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CNeuroMax

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Overview

CNeuroMax is a Machine Learning workspace for model fitting (Deep Learning + Neuroevolution + HPO w/ Oríon), testing and serving (with Lightning Apps) AI/ML models. CNeuroMax aims to:

1. Reduce code & configuration boilerplate with:

2. Simplify machine learning workflows:

  • Hyperparameter optimization with Orion, AutoRL-Sweepers & Optuna
  • SLURM job definition, queuing and monitoring with Submitit through its Hydra Launcher plugin.
  • Docker / Apptainer environment containerization for both regular & SLURM-based execution.
  • Transition from regular execution to SLURM-based execution by only swapping container technology and as little as a single Hydra configuration field.

3. Automate workspace & coding processes:

  • Package upgrades through Renovate.
  • Docstring documentation generation with Sphinx.
  • Pre-commit formatting & linting hooks with pre-commit.
  • Documentation/Docker image validation/deployment, formatting, linting, type-checking & unit tests upon contribution to the main branch using GitHub Actions.

4. Facilitate researcher collaboration through:

  • An object-oriented structure for code sharing & reusability.

  • A mono-repository workspace with task/experiment-specific subdirectories.

  • A very informative & clear to navigate Python API reference thanks to Autodoc and plugins like sphinx-autodoc-typehints and sphinx-paramlinks.

  • Shared logging with a Weights & Biases team space.

5. Promote high-quality and reproducible code by:

6. Smoothen up rough edges by providing:

  • Extensive documentation on how to install/execute on regular & SLURM-based systems.
  • Unassuming guides on how to contribute to the codebase.
  • Tutorials on i) how to facilitate code transport across machines & ii) how to prune unrelated components of the library for paper publication.

High-level repository tree:

cneuromax/
├─ .github/                  <-- Config files for GitHub Actions (tests, containers, etc)
├─ cneuromax/                <-- Root
│  ├─ fitting/               <-- Model fitting code
│  │  ├─ deeplearning/       <-- Deep Learning code
│  │  │  ├─ datamodule/      <-- Lightning DataModules
│  │  │  ├─ litmodule/       <-- Lightning Modules
│  │  │  │  └─ nnmodule/     <-- PyTorch Modules
│  │  │  ├─ utils/           <-- Deep Learning utilities
│  │  │  ├─ config.py        <-- Deep Learning structured configs
│  │  │  ├─ runner.py        <-- Deep Learning task runner
│  │  │  ├─ store.py         <-- Deep Learning configs storing
│  │  │  └─ train.py         <-- Deep Learning training function
│  │  ├─ deeplneuroevo/      <-- Deep Learning + Neuroevolution code
│  │  ├─ neuroevolution/     <-- Neuroevolution code
│  │  │  ├─ agent/           <-- Neuroevolution agents (encapsulate networks)
│  │  │  ├─ net/             <-- Neuroevolution networks
│  │  │  ├─ space/           <-- Neuroevolution spaces (where agents get evaluated)
│  │  │  ├─ utils/           <-- Neuroevolution utilities
│  │  │  ├─ config.py        <-- Neuroevolution structured configs
│  │  │  ├─ evolve.py        <-- Neuroevolution evolution function
│  │  │  └─ runner.py        <-- Neuroevolution task runner
│  │  ├─ utils/              <-- Fitting utililities
│  │  ├─ config.py           <-- Fitting structured configs
│  │  ├─ runner.py           <-- Fitting task runner
│  │  └─ store.py            <-- Fitting configs storing
│  ├─ projects/              <-- Contains all existing projects
│  │  │
│  │  │                          ******************************************
│  │  └─ my_new_project/     <-- ******** Your new project folder *********
│  │     ├─ task/            <-- *********** Your task folder *************
│  │     │  └─ config.yaml   <-- ****** Your task configuration file ******
│  │     ├─ datamodule.py    <-- ******* Your Lightning DataModule ********
│  │     ├─ litmodule.py     <-- ********* Your Lightning Module **********
│  │     └─ nnmodule.py      <-- ********** Your PyTorch Module ***********
│  │                             ******************************************
│  │
│  ├─ serving/               <-- Contains the code to create apps (cozmo inference, etc)
│  ├─ testing/               <-- Contains code for more complex testing of models
│  ├─ utils/                 <-- CNeuroMax utilities
│  ├─ __init__.py            <-- Sets up Beartype
│  ├─ __main__.py            <-- Entry-point
│  ├─ config.py              <-- Base structured configs
│  ├─ runner.py              <-- Base task runner
│  └─ store.py               <-- Base configs storing
├─ docs/                     <-- Documentation files
├─ .devcontainer.json        <-- VSCode container development config
├─ .gitignore                <-- Files to not track with Git/GitHub
├─ .pre-commit-config.yaml   <-- Pre-"git commit" actions config (format, lint, etc)
├─ .yamllint.yaml            <-- YAML files config
├─ Dockerfile                <-- To build the Docker image
├─ LICENSE                   <-- MIT License file
├─ README.md                 <-- Repository description file
├─ pyproject.toml            <-- Python code & dependencies config
└─ renovate.json             <-- Renovate Bot config (keeps dependencies up-to-date)

Additional information:

CNeuroMax is developed in the context of the Courtois Project on Neuronal Modelling, also known as CNeuroMod. Launched in 2018, CNeuroMod aims to create more human-like AI models by training them to emulate both human brain dynamics and behaviour. Phase I (2018-2023) of the project saw large-scale data acquisition and preliminary unimodal modelling. Phase II (2023-2027) of the project aims to create multimodal phantom models of the subjects. CNeuroMax is used as the framework to train these phantom models.