jgendra · HarrisIp · Jun 5, 2026 · Jun 8, 2026 · Jun 8, 2026 · Jun 13, 2026
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,12 @@
-# Taken from https://github.com/github/gitignore
+### Manual additions
+# Generated Data
+*.npz
+*.json
+
+# Model weights
+weights/
+
+### Taken from https://github.com/github/gitignore
 
 ### Python
 # Byte-compiled / optimized / DLL files

diff --git a/README.md b/README.md
@@ -90,15 +90,12 @@ and **Bonferroni** correction for planned comparisons.
 NeuroAI-Project13/
 ├── README.md
 ├── environment.yml          # pinned conda environment
-├── configs/                 # experiment configs (task × condition × seed)
 ├── src/
 │   ├── models/              # CTRNN definition + Euler integration
-│   ├── tasks/               # NeuroGym task wrappers (dt=20 ms)
 │   ├── training/            # training loop, loss functions, BPTT
-│   ├── analysis/            # PID / ΦID / MI / Fisher pipelines
-│   └── stats/               # permutation tests, bootstrap, effect sizes
-├── notebooks/               # exploratory analysis + figure generation
-├── results/                 # checkpoints, saved activations, metric outputs
+│   └── analysis/            # PID / ΦID / MI / Fisher pipelines
+├── notebooks/               # exploratory analysis + throwaway/example files
+├── results/                 # saved model weights/activations, metric outputs
 ├── figures/                 # final figures
 └── docs/                    # technical note, references
 ```
@@ -148,14 +145,6 @@ python -m src.stats.run_tests --metrics results/metrics/
 Planning and progress are tracked on the repo's **Projects** tab (Roadmap / Board / Table views).
 Key dates: final roadmap **8 June**, midway presentation **17 June**, final presentation **15 July 2026**.
 
-## Team
-
-Group project (3 members):
-
-- Jan Casas Gendra
-- Jean-Pasqual Sindermann
-- Wang Chak Ip
-
 ## References
 
 - Williams & Beer (2010), *Nonnegative Decomposition of Multivariate Information* — [arXiv:1004.2515](https://doi.org/10.48550/arXiv.1004.2515)

diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,17 @@
+name: neuroai-project13
+channels:
+  - nvidia
+  - pytorch
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - pytorch=2.4.1
+  - pytorch-cuda=12.1
+  - pip:
+    - numpy
+    - scipy
+    - matplotlib
+    - seaborn
+    - neurogym==2.3.1
+    - jupyter
diff --git a/figures/.gitkeep b/figures/.gitkeep
diff --git a/figures/learning_curves/context/CTRNN_01.png b/figures/learning_curves/context/CTRNN_01.png
diff --git a/figures/learning_curves/perceptual/CTRNN_01.png b/figures/learning_curves/perceptual/CTRNN_01.png
diff --git a/notebooks/01_poc_training.ipynb b/notebooks/01_poc_training.ipynb
diff --git a/notebooks/02_poc_analysis.ipynb b/notebooks/02_poc_analysis.ipynb
diff --git a/notebooks/03_neurogym_tour.ipynb b/notebooks/03_neurogym_tour.ipynb
diff --git a/notebooks/04_minimal_product.ipynb b/notebooks/04_minimal_product.ipynb
