EHRQC 0.4
Package for performing QC on Electronic Health Record (EHR) data
License: MIT
Requires Python: >=3.6

# EHRQC

## Introduction
The performance of the Machine Learning (ML) models is primarily dependent on the underlying data on which it is trained on. Therefore, it is very essential to ensure that the training data is of the highest quality possible. It is a standard practice to perform operations related to handling of the missing values, and outliers before feeding it to machine learning algorithms, for which there are well established procedures and dedicated libraries currently. However, they are generic in nature and do not cover the domain specific nuances. For instance, non standard data sanity checks are to be performed in addition, to remove further errors in the Electronic Health Records (EHRs) that are specific to the medical domain. This utility is aimed at providing functions that can summarize the errors that are specific to the healthcare domain in the data through various visualizations.

## System architecture

![image](https://user-images.githubusercontent.com/56529301/133012627-875f2643-2d43-4e9e-b97b-8f0424cfa94e.png)

## Example Output

Refer [demographics.html](https://github.com/ryashpal/EHRQC/blob/master/demographics.html), [vitals.html](https://github.com/ryashpal/EHRQC/blob/master/vitals.html), [lab_measurements.html](https://github.com/ryashpal/EHRQC/blob/master/lab_measurements.html), [vitals_anomalies.html](https://github.com/ryashpal/EHRQC/blob/master/vitals_anomalies.html), and [lab_measurements_anomalies.html](https://github.com/ryashpal/EHRQC/blob/master/lab_measurements_anomalies.html)

## Installation Guide

Install the following libraries

    pip install numpy
    pip install matplotlib
    pip install yattag
    pip install scipy
    pip install sklearn
    pip install pandas

Then install EHRQC

    pip install EHRQC

## User Guide

### Extract Demographic data from OMOP schema

    from qc.extract import extractOmopDemographics as extractOmopDemographics

    omopDemographicsDf = extractOmopDemographics()
    omopDemographicsDf.head()

### Extract Vitals data from OMOP schema

    from qc.extract import extractMimicOmopVitals as extractMimicOmopVitals

    mimicOmopVitalsDf = extractMimicOmopVitals()
    mimicOmopVitalsDf.head()

### Extract Lab Measurements data from OMOP schema

    from qc.extract import extractOmopLabMeasurements as extractOmopLabMeasurements

    omopLabMeasurementsDf = extractOmopLabMeasurements()
    omopLabMeasurementsDf.head()

### Extract Demographic data from MIMIC schema

    from qc.extract import extractMimicDemographics as extractMimicDemographics

    mimicDemographicsDf = extractMimicDemographics()
    mimicDemographicsDf.head()

### Extract Vitals data from MIMIC schema

    from qc.extract import extractMimicVitals as extractMimicVitals

    mimicVitalsDf = extractMimicVitals()
    mimicVitalsDf.head()

### Extract Lab Measurements data from MIMIC schema

    from qc.extract import extractMimicLabMeasurements as extractMimicLabMeasurements

    mimicLabMeasurementsDf = extractMimicLabMeasurements()
    mimicLabMeasurementsDf.head()

### Demographics Graphs Example 1

    import qc.demographicsGraphs as demographicsGraphs

    data = [
        [0, 1, 2, 'male', 'white', date.fromisoformat('2020-09-13'), date.fromisoformat('2021-09-13')], 
        [2, 3, 4, np.nan, 'white', date.fromisoformat('2020-09-14'), date.fromisoformat('2021-09-13')], 
        [4, 5, 6, 'female', 'black', date.fromisoformat('2020-09-15'), date.fromisoformat('2021-09-13')], 
        [6, 7, 8, np.nan, 'asian', date.fromisoformat('2020-09-14'), date.fromisoformat('2021-09-13')]]
    demographicsGraphs.plot(pd.DataFrame(data, columns=['age', 'weight', 'height', 'gender', 'ethnicity', 'dob', 'dod']))

### Demographics Graphs Example 2

    import qc.demographicsGraphs as demographicsGraphs

    df = dbUtils._getDemographics()
    demographicsGraphs.plot(df)

