feat:LLM code

cluster/experiment1.sh

@@ -1,7 +1,12 @@
 #!/bin/bash
 
-#cd /the/place/where/everything/happens
-conda run -n neural-graph \
-  python /somewhere/do_thework.py
-echo "Some success message"
+cd /groups/saalfeld/home/allierc/Graph/NeuralGraph
+
+# Activate conda environment
+source /groups/saalfeld/home/allierc/miniforge3/etc/profile.d/conda.sh
+conda activate neural-graph
+
+python GNN_LLM.py
+
+echo "Experiment completed"
 

config/signal/signal_fig_2 copy.yaml

@@ -0,0 +1,72 @@
+description: "Figure 2 baseline - 1000 neurons, 4 types, no noise, no external inputs"
+dataset: "signal_fig_2"
+
+simulation:
+  connectivity_type: "Lorentz"
+  connectivity_init: [0, 0.1]
+  # params: [g, s, c]
+  # du = -c * u + s * torch.tanh(u) + g * msg
+  params:
+    [[10.0, 1.0, 1.0], [10.0, 2.0, 1.0], [10.0, 1.0, 2.0], [10.0, 2.0, 2.0]]
+  phi: "tanh"
+  n_neurons: 1000
+  n_neuron_types: 4
+  n_frames: 100000
+  delta_t: 0.01
+  dpos_init: 0
+  boundary: "no"
+  start_frame: -1000
+
+graph_model:
+  signal_model_name: "PDE_N2"
+  particle_model_name: ""
+  mesh_model_name: ""
+  prediction: "first_derivative"
+
+  input_size: 1
+  output_size: 1
+  hidden_dim: 64
+  n_layers: 3
+
+  input_size_update: 3
+  n_layers_update: 3
+  hidden_dim_update: 64
+
+  aggr_type: "add"
+  embedding_dim: 2
+  update_type: "none"
+
+plotting:
+  colormap: "tab10"
+  arrow_length: 1
+  xlim: [-4, 4]
+  ylim: [-8, 8]
+  label_style: "greek"
+  mlp0_xlim: [-5, 5]
+  mlp0_ylim: [-8, 8]
+  mlp1_xlim: [-5, 5]
+  mlp1_ylim: [-1.1, 1.1]
+
+training:
+  n_epochs: 10
+  n_runs: 1
+  device: "auto"
+
+  batch_size: 8
+  small_init_batch_size: False
+
+  seed: 16
+
+  data_augmentation_loop: 50
+
+  sparsity: "replace_embedding_function"
+  sparsity_freq: 4
+  cluster_method: "distance_plot"
+  cluster_distance_threshold: 0.1
+  fix_cluster_embedding: True
+
+  learning_rate_W_start: 1.0E-3
+  learning_rate_start: 5.0E-4
+  learning_rate_embedding_start: 7.50E-4
+
+  coeff_lin_phi_zero: 1.0

config/signal/signal_fig_3.yaml

@@ -0,0 +1,96 @@
+description: "test neuro-neuron dependent structure matrix modulation     noise_model_level: 1  batch_size: 8"
+dataset: "signal_fig_3"
+
+simulation:
+  connectivity_type: "Lorentz"
+  connectivity_init: [0, 0.1]
+  external_input_type: "visual"
+  external_input_mode: "multiplicative"
+  # params: [a, b, g, s, w, h]
+  # a: decay, b: offset, g: gain, s: self-recurrence, w: width, h: threshold   MLP1((u-h)/w)
+  params:
+    [
+      [1.0, 0.0, 10.0, 1.0, 1.0, 0.0],
+      [1.0, 0.0, 10.0, 2.0, 2.0, 0.0],
+      [2.0, 0.0, 10.0, 1.0, 4.0, 0.0],
+      [2.0, 0.0, 10.0, 2.0, 8.0, 0.0],
+    ]
+  phi: "tanh"
+  n_neurons: 2048
+  n_input_neurons: 1024
+  n_neuron_types: 4
+  n_frames: 50000
+  delta_t: 0.01
+  dpos_init: 0
+  boundary: "no"
+  start_frame: -10000
+  node_value_map: "video_bisons_32.tif"
+  noise_model_level: 1
+
+graph_model:
+  signal_model_name: "PDE_N4"
+  particle_model_name: ""
+  mesh_model_name: ""
+  prediction: "first_derivative"
+
+  input_size: 3
+  output_size: 1
+  hidden_dim: 64
+  n_layers: 5
+
+  input_size_update: 3
+  n_layers_update: 3
+  hidden_dim_update: 64
+
+  input_size_nnr_f: 3
+  n_layers_nnr_f: 5
+  hidden_dim_nnr_f: 128
+  output_size_nnr_f: 1
+  outermost_linear_nnr_f: True
+  omega_f: 30
+
+  aggr_type: "add"
+  embedding_dim: 2
+  update_type: "none"
+
+plotting:
+  colormap: "tab10"
+  arrow_length: 1
+  xlim: [-5, 5]
+  ylim: [0, 0.3]
+  label_style: "greek"
+
+claude:
+  n_epochs: 5
+  data_augmentation_loop: 10
+  n_iter_block: 1024
+
+training:
+  n_epochs: 10
+  n_runs: 1
+  device: "auto"
+
+  batch_size: 1
+  small_init_batch_size: True
+
+  data_augmentation_loop: 50
+
+  learn_external_input: True
+
+  sparsity: "replace_embedding_function"
+  sparsity_freq: 4
+  cluster_method: "distance_plot"
+  cluster_distance_threshold: 0.1
+  fix_cluster_embedding: True
+
+  coeff_W_L1: 1.0E-12
+  coeff_edge_diff: 10
+  coeff_update_diff: 5
+  coeff_lin_phi_zero: 1.0
+
+  learning_rate_W_start: 2.0E-3
+  learning_rate_start: 5.0E-4
+  learning_rate_embedding_start: 5.0E-3
+
+  learning_rate_NNR_f: 1.0E-5
+

config/signal/signal_fig_supp_10 copy.yaml

@@ -0,0 +1,73 @@
+description: "Figure supp 10 Noise test - 1000 neurons, 4 types, no noise, no external inputs"
+dataset: "signal_fig_supp_10"
+
+simulation:
+  connectivity_type: "Lorentz"
+  connectivity_init: [0, 0.1]
+  # params: [g, s, c]
+  # du = -c * u + s * torch.tanh(u) + g * msg
+  params:
+    [[10.0, 1.0, 1.0], [10.0, 2.0, 1.0], [10.0, 1.0, 2.0], [10.0, 2.0, 2.0]]
+  phi: "tanh"
+  n_neurons: 1000
+  n_neuron_types: 4
+  n_frames: 100000
+  delta_t: 0.01
+  dpos_init: 0
+  boundary: "no"
+  start_frame: -1000
+  noise_model_level: 7.2
+
+graph_model:
+  signal_model_name: "PDE_N2"
+  particle_model_name: ""
+  mesh_model_name: ""
+  prediction: "first_derivative"
+
+  input_size: 1
+  output_size: 1
+  hidden_dim: 64
+  n_layers: 3
+
+  input_size_update: 3
+  n_layers_update: 3
+  hidden_dim_update: 64
+
+  aggr_type: "add"
+  embedding_dim: 2
+  update_type: "none"
+
+plotting:
+  colormap: "tab10"
+  arrow_length: 1
+  xlim: [-4, 4]
+  ylim: [-8, 8]
+  label_style: "greek"
+  mlp0_xlim: [-5, 5]
+  mlp0_ylim: [-8, 8]
+  mlp1_xlim: [-5, 5]
+  mlp1_ylim: [-1.1, 1.1]
+
+training:
+  n_epochs: 10
+  n_runs: 1
+  device: "auto"
+
+  batch_size: 1
+  small_init_batch_size: False
+
+  seed: 16
+
+  data_augmentation_loop: 50
+
+  sparsity: "replace_embedding_function"
+  sparsity_freq: 4
+  cluster_method: "distance_plot"
+  cluster_distance_threshold: 0.1
+  fix_cluster_embedding: True
+
+  learning_rate_W_start: 1.0E-4
+  learning_rate_start: 5.0E-5
+  learning_rate_embedding_start: 5.0E-4
+
+  coeff_lin_phi_zero: 1.0

config/signal/signal_fig_supp_11.yaml

@@ -0,0 +1,75 @@
+description: "Figure supp 11 - 8000 neurons, 4 types, little noise, no external inputs"
+dataset: "signal_fig_supp_11"
+
+simulation:
+  connectivity_type: "Lorentz"
+  connectivity_init: [0, 0.1]
+  # params: [g, s, c]
+  # du = -c * u + s * torch.tanh(u) + g * msg
+  params:
+    [[10.0, 1.0, 1.0], [10.0, 2.0, 1.0], [10.0, 1.0, 2.0], [10.0, 2.0, 2.0]]
+  phi: "tanh"
+  n_neurons: 8000
+  n_neuron_types: 4
+  n_frames: 100000
+  delta_t: 0.01
+  dpos_init: 0
+  boundary: "no"
+  start_frame: -1000
+  noise_model_level: 1
+
+graph_model:
+  signal_model_name: "PDE_N2"
+  particle_model_name: ""
+  mesh_model_name: ""
+  prediction: "first_derivative"
+
+  input_size: 1
+  output_size: 1
+  hidden_dim: 64
+  n_layers: 3
+
+  input_size_update: 3
+  n_layers_update: 3
+  hidden_dim_update: 64
+
+  aggr_type: "add"
+  embedding_dim: 2
+  update_type: "none"
+
+plotting:
+  colormap: "tab10"
+  arrow_length: 1
+  xlim: [-4, 4]
+  ylim: [-8, 8]
+  label_style: "greek"
+  mlp0_xlim: [-5, 5]
+  mlp0_ylim: [-8, 8]
+  mlp1_xlim: [-5, 5]
+  mlp1_ylim: [-1.1, 1.1]
+
+training:
+  n_epochs: 10
+  n_runs: 1
+  device: "auto"
+
+  batch_size: 1
+  small_init_batch_size: False
+
+  seed: 16
+
+  data_augmentation_loop: 15
+
+  sparsity: "replace_embedding_function"
+  sparsity_freq: 4
+  cluster_method: "distance_plot"
+  cluster_distance_threshold: 0.1
+  fix_cluster_embedding: True
+
+  learning_rate_W_start: 1.0E-3
+  learning_rate_start: 5.0E-5
+  learning_rate_embedding_start: 5.0E-4
+
+
+  coeff_lin_phi_zero: 1.0
+  coeff_edge_diff: 100