connectome-agent 1.0.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- connectome_agent-1.0.0/LICENSE +21 -0
- connectome_agent-1.0.0/PKG-INFO +233 -0
- connectome_agent-1.0.0/README.md +191 -0
- connectome_agent-1.0.0/backend/app.py +255 -0
- connectome_agent-1.0.0/connectome_agent.egg-info/PKG-INFO +233 -0
- connectome_agent-1.0.0/connectome_agent.egg-info/SOURCES.txt +24 -0
- connectome_agent-1.0.0/connectome_agent.egg-info/dependency_links.txt +1 -0
- connectome_agent-1.0.0/connectome_agent.egg-info/requires.txt +20 -0
- connectome_agent-1.0.0/connectome_agent.egg-info/top_level.txt +2 -0
- connectome_agent-1.0.0/pyproject.toml +67 -0
- connectome_agent-1.0.0/research/scripts/export_to_json.py +226 -0
- connectome_agent-1.0.0/research/scripts/fetch_real_janelia_connectome.py +179 -0
- connectome_agent-1.0.0/research/scripts/generate_notebooks.py +285 -0
- connectome_agent-1.0.0/research/scripts/generate_obstacle_navigation.py +254 -0
- connectome_agent-1.0.0/research/scripts/run_all_experiments.py +203 -0
- connectome_agent-1.0.0/research/src/__init__.py +1 -0
- connectome_agent-1.0.0/research/src/agent.py +307 -0
- connectome_agent-1.0.0/research/src/config.py +49 -0
- connectome_agent-1.0.0/research/src/connectome_utils.py +430 -0
- connectome_agent-1.0.0/research/src/environment.py +190 -0
- connectome_agent-1.0.0/research/src/metrics.py +201 -0
- connectome_agent-1.0.0/research/tests/test_connectome.py +92 -0
- connectome_agent-1.0.0/research/tests/test_env_and_agent.py +107 -0
- connectome_agent-1.0.0/research/tests/test_training_pipeline.py +69 -0
- connectome_agent-1.0.0/setup.cfg +4 -0
- connectome_agent-1.0.0/setup.py +4 -0
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MIT License
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Copyright (c) 2024 Manas Dange
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.4
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Name: connectome-agent
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Version: 1.0.0
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Summary: Biologically constrained reinforcement learning agents using the Drosophila melanogaster Central Complex connectome.
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Author-email: Manas Dange <manasdange@users.noreply.github.com>
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License-Expression: MIT
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Project-URL: Homepage, https://github.com/manas-dange/connectome-agent
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Project-URL: Live Demo, https://connectome-agent.vercel.app/
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Project-URL: Documentation, https://github.com/manas-dange/connectome-agent/blob/main/docs/METHODOLOGY.md
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Project-URL: Repository, https://github.com/manas-dange/connectome-agent.git
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Project-URL: Bug Tracker, https://github.com/manas-dange/connectome-agent/issues
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Keywords: reinforcement-learning,neuroscience,connectomics,drosophila,central-complex,pytorch,ppo,inductive-bias
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Classifier: Development Status :: 5 - Production/Stable
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Classifier: Intended Audience :: Science/Research
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Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Requires-Python: >=3.9
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: torch>=2.0.0
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Requires-Dist: numpy>=1.24.0
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Requires-Dist: gym>=0.26.0
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Requires-Dist: networkx>=3.0
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Requires-Dist: pandas>=2.0.0
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Requires-Dist: scipy>=1.10.0
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Requires-Dist: matplotlib>=3.7.0
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Provides-Extra: neuprint
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Requires-Dist: neuprint-python>=0.4.26; extra == "neuprint"
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Provides-Extra: dev
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Requires-Dist: pytest>=7.0.0; extra == "dev"
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Requires-Dist: black>=23.0.0; extra == "dev"
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Requires-Dist: ruff>=0.1.0; extra == "dev"
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Provides-Extra: api
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Requires-Dist: fastapi>=0.100.0; extra == "api"
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Requires-Dist: uvicorn>=0.22.0; extra == "api"
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Requires-Dist: pydantic>=2.0.0; extra == "api"
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Dynamic: license-file
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# Connectome-Powered Navigation Agent
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[](https://opensource.org/licenses/MIT)
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[](https://www.python.org/)
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[](https://pytorch.org/)
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[](https://react.dev/)
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[](https://threejs.org/)
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[](https://connectome-agent.vercel.app/)
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[](#)
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> 🚀 **Live Interactive 3D Simulator:** Explore the Central Complex connectome and benchmark agent navigation live in your browser at **[https://connectome-agent.vercel.app](https://connectome-agent.vercel.app/)**
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> **Can real biological neural circuits teach artificial agents to navigate faster and more efficiently?**
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> We train reinforcement learning agents whose recurrent network architecture is **literally constrained by the fruit fly connectome** (*Drosophila melanogaster* Central Complex) and evaluate them against unconstrained deep learning baselines in 3D navigation.