### Vitals Graphs Example 1

    import qc.vitalsGraphs as vitalsGraphs

    data = [
        [0, 1, 2], 
        [2, np.nan, 4], 
        [4, 5, np.nan], 
        [0, 1, 2], 
        [2, 3, 4], 
        [4, 5, np.nan], 
        [0, 1, 2], 
        [2, 3, 4], 
        [4, 5, 6], 
        [6, 7, np.nan]]
    vitalsGraphs.plot(pd.DataFrame(data, columns=['heartrate', 'sysbp', 'diabp']))

### Vitals Graphs Example 2

    import qc.vitalsGraphs as vitalsGraphs

    df = dbUtils._getVitals()
    vitalsGraphs.plot(df)

### Lab Measurements Graphs Example 1

    import qc.labMeasurementsGraphs as labMeasurementsGraphs

    data = [
        [0, 1, 2], 
        [2, np.nan, 4], 
        [4, 5, np.nan], 
        [0, 1, 2], 
        [2, 3, 4], 
        [4, 5, np.nan], 
        [0, 1, 2], 
        [2, 3, 4], 
        [4, 5, 6], 
        [6, 7, np.nan]]
    labMeasurementsGraphs.plot(pd.DataFrame(data, columns=['glucose', 'hemoglobin', 'anion_gap']))

### Lab Measurements Graphs Example 2

    import qc.labMeasurementsGraphs as labMeasurementsGraphs

    df = dbUtils._getLabMeasurements()
    labMeasurementsGraphs.plot(df)

### Missing Data Imputation Method Comparison Example 1

    import qc.missingDataImputation as missingDataImputation

    df = dbUtils._getVitals()
    df = df.dropna()
    meanR2, medianR2, knnR2, mfR2, emR2, miR2 = missingDataImputation.compare()
    print(meanR2, medianR2, knnR2, mfR2, emR2, miR2)

### Missing Data Imputation Method Comparison Example 2

    import qc.missingDataImputation as missingDataImputation

    df = dbUtils._getLabMeasurements()
    df = df.dropna()
    meanR2, medianR2, knnR2, mfR2, emR2, miR2 = missingDataImputation.compare()
    print(meanR2, medianR2, knnR2, mfR2, emR2, miR2)

### Missing Data Imputation Example 1

    import qc.missingDataImputation as missingDataImputation

    df = dbUtils._getVitals()
    imputedDf = missingDataImputation.impute(df, 'miss_forest')

### Vitals Anomaly Graphs Example

    import qc.vitalsAnomalies as vitalsAnomalies

    df = dbUtils._getVitals()
    vitalsAnomalies.plot(df)

### Lab Measurements Anomaly Graphs Example

    import qc.labMeasurementsAnomalies as labMeasurementsAnomalies

    df = dbUtils._getVitals()
    labMeasurementsAnomalies.plot(df)

### Running the Pipeline Example

    from qc.pipeline import run

    data = run(source='mimic', type='demographics', graph=True, impute_missing=True)
    print(data.head())

    ## source -> Can be one of 'mimic' or 'omop'  
    ## type -> Can be one of 'demographics', 'vitals', 'lab_measurements'  
    ## graph -> If true, the EDA graph will be generated  
    ## impute_missing -> If true, missing values will be imputed based on the best imputation method for the given data

## Acknowledgements

<img src="https://user-images.githubusercontent.com/56529301/155898403-c453ab3f-df17-45c8-ac0a-b314461f5e8f.png" alt="the-alfred-hospital-logo" width="100"/>
<img src="https://user-images.githubusercontent.com/56529301/155898442-ba8dcbb1-14dd-4c8b-96e6-e02c6a632c0e.png" alt="the-alfred-hospital-logo" width="150"/>
<img src="https://user-images.githubusercontent.com/56529301/155898475-a5244ab5-e16e-4e5d-b562-6a89a7c2b7b7.png" alt="Superbug_AI_Branding_FINAL" width="150"/>