/MIT-LCP/mimic-code/pull/1360
    • mimic-iv/buildmimic/sqlite/README: mention sqlalchemy requirement by @schu in https://github.com/MIT-LCP/mimic-code/pull/1361
    • mimic-iv/buildmimic/sqlite/README: remove "edit step" by @schu in https://github.com/MIT-LCP/mimic-code/pull/1362

    New Contributors

    • @schu made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1360
    • @nragusa made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1425

    Full Changelog

    https://github.com/MIT-LCP/mimic-code/compare/v2.2.1...v2.3.0

    Source code(tar.gz)
    Source code(zip)
  • v2.2.1(Jul 11, 2022)

    This release updates the MIMIC Code repository to align with MIMIC-IV v2.0. It also contains many bug fixes.

    Change log:

    • This version (v2.2.1) fixes a bug in the workflow generating tables on BigQuery occurring in v2.2.0. The rest of the changes below are in comparison to v2.1.1.
    • Build MIMIC scripts
      • Updated PostgreSQL build scripts for MIMIC-IV v2.0 (#1328, thanks @alexmbennett2)
      • Added SQLite build of MIMIC-IV (thanks @armando-fandango) and updated for MIMIC-IV v2.0
      • Fixed MySQL build code (thanks @mdsung) and updated for MIMIC-IV v2.0
      • Updated DuckDB code to work with MIMIC-IV v2.0
    • Concept improvements
      • The generation of BigQuery tables by the GitHub action no longer prints rows to the standard output
      • Fixed incompatibility of convert_bigquery_to_postgres.sh on Mac OS X. The script should run on both Mac OS X and Ubuntu now.
      • Fixed imputation of cell counts (#1208, thanks @duanxiangjie)
      • Added an initial concept mapping of labs to LOINC (thanks @a-chahin). This mapping will continue to be improved in this repository.
      • Fixed matching of GCS value with prior value in the last 6 hours (#1248, thanks @prockenschaub)
      • Added mapping tables for standard concepts for waveform data (#1321 and #1322, thanks @a-chahin)

    Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.1.1...v2.2.1

    Source code(tar.gz)
    Source code(zip)
  • v2.2.0(Jul 11, 2022)

    This release updates the MIMIC Code repository to align with MIMIC-IV v2.0. It also contains many bug fixes.

    Change log:

    • Build MIMIC scripts
      • Updated PostgreSQL build scripts for MIMIC-IV v2.0 (#1328, thanks @alexmbennett2)
      • Added SQLite build of MIMIC-IV (thanks @armando-fandango) and updated for MIMIC-IV v2.0
      • Fixed MySQL build code (thanks @mdsung) and updated for MIMIC-IV v2.0
      • Updated DuckDB code to work with MIMIC-IV v2.0
    • Concept improvements
      • The generation of BigQuery tables by the GitHub action no longer prints rows to the standard output
      • Fixed incompatibility of convert_bigquery_to_postgres.sh on Mac OS X. The script should run on both Mac OS X and Ubuntu now.
      • Fixed imputation of cell counts (#1208, thanks @duanxiangjie)
      • Added an initial concept mapping of labs to LOINC (thanks @a-chahin). This mapping will continue to be improved in this repository.
      • Fixed matching of GCS value with prior value in the last 6 hours (#1248, thanks @prockenschaub)
      • Added mapping tables for standard concepts for waveform data (#1321 and #1322, thanks @a-chahin)

    Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.1.1...v2.2.0

    Source code(tar.gz)
    Source code(zip)
  • v2.1.1(Dec 15, 2021)

    This is a bug fix release to ensure concepts are created correctly.

    Change log:

    • Rather than redirect the GitHub action output to /dev/null, the make concept query now uses bq query --quiet. This makes it easier to see where the script fails in the case of an error.
    • Fix syntax bugs in the norepinephrine / norepinephrine_equivalent_dose / ventilation queries
    • Various query changes are carried forward to postgresql scripts (vasoactive, ntprobnp, ventilation)
    • Use bg specimen in the severity score queries rather than specimen_pred

    Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.1.0...v2.1.1

    Source code(tar.gz)
    Source code(zip)
  • v2.1.0(Dec 15, 2021)

    This release fixes blood gas and (postgres) vent/oxygen delivery queries, adds the ntprobnp column to the cardiac_marker concept, and improves aux scripts for generating concepts in MIMIC-III.

    Change log:

    • Allow extra options to be passed to psql calls with MIMIC-III by @juliangilbey in https://github.com/MIT-LCP/mimic-code/pull/1195
    • A single table aggregating vasoactive agents is now available as vasoactive_agent, see https://github.com/MIT-LCP/mimic-code/pull/1203
    • Include BNP in cardiac markers concept by @pedrogemal in https://github.com/MIT-LCP/mimic-code/pull/1204
    • Fixed first day blood gas queries to use the specimen data present in labevents rather than a no-longer existing probabilistic prediction of speciment, https://github.com/MIT-LCP/mimic-code/pull/1209
    • Same PR as above, propagated previous vent/oxygen delivery changes to the postgres scripts and improved tests https://github.com/MIT-LCP/mimic-code/pull/1209

    Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.0.0...v2.1.0

    Source code(tar.gz)
    Source code(zip)
  • v2.0.0(Dec 7, 2021)

    This is the first release with the new repository organization where all MIMIC related code is located here, including MIMIC-III, MIMIC-IV, MIMIC-IV-ED, and MIMIC-CXR. Many thanks to @briangow for so much effort in doing this reorganization!

    Change log:

    • A GitHub action workflow now regenerates BigQuery tables for MIMIC-IV upon publish of a release, ensuring BigQuery is synchronized with the latest release of the code.
    • Added MIMIC-IV and MIMIC-IV-ED build scripts.
    • Added MIMIC-IV and MIMIC-IV-ED concepts.
    • Added code for parsing MIMIC-CXR DICOMs (dcm) and deidentified free-text reports (txt) - this is the mimic-iv-cxr subfolder here (the mimic-iv prefix helps clarify this data can be used with MIMIC-IV - i.e. mimic-iv-cxr is synonymous with MIMIC-CXR).
    • Added version of MIMIC-IV concepts in the PostgreSQL dialect. These concepts are (mostly) automatically generated using a shell script from the BigQuery syntax.
    • Various bug fixes for MIMIC concepts.
    Source code(tar.gz)
    Source code(zip)
  • v1.4.2(May 16, 2019)

    Changelog:

    • Added an example R markdown notebook which uses BigQuery to connect to MIMIC
    • Filtered non-IV vancomycin administrations from the vancomycin dosing notebook
    • Documentation on a common failure case when building MIMIC
    • Added a contributed dplyr tutorial
    • Fixed logic in identifying central/arterial lines in metavision
    • Adjusted the calculation of UO in KDIGO to look backward; this will result in overestimation of UO and thus fewer AKI cases (before, the estimate was too low and AKI cases were potentially inflated)
    • Improve comments in various scripts
    Source code(tar.gz)
    Source code(zip)
  • v1.4.1(Sep 7, 2018)

    This is the latest release of the code repository. It contains a number of improvements in the build scripts and many more concepts. This build is for use with MIMIC-III v1.4.

    Source code(tar.gz)
    Source code(zip)
  • v1.4(Jul 2, 2017)

  • v1.3(Sep 6, 2016)

  • v1.2(Dec 4, 2015)

Owner
MIT Laboratory for Computational Physiology
Research on improving health care through data analysis, including use of MIMIC-III and other data sources
MIT Laboratory for Computational Physiology
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