Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…

…Link into devel

# Conflicts:
#	Scripts/Models (Under Development)/EGO/Using EMComposition/EGO Model - CSW with Simple Integrator.py

README.rst

@@ -172,13 +172,13 @@ To run the tutorial locally, you must run python 3.5 and install additional pack
 
 ::
 
-    pip install psyneulink[tutorial]
+    pip install "psyneulink[tutorial]"
 
 or if you downloaded the source:
 
 ::
 
-    pip install .[tutorial]
+    pip install ".[tutorial]"
 
 
 To access the tutorial, make sure you fulfill the requirements mentioned above, download the tutorial notebook (/tutorial/PsyNeuLink Tutorial.ipynb), then run the terminal command

Scripts/Models (Under Development)/EGO/Using EMComposition/DeclanParams.py

@@ -0,0 +1,93 @@
+"""
+DECLAN Params: **************************************************************************
+√ episodic_lr = 1  # learning rate for the episodic pathway
+√ temperature = 0.1  # temperature for EM retrieval (lower is more argmax-like)
+√ n_optimization_steps = 10  # number of update steps
+sim_thresh = 0.8 # threshold for discarding bad seeds -- can probably ignore this for now
+Filter runs whose context representations are too uniform (i.e. not similar to "checkerboard" foil)
+
+May need to pad the context reps because there will be 999 reps
+def filter_run(run_em, thresh=0.8):
+    foil = np.zeros([4,4])
+    foil[::2, ::2] = 1
+    foil[1::2, 1::2] = 1
+    run_em = run_em.reshape(200, 5, 11).mean(axis=1)
+    mat = cosine_similarity(run_em, run_em)
+    vec = mat[:160, :160].reshape(4, 40, 4, 40).mean(axis=(1, 3)).ravel()
+    return cosine_similarity(foil.reshape(1, -1), vec.reshape(1, -1))[0][0]
+
+# Stack the model predictions (should be 999x11), pad with zeros, and reshape into trials for averaging.
+em_preds = np.vstack([em_preds, np.zeros([1,11])]).reshape(-1,5,11)
+
+# Stack the ground truth states (should be 999x11), pad with zeros, and reshape into trials for averaging.
+ys = np.vstack([data_loader.dataset.ys.cpu().numpy(), np.zeros([1,11])]).reshape(-1,5,11)
+
+# compute the probability as a performance metric
+def calc_prob(em_preds, test_ys):
+    em_preds, test_ys = em_preds[:, 2:-1, :], test_ys[:, 2:-1, :]
+    em_probability = (em_preds*test_ys).sum(-1).mean(-1)
+    trial_probs = (em_preds*test_ys)
+    return em_probability, trial_probs
+
+Calculate the retrieval probability of the correct response as a performance metric (probs)
+probs, trial_probs = calc_prob(em_preds, test_ys)
+"""
+from psyneulink.core.llvm import ExecutionMode
+from psyneulink.core.globals.keywords import ALL, ADAPTIVE, CONTROL, CPU, Loss, MPS, OPTIMIZATION_STEP, RUN, TRIAL
+
+model_params = dict(
+
+    # Names:
+    name = "EGO Model CSW",
+    state_input_layer_name = "STATE",
+    previous_state_layer_name = "PREVIOUS STATE",
+    context_layer_name = 'CONTEXT',
+    em_name = "EM",
+    prediction_layer_name = "PREDICTION",
+
+    # Structural
+    state_d = 11, # length of state vector
+    previous_state_d = 11, # length of state vector
+    context_d = 11, # length of context vector
+    memory_capacity = ALL, # number of entries in EM memory; ALL=> match to number of stims
+    memory_init = (0,.0001),  # Initialize memory with random values in interval
+    # memory_init = None,  # Initialize with zeros
+    concatenate_keys = False,
+    # concatenate_keys = True,
+
+    # environment
+    # curriculum_type = 'Interleaved',
+    curriculum_type = 'Blocked',
+    # num_stims = 100,  # Integer or ALL
+    num_stims = ALL,  # Integer or ALL
+
+    # Processing
+    integration_rate = .69, # rate at which state is integrated into new context
+    # state_weight = 1, # weight of the state used during memory retrieval
+    # context_weight = 1, # weight of the context used during memory retrieval
+    state_weight = .5, # weight of the state used during memory retrieval
+    context_weight = .5, # weight of the context used during memory retrieval
+    normalize_field_weights = False, # whether to normalize the field weights during memory retrieval
+    # normalize_field_weights = True, # whether to normalize the field weights during memory retrieval
+    # softmax_temperature = None, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
+    softmax_temperature = .1, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
+    # softmax_temperature = ADAPTIVE, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
+    # softmax_temperature = CONTROL, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
+    # softmax_threshold = None, # threshold used to mask out small values in softmax
+    softmax_threshold = .001, # threshold used to mask out small values in softmax
+    enable_learning=[True, False, False], # Enable learning for PREDICTION (STATE) but not CONTEXT or PREVIOUS STATE
+    learn_field_weights = False,
+    loss_spec = Loss.BINARY_CROSS_ENTROPY,
+    # loss_spec = Loss.MSE,
+    learning_rate = .5,
+    # num_optimization_steps = 1,
+    num_optimization_steps = 10,
+    synch_weights = RUN,
+    synch_values = RUN,
+    synch_results = RUN,
+    # execution_mode = ExecutionMode.Python,
+    execution_mode = ExecutionMode.PyTorch,
+    device = CPU,
+    # device = MPS,
+)
+#endregion

Scripts/Models (Under Development)/EGO/EGO Model (sim 2) - CSW using EMComposition with WM.py → Scripts/Models (Under Development)/EGO/Using EMComposition/EGO Model - CSW with RNN.py

@@ -147,8 +147,8 @@
 MEMORY_CAPACITY = 5
 CONSTRUCT_MODEL = True                 # THIS MUST BE SET TO True to run the script
 DISPLAY_MODEL = (                      # Only one of the following can be uncommented:
-    None                             # suppress display of model
-    # {}                               # show simple visual display of model
+    # None                             # suppress display of model
+    {}                               # show simple visual display of model
     # {'show_node_structure': True}    # show detailed view of node structures and projections
 )
 RUN_MODEL = True                       # True => run the model
@@ -404,7 +404,7 @@ def construct_model(model_name:str=MODEL_NAME,
         model = construct_model()
         assert 'DEBUGGING BREAK POINT'
         # print(model.scheduler.consideration_queue)
-        # gs.output_graph_image(model.scheduler.graph, 'EGO_comp-scheduler.png')
+        # gs.output_graph_image(model.scheduler.graph, 'show_graph OUTPUT/EGO_comp-scheduler.png')
 
     if DISPLAY_MODEL is not None:
         if model: