jgendra · jgendra · Jul 4, 2026 · Jul 4, 2026 · Jul 4, 2026 · Jul 4, 2026
diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,9 @@
 # Generated Data
 *.npz
 data/
+# Track coherences in results
+!results/stimulus_coherences/**
+!results/stimulus_coherences/
 
 # Model weights
 weights/
@@ -326,4 +329,7 @@ $RECYCLE.BIN/
 .nfs*
 
 # python-history when using pyenv
-.python-history
+.python-history
+
+# Ignore LLM files
+.claude/
diff --git a/...ts/pid_task_rnn_comparison_h100_mante.png → ...es/pid_task_rnn_comparison_h100_mante.png b/...ts/pid_task_rnn_comparison_h100_mante.png → ...es/pid_task_rnn_comparison_h100_mante.png
diff --git a/...task_rnn_comparison_h100_mante_medium.png → ...task_rnn_comparison_h100_mante_medium.png b/...task_rnn_comparison_h100_mante_medium.png → ...task_rnn_comparison_h100_mante_medium.png
diff --git a/...d_outputs/pid_task_rnn_comparison_h20.png → ...n/figures/pid_task_rnn_comparison_h20.png b/...d_outputs/pid_task_rnn_comparison_h20.png → ...n/figures/pid_task_rnn_comparison_h20.png
diff --git a/...uts/pid_task_rnn_comparison_h20_mante.png → ...res/pid_task_rnn_comparison_h20_mante.png b/...uts/pid_task_rnn_comparison_h20_mante.png → ...res/pid_task_rnn_comparison_h20_mante.png
diff --git a/...tputs/pid_task_rnn_comparison_h20_new.png → ...gures/pid_task_rnn_comparison_h20_new.png b/...tputs/pid_task_rnn_comparison_h20_new.png → ...gures/pid_task_rnn_comparison_h20_new.png
diff --git a/...d_outputs/pid_task_rnn_comparison_h80.png → ...n/figures/pid_task_rnn_comparison_h80.png b/...d_outputs/pid_task_rnn_comparison_h80.png → ...n/figures/pid_task_rnn_comparison_h80.png
diff --git a/...hts/CTRNN_ContextDecisionMaking-v0_h20.pt → ...hts/CTRNN_ContextDecisionMaking-v0_h20.pt b/...hts/CTRNN_ContextDecisionMaking-v0_h20.pt → ...hts/CTRNN_ContextDecisionMaking-v0_h20.pt
diff --git a/...hts/CTRNN_ContextDecisionMaking-v0_h80.pt → ...hts/CTRNN_ContextDecisionMaking-v0_h80.pt b/...hts/CTRNN_ContextDecisionMaking-v0_h80.pt → ...hts/CTRNN_ContextDecisionMaking-v0_h80.pt
diff --git a/.../CTRNN_PerceptualDecisionMaking-v0_h20.pt → .../CTRNN_PerceptualDecisionMaking-v0_h20.pt b/.../CTRNN_PerceptualDecisionMaking-v0_h20.pt → .../CTRNN_PerceptualDecisionMaking-v0_h20.pt
diff --git a/.../CTRNN_PerceptualDecisionMaking-v0_h80.pt → .../CTRNN_PerceptualDecisionMaking-v0_h80.pt b/.../CTRNN_PerceptualDecisionMaking-v0_h80.pt → .../CTRNN_PerceptualDecisionMaking-v0_h80.pt
diff --git a/...hts/Elman_ContextDecisionMaking-v0_h20.pt → ...hts/Elman_ContextDecisionMaking-v0_h20.pt b/...hts/Elman_ContextDecisionMaking-v0_h20.pt → ...hts/Elman_ContextDecisionMaking-v0_h20.pt
diff --git a/...hts/Elman_ContextDecisionMaking-v0_h80.pt → ...hts/Elman_ContextDecisionMaking-v0_h80.pt b/...hts/Elman_ContextDecisionMaking-v0_h80.pt → ...hts/Elman_ContextDecisionMaking-v0_h80.pt
diff --git a/.../Elman_PerceptualDecisionMaking-v0_h20.pt → .../Elman_PerceptualDecisionMaking-v0_h20.pt b/.../Elman_PerceptualDecisionMaking-v0_h20.pt → .../Elman_PerceptualDecisionMaking-v0_h20.pt