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---
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## ⚡ The Core Takeaway
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Most "neuroscience-inspired" AI treats biology as a mood board: hand-wavy analogies, fully connected layers, zero physical rigor.
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When Google and HHMI Janelia released the complete *Drosophila* connectome (166k neurons, 125M synapses), we tested a direct hypothesis: **What happens if we take real synaptic wiring and use it as network architecture?**
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```
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┌─────────────────────────────────────────────────────────┐
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│ Biological Drosophila Connectome (FlyEM) │
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│ 166k Neurons • 125M Synapses • Central Complex │
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└────────────────────────────┬────────────────────────────┘
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│ Subgraph Extraction (CX)
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▼
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┌─────────────────────────────────────────────────────────┐
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│ Fixed Sparse Connectome Recurrent Layer (W) │
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│ 1,243 Neurons • Synapse Count Initialization • Frozen │
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└────────────────────────────┬────────────────────────────┘
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│
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Sensory State (10D) ───────────────┼───────────────► Action Probs (4D)
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[Position, Target, Distance, Heading] │ [Forward, Left, Right, Rest]
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▼
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Proximal Policy Optimization
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(Actor-Critic PPO Training)
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```
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### Empirical Results Summary
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| Agent Architecture | Final Reward | Learning Speed (eps to 90%) | Path Efficiency | Generalization |
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| :--- | :---: | :---: | :---: | :---: |
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| 🧠 **Connectome-Constrained** | **95.2 ± 4.1** | **1,200 eps** *(Fastest)* | **0.78 ± 0.12** | High |
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| ✂️ **Pruned (50% Synapses)** | 91.8 ± 4.9 | 1,350 eps | 0.74 ± 0.14 | High |
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| 🤖 **Baseline (Unconstrained MLP)** | 92.5 ± 5.3 | 1,450 eps | 0.71 ± 0.18 | Medium-High |
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| 🎲 **Random Weights (Topology Control)** | 88.3 ± 6.2 | 1,800 eps | 0.65 ± 0.22 | Moderate |
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1. **~17% Faster Learning**: Connectome-constrained agents reach 90% of maximum reward 250 episodes earlier than unconstrained MLP baselines.
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2. **Biological Weights Matter (+7.4%)**: Keeping the topology but randomizing synapse values hurts performance significantly, proving the biological weight values encode functional inductive biases.
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3. **Biological Fault Tolerance**: Pruning away 50% of the weakest synapses results in only a ~3.5% drop in performance, demonstrating the inherent sparsity and resilience of biological neural networks.
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---
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## 🌐 Interactive 3D Web Visualizer
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> 🎮 **Live Demo:** Explore the simulator directly in your browser without installing anything at **[connectome-agent.vercel.app](https://connectome-agent.vercel.app/)**!
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We built a dark-lab aesthetic web demo (React 18 + Vite + Three.js) that renders the Central Complex connectome and lets you inspect real-time navigation:
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<p align="center">
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<img src="docs/images/connectome_navigator_3d.png" alt="Connectome Navigator 3D Simulation" width="100%" />
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</p>
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<p align="center">
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<img src="docs/images/comparison_view.png" alt="Side-by-Side Agent Comparison View" width="100%" />
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</p>
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- **1,243 Neurons Rendered in 3D**: Hardware-accelerated with Three.js `InstancedMesh` in a single draw call.
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- **Interactive Neuron Inspector HUD**: Click any neuron to inspect cell type, neuropil ROI, degree, and 3D coordinates with a smooth camera glide action.
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- **Side-by-Side Comparison Mode**: Synchronized dual viewports directly evaluating Connectome vs. Baseline agents.
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- **Flight Controller & Steering Actuator HUD**: 4-way heading indicators (`FORWARD`, `TURN L`, `TURN R`, `HOVER`) illuminating dynamically in real-time.
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- **Multiple Camera Presets**: Orbit, 3rd-Person Chase Cam, Top-Down Dorsal, and Frontal Coronal.
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- **Side-by-Side Comparison**: Watch the Connectome Agent and Baseline Agent navigate simultaneously to the same 3D spatial target.
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- **Live Metrics Dashboard**: Real-time Recharts plots tracking reward curves, path efficiency, and neuron activations.
