cell tracking

GNN_particles_Ntype.py

@@ -49,10 +49,8 @@
     config_list = ['arbitrary_3_division_death_tracking']
     # config_list = ['boids_16_256_tracking']
     # config_list = ['arbitrary_64']
-    # config_list = ['arbitrary_3_angle_10']
-    # config_list = ['arbitrary_3_Bernouilli_10']
-    # config_list = ['arbitrary_3_tracking_angle_10']
-    # config_list = ['arbitrary_3_tracking_Bernouilli_10']
+    # config_list = ['arbitrary_3_angle_20','arbitrary_3_angle_30','arbitrary_3_Bernouilli_20','arbitrary_3_Bernouilli_30']
+    # config_list = ['arbitrary_3_tracking_angle_20','arbitrary_3_tracking_angle_30','arbitrary_3_tracking_Bernouilli_20','arbitrary_3_tracking_Bernouilli_20']
 
     seed_list = np.arange(10)
 

config/arbitrary_3_Bernouilli_20.yaml

@@ -0,0 +1,50 @@
+description: 'attraction-repulsion with 3 types particles'
+dataset: 'arbitrary_3_Bernouilli_20'
+
+simulation:
+  params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
+  min_radius: 0
+  max_radius: 0.075
+  n_particles: 4800
+  n_particle_types: 3
+  n_interactions: 3
+  n_frames: 250
+  sigma: 0.005
+  delta_t: 0.1
+  dpos_init: 0
+  boundary: 'periodic'
+  angular_Bernouilli: [-20, 20, 4, 0.5]
+
+graph_model:
+  particle_model_name: 'PDE_A'
+  mesh_model_name: ''
+  prediction: 'first_derivative'
+  input_size: 5
+  output_size: 2
+  hidden_dim: 128
+  n_mp_layers: 5
+  aggr_type: 'mean'
+  embedding_dim: 2
+  update_type: 'none'
+
+plotting:
+  colormap: 'tab10'
+  arrow_length: 2
+  ylim: [-0.04, 0.03]
+
+training:
+  n_epochs: 20
+  batch_size: 8
+  small_init_batch_size: False
+  n_runs: 2
+  sparsity: 'replace_embedding_function'
+  cluster_method: 'distance_plot'
+  data_augmentation: True
+  data_augmentation_loop: 100
+  fix_cluster_embedding: True
+  device: 'auto'
+
+
+
+
+

config/arbitrary_3_Bernouilli_30.yaml

@@ -0,0 +1,50 @@
+description: 'attraction-repulsion with 3 types particles'
+dataset: 'arbitrary_3_Bernouilli_30'
+
+simulation:
+  params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
+  min_radius: 0
+  max_radius: 0.075
+  n_particles: 4800
+  n_particle_types: 3
+  n_interactions: 3
+  n_frames: 250
+  sigma: 0.005
+  delta_t: 0.1
+  dpos_init: 0
+  boundary: 'periodic'
+  angular_Bernouilli: [-30, 30, 4, 0.5]
+
+graph_model:
+  particle_model_name: 'PDE_A'
+  mesh_model_name: ''
+  prediction: 'first_derivative'
+  input_size: 5
+  output_size: 2
+  hidden_dim: 128
+  n_mp_layers: 5
+  aggr_type: 'mean'
+  embedding_dim: 2
+  update_type: 'none'
+
+plotting:
+  colormap: 'tab10'
+  arrow_length: 2
+  ylim: [-0.04, 0.03]
+
+training:
+  n_epochs: 20
+  batch_size: 8
+  small_init_batch_size: False
+  n_runs: 2
+  sparsity: 'replace_embedding_function'
+  cluster_method: 'distance_plot'
+  data_augmentation: True
+  data_augmentation_loop: 100
+  fix_cluster_embedding: True
+  device: 'auto'
+
+
+
+
+

config/arbitrary_3_angle_20.yaml

@@ -0,0 +1,50 @@
+description: 'attraction-repulsion with 3 types particles'
+dataset: 'arbitrary_3_angle_20'
+
+simulation:
+  params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
+  min_radius: 0
+  max_radius: 0.075
+  n_particles: 4800
+  n_particle_types: 3
+  n_interactions: 3
+  n_frames: 250
+  sigma: 0.005
+  delta_t: 0.1
+  dpos_init: 0
+  boundary: 'periodic'
+  angular_sigma: 20
+
+graph_model:
+  particle_model_name: 'PDE_A'
+  mesh_model_name: ''
+  prediction: 'first_derivative'
+  input_size: 5
+  output_size: 2
+  hidden_dim: 128
+  n_mp_layers: 5
+  aggr_type: 'mean'
+  embedding_dim: 2
+  update_type: 'none'
+
+plotting:
+  colormap: 'tab10'
+  arrow_length: 2
+  ylim: [-0.04, 0.03]
+
+training:
+  n_epochs: 20
+  batch_size: 8
+  small_init_batch_size: False
+  n_runs: 2
+  sparsity: 'replace_embedding_function'
+  cluster_method: 'distance_plot'
+  data_augmentation: True
+  data_augmentation_loop: 100
+  fix_cluster_embedding: True
+  device: 'auto'
+
+
+
+
+

