.. CytoBridge documentation master file, created by sphinx-quickstart on Sun Nov 30 21:09:27 2025. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. CytoBridge: ====================================================================================== **CytoBridge** is a Python package designed to provide a unified and extensible framework for modeling cellular dynamics using Spatiotemporal Dynamical Generative Models. Our goal is to connect cutting-edge theoretical frameworks with practical, easy-to-use tools. ---- The core of CytoBridge is to model cellular processes by learning a dynamical model that accounts for various biological phenomena using time-series transcriptomics data (including both scRNA-seq and spatial data): * **Velocity** — instantaneous direction of cell state transitions (Corresponds to **Dynamical OT**) * **Growth** — proliferation and apoptosis rates (Corresponds to **Unbalanced OT, UOT**) * **Score** *(Planned)* — diffusion/noise term modeling stochasticity (Corresponds to **Regularized Unbalanced OT**) * **Interaction** *(Planned)* — cell–cell communication influences (Corresponds to **Unbalanced Mean Field Schrödinger Bridge**) The package is built to be modular, allowing users to easily combine these components to replicate existing models or create novel ones. ---- .. image:: _static/model.png :alt: model :align: center :width: 900px ---- Current Status ============== CytoBridge is currently under active development. The foundational framework is in place, and we have implemented the following models: * **Dynamical OT** (velocity) * **Unbalanced Dynamical OT** (velocity + growth) * **Regularized Unbalanced OT (RUOT)** (velocity + growth + stochasticity) * **Conditional RegularizedOT Unbalanced Flow Matching (CRUFM)** (velocity + growth + stochasticity) * **cytobridge** (velocity + growth + stochasticity + interaction) ---- Roadmap ======= We are continuously working to expand the capabilities of CytoBridge. Our development plan is as follows: - [√] **Phase 1: Stochastic Dynamics & RUOT** - [√] Implementation of the ``score`` component to model stochasticity. - [√] Support for training methods based on the **Regularized Unbalanced Optimal Transport (RUOT)** frameworks. - [√] Integration of simulation-free training methods (e.g., Conditional Flow Matching, Velocity-growth Flow Matching). - [√] Basic plotting functions and downstream analysis. - [√] **Phase 2: Advanced Modeling & Downstream Analysis** - [√] Implementation of the ``interaction`` component for modeling cell-cell communication. - [√] Advanced plotting functions and downstream analysis. - [ ] **Phase 3: Spatiotemporal Dynamics** - [ ] Support for time serise spatial transcriptomics data. - [ ] Advanced plotting functions and downstream analysis. ---- Here’s a polished and reorganized version of your installation and usage instructions, with improved clarity and flow: ---- .. toctree:: :maxdepth: 1 :hidden: Installation .. toctree:: :maxdepth: 1 :hidden: bg/guide_index .. toctree:: :maxdepth: 1 :hidden: refrence .. toctree:: :maxdepth: 1 :hidden: GitHub