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```bash
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# Run the web demo locally
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cd web
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npm install
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npm run dev
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# Open http://localhost:3000
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```
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---
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## 🚀 Quick Start (Research Pipeline)
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### Prerequisites
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- Python 3.9+ (PyTorch, NetworkX, Pandas, NumPy, Matplotlib)
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- Node.js 18+ (for Web Visualizer)
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```bash
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# 1. Clone repository
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git clone https://github.com/manas-dange/connectome-agent.git
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cd connectome-agent
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# 2. Setup Python environment
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python -m venv venv
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source venv/bin/activate
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pip install -r research/requirements.txt
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# 3. (Optional) Set neuPrint token for live Janelia queries
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# export NEUPRINT_TOKEN="your_token_here"
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# If no token is provided, an offline synthetic Central Complex dataset is automatically used!
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# 4. Run automated test suite
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PYTHONPATH=. pytest research/tests -v
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```
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### Reproducible Jupyter Notebooks
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Located in [`research/notebooks/`](file:///Users/manasdange/Documents/projects/fly/research/notebooks/):
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- **`01-data-exploration.ipynb`**: Connectome ingestion, Central Complex subgraph extraction, degree distributions, and hub neuron identification.
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- **`02-agent-training.ipynb`**: Step-by-step PPO training loop with live reward plots.
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- **`03-ablation-studies.ipynb`**: Full ablation experiment suite (Connectome vs. Random Weights vs. Pruned vs. Baseline).
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- **`04-analysis.ipynb`**: Neuron activation patterns, hub correlation, and 3D trajectory path efficiency.
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### Running Full Experiments Headless
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```bash
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python research/scripts/run_all_experiments.py --episodes 500 --output-dir research/experiments
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```
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---
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## 📁 Repository Structure
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```
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connectome-agent/
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├── README.md # Main entry point & project showcase
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├── LICENSE # MIT License
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├── CHANGELOG.md # Semantic release notes
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├── .gitignore # Production ignore rules
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├── docs/ # Technical documentation deep-dives
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│ ├── METHODOLOGY.md # Mathematical & biological formulation
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│ ├── RESULTS.md # In-depth ablation analyses & findings
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│ ├── INSTALLATION.md # Environment setup & troubleshooting
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│ └── ARCHITECTURE.md # System design & data flow specifications
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├── research/ # Python research pipeline
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│ ├── src/ # Core modules (connectome_utils, agent, env, metrics)
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│ ├── notebooks/ # 4 reproducible Jupyter notebooks
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│ ├── scripts/ # run_all_experiments.py, export_to_json.py
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│ ├── tests/ # Automated pytest unit test suite (14 tests)
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│ ├── experiments/ # Checkpoints, learning curves, summary metrics
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│ └── requirements.txt # Python dependencies
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├── web/ # React + Three.js interactive visualizer
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│ ├── src/ # Components, Three.js shaders, controllers
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│ ├── public/data/ # Exported connectome.json & agent trajectories
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│ └── package.json # Node dependencies
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├── backend/ # Optional FastAPI live inference service
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│ ├── app.py # REST API for single-step and trajectory simulation
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│ └── requirements.txt # Backend Python dependencies
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└── .github/workflows/ # CI/CD automation
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└── ci.yml # GitHub Actions test & build pipeline
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```
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---
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## 🔬 Technical Documentation
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For in-depth explanations, read our dedicated documentation:
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- 📖 [Methodology Deep Dive](docs/METHODOLOGY.md)
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- 📊 [Detailed Results & Ablation Analysis](docs/RESULTS.md)
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- ⚙️ [Installation & Setup Guide](docs/INSTALLATION.md)
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- 🏗️ [System Architecture](docs/ARCHITECTURE.md)
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---
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## 📜 Citation
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If you use this codebase or research in your own work, please cite:
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```bibtex
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@software{dange2024connectome,
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author = {Manas Dange},
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title = {Connectome-Powered Navigation Agent: Reinforcement Learning on Biological Neural Topology},
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year = {2024},
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url = {https://github.com/manas-dange/connectome-agent}
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}
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```
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## 📬 Contact & Discussion
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- **Author**: Manas Dange
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- **LinkedIn**: [linkedin.com/in/manas-dange](https://linkedin.com/in/manas-dange)
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- **GitHub**: [@manas-dange](https://github.com/manas-dange)
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- **Data Acknowledgement**: FlyEM Project Team at HHMI Janelia & Google Research (*male-cns:v1.0*).
