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Disease Diagnosis Project - Setup Guide

Quick Start (5 minutes)

Prerequisites

  • Windows with conda/Anaconda installed ✅ (You have this!)
  • OR Linux/WSL with conda installed

Setup Steps

1. Clone/Open Project

cd C:\Users\voan2\Documents\GitHub\AI-CDS-Disease-Diagnosis-Reproduction
# Or on Linux/WSL:
# cd /path/to/AI-CDS-Disease-Diagnosis-Reproduction

2. Create Conda Environment

conda env create -f environment.yml

This installs:

  • Python 3.9
  • numpy, scipy, scikit-learn, gensim, cython
  • sent2vec

3. Activate Environment

conda activate disease-diagnosis

4. Verify Setup

python -c "from utils.Constants import CH_DIR; print('✅ Project path:', CH_DIR)"

5. Run the Code

python CS2V.py

Team Collaboration

What Changed

  • ✅ No more manual path editing! Constants.py auto-detects project location
  • ✅ One-command setup with conda environment.yml
  • ✅ Works on Windows, Linux, Mac - same commands everywhere

For New Team Members

  1. Install Miniconda: https://docs.conda.io/en/latest/miniconda.html
  2. Clone the repository
  3. Run: conda env create -f environment.yml
  4. Run: conda activate disease-diagnosis
  5. Start working!

Environment Management

Activate environment (every time you work)

conda activate disease-diagnosis

Deactivate when done

conda deactivate

Update environment (if environment.yml changes)

conda env update -f environment.yml --prune

Delete environment (if needed)

conda env remove -n disease-diagnosis

Troubleshooting

"conda: command not found"

  • Windows: Open "Anaconda PowerShell Prompt" instead of regular PowerShell
  • Linux/Mac: Run conda init bash then restart terminal

"Module not found" errors

  • Make sure environment is activated: conda activate disease-diagnosis
  • Verify with: conda env list (should show * next to disease-diagnosis)

Path issues

The project now auto-detects its location! If you see path errors:

  1. Ensure you're in the project directory
  2. Check that utils/Constants.py exists
  3. Try: python -c "from utils.Constants import CH_DIR; print(CH_DIR)"

What Was Fixed

Before (Manual Setup Required)

# In utils/Constants.py - everyone had to edit this!
CH_DIR = r"c:\Users\voan2\Documents\GitHub\AI-CDS-Disease-Diagnosis-Reproduction"

After (Auto-Detect)

# Now automatically detects project location
CH_DIR = str(Path(__file__).parent.parent.absolute())

Result: Clone and run - no configuration needed! ✨

Files in This Repo

  • environment.yml - Conda environment specification
  • requirements.txt - Pip requirements (legacy, use environment.yml instead)
  • CS2V.py - Main script
  • utils/Constants.py - Auto-detecting configuration
  • Dataset/ - Training/test data (10-fold cross-validation)
  • BioSentVec_PubMed_MIMICIII-bigram_d700.bin - 20.9GB model file

Ready to go! 🚀