diff --git a/notebooks/05_Full_train_pipeline.ipynb b/notebooks/05_Full_train_pipeline.ipynb
diff --git a/example_rnn/Exercise Handout.pdf → ...ooks/Jan_example_rnn/Exercise Handout.pdf b/example_rnn/Exercise Handout.pdf → ...ooks/Jan_example_rnn/Exercise Handout.pdf
diff --git a/notebooks/Jan_example_rnn/__init__.py b/notebooks/Jan_example_rnn/__init__.py
diff --git a/example_rnn/dyn_rnn/RNN_Lorenz.pt → ...oks/Jan_example_rnn/dyn_rnn/RNN_Lorenz.pt b/example_rnn/dyn_rnn/RNN_Lorenz.pt → ...oks/Jan_example_rnn/dyn_rnn/RNN_Lorenz.pt
diff --git a/example_rnn/dyn_rnn/RNN_VanDerPol.pt → .../Jan_example_rnn/dyn_rnn/RNN_VanDerPol.pt b/example_rnn/dyn_rnn/RNN_VanDerPol.pt → .../Jan_example_rnn/dyn_rnn/RNN_VanDerPol.pt
diff --git a/notebooks/Jan_example_rnn/dyn_rnn/RNN_VanDerPol_100.pt b/notebooks/Jan_example_rnn/dyn_rnn/RNN_VanDerPol_100.pt
diff --git a/notebooks/Jan_example_rnn/dyn_rnn/__init__.py b/notebooks/Jan_example_rnn/dyn_rnn/__init__.py
diff --git a/example_rnn/dyn_rnn/dynRNN.py → notebooks/Jan_example_rnn/dyn_rnn/dynRNN.py b/example_rnn/dyn_rnn/dynRNN.py → notebooks/Jan_example_rnn/dyn_rnn/dynRNN.py
diff --git a/example_rnn/dyn_rnn/main.py → notebooks/Jan_example_rnn/dyn_rnn/main.py b/example_rnn/dyn_rnn/main.py → notebooks/Jan_example_rnn/dyn_rnn/main.py
@@ -2,27 +2,28 @@
 import torch.nn as nn
 import torch.optim as optim
 import matplotlib.pyplot as plt
-from example_rnn.dyn_rnn.dynRNN import DynRNN
+from notebooks.example_rnn.dyn_rnn.dynRNN import DynRNN
 
 # Define task directory
-dir = "dynrnn/"
+dir = "example_rnn/dyn_rnn/"
 
 # hyperparameters
 BATCH_SIZE = 1   # not really used here, since we train on a single trajectory
-EPOCHS = 1000   
+EPOCHS = 100   
 LEARNING_RATE = 1e-3
 
 # Choose dynamical system
-system = 'Lorenz'  # 'VanDerPol' or 'Lorenz'
+system = 'VanDerPol'  # 'VanDerPol' or 'Lorenz'
 
 if __name__ == "__main__":
 
     y_true = torch.load(f'{dir}y_{system}.pt', weights_only=True)  # Size (300, 2) or (300, 3)
-    # print(y_true.shape)
+    print(y_true.shape)
 
     n_timesteps, dim = y_true.shape
 
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+    print(f"Using device: {device}")
     y_true = y_true.to(device)
 
     # Create RNN
@@ -85,8 +86,8 @@
             )
 
     # Save trained RNN
-    torch.save(model.state_dict(), f"{dir}RNN_{system}.pt")
-    print(f"Trained RNN saved to {dir}RNN_{system}.pt")
+    torch.save(model.state_dict(), f"{dir}RNN_{system}_{EPOCHS}.pt")
+    print(f"Trained RNN saved to {dir}RNN_{system}_{EPOCHS}.pt")
 
 
     # ===== EVALUATION: AUTOREGRESSIVE ROLLOUT =====

diff --git a/example_rnn/dyn_rnn/utils.py → notebooks/Jan_example_rnn/dyn_rnn/utils.py b/example_rnn/dyn_rnn/utils.py → notebooks/Jan_example_rnn/dyn_rnn/utils.py
diff --git a/example_rnn/dyn_rnn/y_Lorenz.pt → ...books/Jan_example_rnn/dyn_rnn/y_Lorenz.pt b/example_rnn/dyn_rnn/y_Lorenz.pt → ...books/Jan_example_rnn/dyn_rnn/y_Lorenz.pt