diff --git a/.../Elman_PerceptualDecisionMaking-v0_h80.pt → .../Elman_PerceptualDecisionMaking-v0_h80.pt b/.../Elman_PerceptualDecisionMaking-v0_h80.pt → .../Elman_PerceptualDecisionMaking-v0_h80.pt
diff --git a/figures/accuracy_loss/test_accuracy_loss_bars.png b/figures/accuracy_loss/test_accuracy_loss_bars.png
diff --git a/figures/all_time_pid/CTRNN_01.png b/figures/all_time_pid/CTRNN_01.png
diff --git a/figures/all_time_pid/CTRNN_02.png b/figures/all_time_pid/CTRNN_02.png
diff --git a/figures/all_time_pid/CTRNN_03.png b/figures/all_time_pid/CTRNN_03.png
diff --git a/figures/all_time_pid/CTRNN_04.png b/figures/all_time_pid/CTRNN_04.png
diff --git a/figures/all_time_pid/CTRNN_05.png b/figures/all_time_pid/CTRNN_05.png
diff --git a/figures/all_time_pid/CTRNN_06.png b/figures/all_time_pid/CTRNN_06.png
diff --git a/figures/all_time_pid/CTRNN_07.png b/figures/all_time_pid/CTRNN_07.png
diff --git a/figures/all_time_pid/CTRNN_08.png b/figures/all_time_pid/CTRNN_08.png
diff --git a/figures/all_time_pid/CTRNN_09.png b/figures/all_time_pid/CTRNN_09.png
diff --git a/figures/all_time_pid/CTRNN_10.png b/figures/all_time_pid/CTRNN_10.png
diff --git a/figures/learning_curves/.gitkeep b/figures/learning_curves/.gitkeep
diff --git a/figures/learning_curves/context/.gitkeep b/figures/learning_curves/context/.gitkeep
diff --git a/figures/learning_curves/perceptual/.gitkeep b/figures/learning_curves/perceptual/.gitkeep
diff --git a/notebooks/04_minimal_product.ipynb b/notebooks/04_minimal_product.ipynb
@@ -34,7 +34,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "275176ad",
    "metadata": {},
    "outputs": [
@@ -50,7 +50,7 @@
    ],
    "source": [
     "# Configuration\n",
-    "BASE_PATH = \"../src/tasks/data/mante_style\"\n",
+    "BASE_PATH = \"../data\"\n",
     "BATCH_SIZE = 1024 * 2\n",
     "SUBSAMPLE_STEP = 10 # Subsample for Elman RNN (simulate tau=10ms)\n",
     "\n",
@@ -258,7 +258,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "2cdf07a6",
    "metadata": {},
    "outputs": [
@@ -282,7 +282,7 @@
     "if device.type == \"cuda\":\n",
     "    print(f\"   GPU Name: {torch.cuda.get_device_name(0)}\")\n",
     "\n",
-    "WEIGHTS_DIR = \"../src/models/weights/mante_medium\"\n",
+    "WEIGHTS_DIR = \"../elman_vs_ctrnn_comparison/model_weights\" \n",
     "os.makedirs(WEIGHTS_DIR, exist_ok=True)"
    ]
   },

diff --git a/notebooks/05_Full_train_pipeline.ipynb b/notebooks/05_Full_train_pipeline.ipynb
@@ -76,13 +76,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "275176ad",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Configuration (paths are relative to the notebooks/ directory, i.e. repo root via \"..\")\n",
-    "BASE_PATH = \"../src/tasks/data/mante_style\"\n",
+    "BASE_PATH = \"../data\"\n",
     "BATCH_SIZE = 1024 * 8\n",
     "SUBSAMPLE_STEP = 1   # raw trials are dt=10ms; step=1 gives an effective 10ms timestep (750ms -> 75 steps)\n",
     "# Each seeded CTRNN gets its own held-out test set (train/val are shared across seeds of a task).\n",
@@ -1310,7 +1310,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "neuroai-project13",
+   "display_name": "neuroai",
    "language": "python",
    "name": "python3"
   },