INSTALLATION.md

Prophet Installation

Install

pip install prophet

Complete functionality included:

• Prophet model (training, inference, fine-tuning)
• Data processing utilities
• PyTorch & Lightning
• Visualization tools (Matplotlib, Seaborn, Plotly)
• Jupyter notebook support
• Experiment tracking (W&B, TensorBoard)

Usage

from prophet import Prophet

# Train
model = Prophet(
    iv_emb_path="interventions.csv",
    cl_emb_path="cell_lines.csv",
    model_pth="checkpoint.ckpt"
)
model.train(df, iv_col="drug", cl_col="cell_line", readout_col="response")

# Predict
predictions = model.predict(target_ivs=["DRUG1"], target_cls=["CELL1"], save=False)

Verification

import prophet
from prophet import Prophet
print("✅ Prophet ready!")

Help

• Issues: https://github.com/theislab/prophet/issues
• Tutorials: See tutorials/ directory