diff --git a/example_rnn/dyn_rnn/y_VanDerPol.pt → ...ks/Jan_example_rnn/dyn_rnn/y_VanDerPol.pt b/example_rnn/dyn_rnn/y_VanDerPol.pt → ...ks/Jan_example_rnn/dyn_rnn/y_VanDerPol.pt
diff --git a/example_rnn/true_rnn/RNN_Lorenz.pt → ...ks/Jan_example_rnn/true_rnn/RNN_Lorenz.pt b/example_rnn/true_rnn/RNN_Lorenz.pt → ...ks/Jan_example_rnn/true_rnn/RNN_Lorenz.pt
diff --git a/example_rnn/true_rnn/RNN_VanDerPol.pt → ...Jan_example_rnn/true_rnn/RNN_VanDerPol.pt b/example_rnn/true_rnn/RNN_VanDerPol.pt → ...Jan_example_rnn/true_rnn/RNN_VanDerPol.pt
diff --git a/notebooks/Jan_example_rnn/true_rnn/__init__.py b/notebooks/Jan_example_rnn/true_rnn/__init__.py
diff --git a/example_rnn/true_rnn/main.py → notebooks/Jan_example_rnn/true_rnn/main.py b/example_rnn/true_rnn/main.py → notebooks/Jan_example_rnn/true_rnn/main.py
@@ -2,10 +2,10 @@
 import torch.nn as nn
 import torch.optim as optim
 import matplotlib.pyplot as plt
-from example_rnn.true_rnn.trueRNN import TrueRNN
+from notebooks.example_rnn.true_rnn.trueRNN import TrueRNN
 
 # Define task directory
-dir = "true_rnn/"
+dir = "example_rnn/true_rnn/"
 
 # hyperparameters
 BATCH_SIZE = 1   # not really used here, since we train on a single trajectory

diff --git a/example_rnn/true_rnn/trueRNN.py → ...books/Jan_example_rnn/true_rnn/trueRNN.py b/example_rnn/true_rnn/trueRNN.py → ...books/Jan_example_rnn/true_rnn/trueRNN.py
diff --git a/example_rnn/true_rnn/utils.py → notebooks/Jan_example_rnn/true_rnn/utils.py b/example_rnn/true_rnn/utils.py → notebooks/Jan_example_rnn/true_rnn/utils.py
diff --git a/example_rnn/true_rnn/y_Lorenz.pt → ...ooks/Jan_example_rnn/true_rnn/y_Lorenz.pt b/example_rnn/true_rnn/y_Lorenz.pt → ...ooks/Jan_example_rnn/true_rnn/y_Lorenz.pt
diff --git a/example_rnn/true_rnn/y_VanDerPol.pt → ...s/Jan_example_rnn/true_rnn/y_VanDerPol.pt b/example_rnn/true_rnn/y_VanDerPol.pt → ...s/Jan_example_rnn/true_rnn/y_VanDerPol.pt
diff --git a/notebooks/poc_hidden_states.npy b/notebooks/poc_hidden_states.npy
diff --git a/notebooks/recreateRNN.ipynb b/notebooks/recreateRNN.ipynb
diff --git a/roadmap_generator/SETUP_INSTRUCTIONS.md → ...s/roadmap_generator/SETUP_INSTRUCTIONS.md b/roadmap_generator/SETUP_INSTRUCTIONS.md → ...s/roadmap_generator/SETUP_INSTRUCTIONS.md
diff --git a/roadmap_generator/setup_roadmap.py → notebooks/roadmap_generator/setup_roadmap.py b/roadmap_generator/setup_roadmap.py → notebooks/roadmap_generator/setup_roadmap.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,21 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "neuroai-project13"
+version = "0.2.0"
+description = "Information Decomposition in Task-Trained RNNs"
+requires-python = ">=3.11"
+dependencies = [
+    "torch==2.4.1+cu121",
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "seaborn",
+    "neurogym==2.3.1"
+]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["src*"]
diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,14 @@
-matplotlib==3.9.2; python_version >= '3.12'
-numpy==2.1.3; python_version >= '3.12'
-torch==2.5.1; python_version >= '3.12'