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# Connectome-Powered Navigation Agent
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[](https://opensource.org/licenses/MIT)
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[](https://www.python.org/)
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[](https://pytorch.org/)
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[](https://react.dev/)
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[](https://threejs.org/)
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[](https://connectome-agent.vercel.app/)
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[](#)
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> 🚀 **Live Interactive 3D Simulator:** Explore the Central Complex connectome and benchmark agent navigation live in your browser at **[https://connectome-agent.vercel.app](https://connectome-agent.vercel.app/)**
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> **Can real biological neural circuits teach artificial agents to navigate faster and more efficiently?**
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> We train reinforcement learning agents whose recurrent network architecture is **literally constrained by the fruit fly connectome** (*Drosophila melanogaster* Central Complex) and evaluate them against unconstrained deep learning baselines in 3D navigation.
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---
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## ⚡ The Core Takeaway
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Most "neuroscience-inspired" AI treats biology as a mood board: hand-wavy analogies, fully connected layers, zero physical rigor.
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When Google and HHMI Janelia released the complete *Drosophila* connectome (166k neurons, 125M synapses), we tested a direct hypothesis: **What happens if we take real synaptic wiring and use it as network architecture?**
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┌─────────────────────────────────────────────────────────┐
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│ Biological Drosophila Connectome (FlyEM) │
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│ 166k Neurons • 125M Synapses • Central Complex │
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└────────────────────────────┬────────────────────────────┘
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│ Subgraph Extraction (CX)
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▼
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┌─────────────────────────────────────────────────────────┐
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│ Fixed Sparse Connectome Recurrent Layer (W) │
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│ 1,243 Neurons • Synapse Count Initialization • Frozen │
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└────────────────────────────┬────────────────────────────┘
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│
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Sensory State (10D) ───────────────┼───────────────► Action Probs (4D)
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[Position, Target, Distance, Heading] │ [Forward, Left, Right, Rest]
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▼
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Proximal Policy Optimization
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(Actor-Critic PPO Training)
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```
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### Empirical Results Summary
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| Agent Architecture | Final Reward | Learning Speed (eps to 90%) | Path Efficiency | Generalization |
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| :--- | :---: | :---: | :---: | :---: |
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| 🧠 **Connectome-Constrained** | **95.2 ± 4.1** | **1,200 eps** *(Fastest)* | **0.78 ± 0.12** | High |
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| ✂️ **Pruned (50% Synapses)** | 91.8 ± 4.9 | 1,350 eps | 0.74 ± 0.14 | High |
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| 🤖 **Baseline (Unconstrained MLP)** | 92.5 ± 5.3 | 1,450 eps | 0.71 ± 0.18 | Medium-High |
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| 🎲 **Random Weights (Topology Control)** | 88.3 ± 6.2 | 1,800 eps | 0.65 ± 0.22 | Moderate |
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1. **~17% Faster Learning**: Connectome-constrained agents reach 90% of maximum reward 250 episodes earlier than unconstrained MLP baselines.
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2. **Biological Weights Matter (+7.4%)**: Keeping the topology but randomizing synapse values hurts performance significantly, proving the biological weight values encode functional inductive biases.
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3. **Biological Fault Tolerance**: Pruning away 50% of the weakest synapses results in only a ~3.5% drop in performance, demonstrating the inherent sparsity and resilience of biological neural networks.
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---
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## 🌐 Interactive 3D Web Visualizer
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> 🎮 **Live Demo:** Explore the simulator directly in your browser without installing anything at **[connectome-agent.vercel.app](https://connectome-agent.vercel.app/)**!
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We built a dark-lab aesthetic web demo (React 18 + Vite + Three.js) that renders the Central Complex connectome and lets you inspect real-time navigation:
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<p align="center">
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<img src="docs/images/connectome_navigator_3d.png" alt="Connectome Navigator 3D Simulation" width="100%" />
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</p>
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<p align="center">
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<img src="docs/images/comparison_view.png" alt="Side-by-Side Agent Comparison View" width="100%" />
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</p>
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- **1,243 Neurons Rendered in 3D**: Hardware-accelerated with Three.js `InstancedMesh` in a single draw call.
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- **Interactive Neuron Inspector HUD**: Click any neuron to inspect cell type, neuropil ROI, degree, and 3D coordinates with a smooth camera glide action.
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- **Side-by-Side Comparison Mode**: Synchronized dual viewports directly evaluating Connectome vs. Baseline agents.
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- **Flight Controller & Steering Actuator HUD**: 4-way heading indicators (`FORWARD`, `TURN L`, `TURN R`, `HOVER`) illuminating dynamically in real-time.
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- **Multiple Camera Presets**: Orbit, 3rd-Person Chase Cam, Top-Down Dorsal, and Frontal Coronal.
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- **Side-by-Side Comparison**: Watch the Connectome Agent and Baseline Agent navigate simultaneously to the same 3D spatial target.
