Medication-Labtests

Repository for Medication <> Lab Test interaction discovery analysis.

Directory Structure

.
├── data                    # Datasets - Not pushed (Drive link in [dataset section](##Dataset))
├── docs                    # Documentation files (Will update shortly)
├── old                    # Previous version
|    ├── src                     # Source Code 
|    │   ├── preprocessing               # Data Preprocessing
|    |   |   ├── preprocess.py             # Data Loading and preprocessing class
|    |   |   └── stratify.py               # Stratification class
|    │   ├── analysis                    # Data Analysis
|    |   |   ├── analysis.py               # Analysis Parent Class
|    |   |   ├── inputevents_analysis.py   # Inputevents table - Before and After, regression and trend analysis
|    |   |   ├── presc_analysis.py         # Prescriptions table - Before and After, regression and trend analysis
|    |   |   └── time_effect_analysis.py   # Time effct analysis
|    │   ├── modeling                    # Data Modeling
|    │   └── visualize                   # Visualization of data analysis
|    |       └── time_effect_visualize.py   # Time effct Visualization
|    ├── notebooks                     # Notebook files
|    │   ├── Dataset                     # Datset access
|    │   ├── Drugs                       # Drug data taken from chartevents table
|    │   ├── Medication                  # Medication data from inputevents_mv (Metavision) table
|    │   ├── Medication-Regression       # Medication data from inputevents_mv (Metavision) table + Regression done to perform analysis
|    │   ├── Prescription                # Prescription data from prescription table
|    │   ├── Others                      # MIMIC Extract and Other analysis
|    |   └── sql_queries                 # SQL Queries used to read from MIMIC-III Postgre SQL
|    ├── pipeline                # Automation pipelines and scripts Database
|    └── plots                   # Plots for data analysis and visualization (Older plots on drive - check [plots section](##Plots))
├── mimic-notebook-analysis                     # MIMIC Notebook files
├── hirid-notebook-analysis                     # HIRID Notebook files
├── src                     # Source Code 
│   ├── parsers               # Dataset parsers
|   |   ├── parser.py             # Parser interface
|   |   ├── mimic.py              # MIMIC Dataset Parser
|   |   └── hirid.py              # MIMIC Dataset Parser
│   ├── modling               # Data Analysis and modeling
|   |   ├── querier.py            # dataset querier - lab test <> medication pair generation code
|   |   ├── discovery.py          # Before and After and trend analysis
|   |   └── plots.py              # Time effct analysis
│   └── utils                 # Utils functions and classes
|       ├── utils.py              # utils
|       └── constants.py          # Constant values - lab id mappings for all datasets
├── results                 # Results 
└── README.md

Dataset

Drive Link to Datasets : https://drive.google.com/drive/folders/1-ARL03M0t8yGB3xiy_k1lhmQBHJWToFK?usp=share_link

.
├── mimic_extract                                            # MIMIC Extract Dataset
├── mimiciii                                                 # MIMIC-III Dataset
├── hirid-a-high-time-resolution-icu-dataset-1.1.1           # HIRID Dataset 
└── itemid_to_variable_map.csv                               # MIMIC Extract - itemid to lab test/medication mapping

Results

Needs to be updated

Plots

Needs to be updated

Running Code

1. Setup VM (With the repo as root directory). Recommend using Python 3.9.6

   python3 -m venv venv
   pip3 install -r requirements.txt

2. Use either main.py or main.ipynb to run the code