config/arbitrary_3_angle_30.yaml

@@ -0,0 +1,50 @@
+description: 'attraction-repulsion with 3 types particles'
+dataset: 'arbitrary_3_angle_30'
+
+simulation:
+  params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
+  min_radius: 0
+  max_radius: 0.075
+  n_particles: 4800
+  n_particle_types: 3
+  n_interactions: 3
+  n_frames: 250
+  sigma: 0.005
+  delta_t: 0.1
+  dpos_init: 0
+  boundary: 'periodic'
+  angular_sigma: 30
+
+graph_model:
+  particle_model_name: 'PDE_A'
+  mesh_model_name: ''
+  prediction: 'first_derivative'
+  input_size: 5
+  output_size: 2
+  hidden_dim: 128
+  n_mp_layers: 5
+  aggr_type: 'mean'
+  embedding_dim: 2
+  update_type: 'none'
+
+plotting:
+  colormap: 'tab10'
+  arrow_length: 2
+  ylim: [-0.04, 0.03]
+
+training:
+  n_epochs: 20
+  batch_size: 8
+  small_init_batch_size: False
+  n_runs: 2
+  sparsity: 'replace_embedding_function'
+  cluster_method: 'distance_plot'
+  data_augmentation: True
+  data_augmentation_loop: 100
+  fix_cluster_embedding: True
+  device: 'auto'
+
+
+
+
+

config/arbitrary_3_division_death.yaml

@@ -3,7 +3,7 @@ dataset: 'arbitrary_3_division_death'
 
 simulation:
   params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
-  cell_cycle_length: [-1]
+  cell_cycle_length: [100, 125, 200]
   cell_death_rate: [1,2,3]
   min_radius: 0
   max_radius: 0.075
@@ -12,7 +12,7 @@ simulation:
   n_interactions: 3
   has_cell_division: True
   n_particles_max: 20000
-  n_frames: 2000
+  n_frames: 1000
   sigma: 0.005
   delta_t: 0.025
   dpos_init: 0

config/arbitrary_3_division_death_tracking.yaml

@@ -3,7 +3,7 @@ dataset: 'arbitrary_3_division_death'
 
 simulation:
   params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
-  cell_cycle_length: [-1]
+  cell_cycle_length: [100, 125, 200]
   cell_death_rate: [1,2,3]
   min_radius: 0
   max_radius: 0.075
@@ -12,7 +12,7 @@ simulation:
   n_interactions: 3
   has_cell_division: True
   n_particles_max: 20000
-  n_frames: 2000
+  n_frames: 1000
   sigma: 0.005
   delta_t: 0.025
   dpos_init: 0

config/arbitrary_3_tracking_Bernouilli_20.yaml

@@ -0,0 +1,52 @@
+description: 'attraction-repulsion with 3 types particles'
+dataset: 'arbitrary_3_Bernouilli_20'
+
+simulation:
+  params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
+  min_radius: 0
+  max_radius: 0.075
+  n_particles: 4800
+  n_particle_types: 3
+  n_interactions: 3
+  n_frames: 250
+  sigma: 0.005
+  delta_t: 0.1
+  dpos_init: 0
+  boundary: 'periodic'
+
+graph_model:
+  particle_model_name: 'PDE_A'
+  mesh_model_name: ''
+  prediction: 'first_derivative'
+  input_size: 5
+  output_size: 2
+  hidden_dim: 128
+  n_mp_layers: 5
+  aggr_type: 'mean'
+  embedding_dim: 2
+  update_type: 'none'
+
+plotting:
+  colormap: 'tab10'
+  arrow_length: 2
+  ylim: [-0.04, 0.03]
+
+training:
+  n_epochs: 20
+  has_no_tracking: True
+  batch_size: 1
+  small_init_batch_size: True
+  n_runs: 2
+  sparsity: 'replace_embedding_function'
+  cluster_method: 'distance_plot'
+  data_augmentation: True
+  data_augmentation_loop: 200
+  fix_cluster_embedding: True
+  device: 'auto'
+  coeff_loss1: 1
+  coeff_loss2: 1
+
+
+
+
+

config/arbitrary_3_tracking_Bernouilli_30.yaml

@@ -0,0 +1,52 @@
+description: 'attraction-repulsion with 3 types particles'
+dataset: 'arbitrary_3_Bernouilli_30'
+
+simulation:
+  params: [[1.6233, 1.0413, 1.6012, 1.5615], [1.7667, 1.8308, 1.0855, 1.9055], [1.7226, 1.7850, 1.0584, 1.8579]]
+  min_radius: 0
+  max_radius: 0.075
+  n_particles: 4800
+  n_particle_types: 3
+  n_interactions: 3
+  n_frames: 250
+  sigma: 0.005
+  delta_t: 0.1
+  dpos_init: 0
+  boundary: 'periodic'
+
+graph_model:
+  particle_model_name: 'PDE_A'
+  mesh_model_name: ''
+  prediction: 'first_derivative'
+  input_size: 5
+  output_size: 2
+  hidden_dim: 128
+  n_mp_layers: 5
+  aggr_type: 'mean'
+  embedding_dim: 2
+  update_type: 'none'
+
+plotting:
+  colormap: 'tab10'
+  arrow_length: 2
+  ylim: [-0.04, 0.03]
+
+training:
+  n_epochs: 20
+  has_no_tracking: True
+  batch_size: 1
+  small_init_batch_size: True
+  n_runs: 2
+  sparsity: 'replace_embedding_function'
+  cluster_method: 'distance_plot'
+  data_augmentation: True
+  data_augmentation_loop: 200
+  fix_cluster_embedding: True
+  device: 'auto'
+  coeff_loss1: 1
+  coeff_loss2: 1
+
+
+
+
+