Data-Driven Modeling and Decision Support for Personalized Precision Oncology

Introduction

This repository contains the code and Jupyter notebooks for our project on data-driven modeling and decision support systems in personalized precision oncology. We leverage techniques such as Physiologically Based Pharmacokinetic (PBPK) models, Neural Ordinary Differential Equations (Neural ODEs), and Reinforcement Learning (RL) to create dynamic, personalized treatment plans for cancer therapies.

Contents

• MIRDcell.14 with Atlide: MIRD cell calculations with Atlide integration.
• Tumor_Growth_Model: Models for simulating tumor growth dynamics.
• UBC-PSMA-PBPK-Model-Matlab: Matlab version of the PBPK model for PSMA.
• VirtualPatientsSimBiologyModelAnalyzerExample: An example analyzer for virtual patient simulation biology models.
• antibiotics: Exploratory code related to antibiotic treatment modeling.
• frankstein: A collection of cleaned and processed notebooks.
• nvidia-modulus-pinn-training: Training modules using Nvidia Modulus for Physics-Informed Neural Networks (PINN).
• papers_reviewed: Documentation and notes on reviewed papers relevant to the project.
• pbpk-model: The main PBPK model implemented in Python.
• 01 - The Problem.ipynb: Notebook discussing the problem statement and objectives.
• 02 - Basic PBPK Model.ipynb: Notebook outlining the basic PBPK model.
• 03 - Three Compartment PBPK.ipynb: A three-compartment PBPK model implementation.
• PRRT Treatment Planning.ipynb: A notebook detailing the treatment planning for Peptide Receptor Radionuclide Therapy (PRRT).
• 04 - UBC_PBRPK - Data-Driven - Regression.ipynb: A comprehensive regression analysis within the PBPK modeling for data-driven insights.
• 05 - UBC_PBRPK - Data-Driven - RNN.ipynb: Implementing Recurrent Neural Networks (RNN) for dynamic modeling in PBPK frameworks.
• Connect2Matlab.ipynb: This notebook outlines the process of connecting Python-based PBPK models with MATLAB for extended analyses and simulations.
• 06 - Neural ODE - PINN Approach.ipynb: Notebook on integrating Neural ODE with PINN approach.
• Lu-DOTATATE Therapy - Insilico Analysis.ipynb: Insilico analysis of Lu-DOTATATE therapy.
• PRRT_Treatment_Planning_Tutorial.md: Tutorial on treatment planning for Peptide Receptor Radionuclide Therapy (PRRT).

Additional Resources

For more comprehensive insights into our project's scope and methodologies, please visit our detailed portfolio page at the SAIL Lab: Data-Driven Modeling and Decision Support for Personalized Precision Oncology

We hope this repository will aid researchers and practitioners in the field of oncology to develop more precise and personalized treatment strategies.