For both homework and project, we will use MIMIC-III Critical Care Database. This page describes information about the dataset and procedures to obtain the dataset.


MIMIC-III is a large, openly-available database comprising deidentified health-related data associated with over forty thousand patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012.

Among the types of data included are:

  1. General - Patient demographics, hospital admissions & discharge dates, room tracking, death dates (in or out of the hospital), ICD-9 codes, unique code for health care provider and type (RN, MD, RT, etc). All dates are surrogate dates because of privacy issues, but time intervals (even those between multiple admissions of the same patient) are preserved.
  2. Physiological - Hourly vital sign metrics, SAPS, SOFA, ventilator settings, etc.
  3. Medications - IV meds, provider order entry data, etc.
  4. Lab Tests - Chemistry, hematology, ABGs, imaging, etc.
  5. Fluid Balance - Intake (solutions, blood, etc) and output (urine, estimated blood loss, etc).
  6. Notes & Reports - Discharge summary, nursing progress notes, etc; cardiac catheterization, ECG, radiology, and echo reports.

MIMIC supports a diverse range of analytic studies spanning epidemiology, clinical decision-rule improvement, and electronic tool development. It is notable for three factors:

  1. it is publicly and freely available
  2. it encompasses a diverse and very large population of ICU patients
  3. it contains high temporal resolution data including lab results, electronic documentation, and bedside monitor trends and waveforms.

Request MIMIC Access

During this course, we will be working with the MIMIC database. MIMIC, although de-identified, still contains detailed information regarding the clinical care of patients, and must be treated with appropriate care and respect.

You must finish CITI training first to get MIMIC access.Do NOT request access individually.

We will collect all student information and send a batch request to MIT, after which you'll be notified and send the access request.

Bootcamp Training Material

Throughout the training exercises on this site we will use a small sample data set. If you followed the instructions documented on the environment setup page to set up your environment, you will find the sample data in the /bigdata-bootcamp/data folder in the virtual environment.

There are two data files with names case.csv and control.csv respectively. For the purpose of these exercises we will define patients who developed heart failure (HF) at some time point as case patients, and those who didn't develop HF as control patients.

Each line of the sample data file consists of a tuple structured as (patient-id, event-id, timestamp, value), below are a few lines as an example:

  • patient-id is just a patient identifier (id) in order to differentiate records from different patients. For example, the portion of data we show above is all about the same patient, who has an id of 020E860BD31CAC69.
  • event-id encodes all the clinical events that a patient has had. For example, DRUG00440128228 indicates that the patient was taking a drug identified by a National Drug Code of 00440128228. The numbers in DIAG486 are the first 3 digits of an ICD9 code, which in this case is the code for Pneumonia. For this data an event-id of PAYMENT means that the patient made a payment with the corresponding dollar amount.
  • timestamp indicates the date at which the event on that row happened. Here the timestamp is not formatted as a real date but rather as an offset from an unspecified start point. This is done both to improve the simplicity of processing and to protect the privacy of the patients' data.
  • value is the associated value for an event. See the below table for a detailed description data in the value field.
event typesample event-odvalue meaningexample
diagnostic codeDIAG486Will always be 1.0 for diagnose events1.0
drug consumptionDRUG00440128228Dosage of the drug30
paymentPAYMENTAmount of payment made on timestamp date15000
heartfailureheartfailureIndicator of heart failure event1.0