+# Core ML — CUDA 12.1 build, compatible with all team GPUs + Python 3.11
+torch==2.3.1; python_version >= '3.11'
+--extra-index-url https://download.pytorch.org/whl/cu121
+
+# Numerics & stats
+numpy==1.26.4; python_version >= '3.11'
+scipy==1.13.1; python_version >= '3.11'
+
+# Visualization
+matplotlib==3.9.2; python_version >= '3.11'
+seaborn==0.13.2; python_version >= '3.11'
+
+# NeuroGym tasks
+neurogym==2.3.1; python_version >= '3.11'
diff --git a/results/model_activations/.gitkeep b/results/model_activations/.gitkeep
diff --git a/results/model_activations/context/CTRNN_01.npy b/results/model_activations/context/CTRNN_01.npy
diff --git a/results/model_activations/perceptual/CTRNN_01.npy b/results/model_activations/perceptual/CTRNN_01.npy
diff --git a/results/model_weights/.gitkeep b/results/model_weights/.gitkeep
diff --git a/results/model_weights/CTRNN_ContextDecisionMaking-v0_h20.pt b/results/model_weights/CTRNN_ContextDecisionMaking-v0_h20.pt
diff --git a/results/model_weights/CTRNN_ContextDecisionMaking-v0_h80.pt b/results/model_weights/CTRNN_ContextDecisionMaking-v0_h80.pt
diff --git a/results/model_weights/CTRNN_PerceptualDecisionMaking-v0_h20.pt b/results/model_weights/CTRNN_PerceptualDecisionMaking-v0_h20.pt
diff --git a/results/model_weights/CTRNN_PerceptualDecisionMaking-v0_h80.pt b/results/model_weights/CTRNN_PerceptualDecisionMaking-v0_h80.pt
diff --git a/results/model_weights/Elman_ContextDecisionMaking-v0_h20.pt b/results/model_weights/Elman_ContextDecisionMaking-v0_h20.pt
diff --git a/results/model_weights/Elman_ContextDecisionMaking-v0_h80.pt b/results/model_weights/Elman_ContextDecisionMaking-v0_h80.pt
diff --git a/results/model_weights/Elman_PerceptualDecisionMaking-v0_h20.pt b/results/model_weights/Elman_PerceptualDecisionMaking-v0_h20.pt
diff --git a/results/model_weights/Elman_PerceptualDecisionMaking-v0_h80.pt b/results/model_weights/Elman_PerceptualDecisionMaking-v0_h80.pt
diff --git a/results/model_weights/context/CTRNN_01.pt b/results/model_weights/context/CTRNN_01.pt
diff --git a/results/model_weights/perceptual/CTRNN_01.pt b/results/model_weights/perceptual/CTRNN_01.pt
diff --git a/results/pid_outputs/.gitkeep b/results/pid_outputs/.gitkeep
diff --git a/results/pid_outputs/pid_task_rnn_comparison_h100_mante.png b/results/pid_outputs/pid_task_rnn_comparison_h100_mante.png
diff --git a/results/pid_outputs/pid_task_rnn_comparison_h100_mante_medium.png b/results/pid_outputs/pid_task_rnn_comparison_h100_mante_medium.png
diff --git a/results/pid_outputs/pid_task_rnn_comparison_h20.png b/results/pid_outputs/pid_task_rnn_comparison_h20.png
diff --git a/results/pid_outputs/pid_task_rnn_comparison_h20_mante.png b/results/pid_outputs/pid_task_rnn_comparison_h20_mante.png
diff --git a/results/pid_outputs/pid_task_rnn_comparison_h20_new.png b/results/pid_outputs/pid_task_rnn_comparison_h20_new.png
diff --git a/results/pid_outputs/pid_task_rnn_comparison_h80.png b/results/pid_outputs/pid_task_rnn_comparison_h80.png