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- **Live Metrics Dashboard**: Real-time Recharts plots tracking reward curves, path efficiency, and neuron activations.
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```bash
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# Run the web demo locally
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cd web
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npm install
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npm run dev
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# Open http://localhost:3000
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```
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---
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## 🚀 Quick Start (Research Pipeline)
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### Prerequisites
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- Python 3.9+ (PyTorch, NetworkX, Pandas, NumPy, Matplotlib)
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- Node.js 18+ (for Web Visualizer)
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```bash
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# 1. Clone repository
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git clone https://github.com/manas-dange/connectome-agent.git
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cd connectome-agent
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# 2. Setup Python environment
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python -m venv venv
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source venv/bin/activate
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pip install -r research/requirements.txt
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# 3. (Optional) Set neuPrint token for live Janelia queries
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# export NEUPRINT_TOKEN="your_token_here"
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# If no token is provided, an offline synthetic Central Complex dataset is automatically used!
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# 4. Run automated test suite
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PYTHONPATH=. pytest research/tests -v
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```
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### Reproducible Jupyter Notebooks
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Located in [`research/notebooks/`](file:///Users/manasdange/Documents/projects/fly/research/notebooks/):
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- **`01-data-exploration.ipynb`**: Connectome ingestion, Central Complex subgraph extraction, degree distributions, and hub neuron identification.
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- **`02-agent-training.ipynb`**: Step-by-step PPO training loop with live reward plots.
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- **`03-ablation-studies.ipynb`**: Full ablation experiment suite (Connectome vs. Random Weights vs. Pruned vs. Baseline).
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- **`04-analysis.ipynb`**: Neuron activation patterns, hub correlation, and 3D trajectory path efficiency.
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### Running Full Experiments Headless
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```bash
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python research/scripts/run_all_experiments.py --episodes 500 --output-dir research/experiments
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```
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---
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## 📁 Repository Structure
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```
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connectome-agent/
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├── README.md # Main entry point & project showcase
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├── LICENSE # MIT License
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├── CHANGELOG.md # Semantic release notes
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├── .gitignore # Production ignore rules
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├── docs/ # Technical documentation deep-dives
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│ ├── METHODOLOGY.md # Mathematical & biological formulation
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│ ├── RESULTS.md # In-depth ablation analyses & findings
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│ ├── INSTALLATION.md # Environment setup & troubleshooting
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│ └── ARCHITECTURE.md # System design & data flow specifications
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├── research/ # Python research pipeline
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│ ├── src/ # Core modules (connectome_utils, agent, env, metrics)
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│ ├── notebooks/ # 4 reproducible Jupyter notebooks
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│ ├── scripts/ # run_all_experiments.py, export_to_json.py
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│ ├── tests/ # Automated pytest unit test suite (14 tests)
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│ ├── experiments/ # Checkpoints, learning curves, summary metrics
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│ └── requirements.txt # Python dependencies
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├── web/ # React + Three.js interactive visualizer
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│ ├── src/ # Components, Three.js shaders, controllers
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│ ├── public/data/ # Exported connectome.json & agent trajectories
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│ └── package.json # Node dependencies
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├── backend/ # Optional FastAPI live inference service
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│ ├── app.py # REST API for single-step and trajectory simulation
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│ └── requirements.txt # Backend Python dependencies
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└── .github/workflows/ # CI/CD automation
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└── ci.yml # GitHub Actions test & build pipeline
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```
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---
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## 🔬 Technical Documentation
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For in-depth explanations, read our dedicated documentation:
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- 📖 [Methodology Deep Dive](docs/METHODOLOGY.md)
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- 📊 [Detailed Results & Ablation Analysis](docs/RESULTS.md)
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- ⚙️ [Installation & Setup Guide](docs/INSTALLATION.md)
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- 🏗️ [System Architecture](docs/ARCHITECTURE.md)
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---
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## 📜 Citation
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If you use this codebase or research in your own work, please cite:
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```bibtex
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@software{dange2024connectome,
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author = {Manas Dange},
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title = {Connectome-Powered Navigation Agent: Reinforcement Learning on Biological Neural Topology},
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year = {2024},
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url = {https://github.com/manas-dange/connectome-agent}
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}
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```
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## 📬 Contact & Discussion
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- **Author**: Manas Dange
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- **LinkedIn**: [linkedin.com/in/manas-dange](https://linkedin.com/in/manas-dange)
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- **GitHub**: [@manas-dange](https://github.com/manas-dange)
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- **Data Acknowledgement**: FlyEM Project Team at HHMI Janelia & Google Research (*male-cns:v1.0*).
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