complete modularized rnn

nn4n/criterion/firing_rate_loss.py

@@ -2,17 +2,7 @@
 import torch.nn as nn
 import torch.nn.functional as F
 
-
-class CustomLoss(nn.Module):
-    def __init__(self, batch_first=True):
-        super().__init__()
-        self.batch_first = batch_first
-
-    def forward(self, **kwargs):
-        pass
-
-
-class FiringRateLoss(CustomLoss):
+class FiringRateLoss(nn.Module):
     def __init__(self, metric="l2", **kwargs):
         super().__init__(**kwargs)
         assert metric in ["l1", "l2"], "metric must be either l1 or l2"
@@ -29,7 +19,7 @@ def forward(self, states, **kwargs):
             return F.mse_loss(mean_fr, torch.zeros_like(mean_fr), reduction="mean")
 
 
-class FiringRateDistLoss(CustomLoss):
+class FiringRateDistLoss(nn.Module):
     def __init__(self, metric="sd", **kwargs):
         super().__init__(**kwargs)
         valid_metrics = ["sd", "cv", "mean_ad", "max_ad"]
@@ -63,15 +53,12 @@ def forward(self, states, **kwargs):
             return torch.max(torch.abs(mean_fr - avg_mean_fr))
 
 
-class StatePredictionLoss(CustomLoss):
+class StatePredictionLoss(nn.Module):
     def __init__(self, tau=1, **kwargs):
         super().__init__(**kwargs)
         self.tau = tau
 
     def forward(self, states, **kwargs):
-        if not self.batch_first:
-            states = states.transpose(0, 1)
-
         # Ensure the sequence is long enough for the prediction window
         assert (
             states.shape[1] > self.tau

nn4n/criterion/rnn_loss.py

@@ -35,7 +35,6 @@ class RNNLoss(nn.Module):
     def __init__(self, model, **kwargs):
         super().__init__()
         self.model = model
-        self.batch_first = model.batch_first
         if type(self.model) != CTRNN:
             raise TypeError("model must be CTRNN")
         self._init_losses(**kwargs)
@@ -103,8 +102,6 @@ def _loss_fr(self, states, **kwargs):
         This compute the L2 norm (for now) of the hidden states across all timesteps and batch_size
         Then take the square of the mean of the norm
         """
-        if not self.batch_first:
-            states = states.transpose(0, 1)
         mean_fr = torch.mean(states, dim=(0, 1))
         # return torch.pow(torch.mean(states, dim=(0, 1)), 2).mean() # this might not be correct
         # return torch.norm(states, p='fro')**2/states.numel() # this might not be correct
@@ -119,8 +116,6 @@ def _loss_fr_sd(self, states, **kwargs):
         Parameters:
         - states: size=(batch_size, n_timesteps, hidden_size), hidden states of the network
         """
-        if not self.batch_first:
-            states = states.transpose(0, 1)
         avg_fr = torch.mean(states, dim=(0, 1))
         return avg_fr.std()
 
@@ -133,8 +128,6 @@ def _loss_fr_cv(self, states, **kwargs):
         Parameters:
         - states: size=(batch_size, n_timesteps, hidden_size), hidden states of the network
         """
-        if not self.batch_first:
-            states = states.transpose(0, 1)
         avg_fr = torch.mean(torch.sqrt(torch.square(states)), dim=(0, 1))
         return avg_fr.std() / avg_fr.mean()
 

nn4n/layer/__init__.py

@@ -1,4 +1,4 @@
 from .linear_layer import LinearLayer
 from .hidden_layer import HiddenLayer
 from .recurrent_layer import RecurrentLayer
-from .rnn import RNN
+from .rnn import RNN

nn4n/layer/base_layer.py

@@ -6,295 +6,17 @@
 
 class BaseLayer(nn.Module):
     """
-    Linear Layer with optional sparsity, excitatory/inhibitory, and plasticity constraints.
-    The layer is initialized by passing specs in layer_struct.
-
-    Required keywords in layer_struct:
-        - input_dim: dimension of input
-        - output_dim: dimension of output
-        - weight: weight matrix init method/init weight matrix, default: 'uniform'
-        - bias: bias vector init method/init bias vector, default: 'uniform'
-        - sparsity_mask: mask for sparse connectivity
-        - ei_mask: mask for Dale's law
-        - plasticity_mask: mask for plasticity
+    nn4n Layer class
     """
 
-    def __init__(
-        self,
-        input_dim: int,
-        output_dim: int,
-        weight: str = "uniform",
-        bias: str = "uniform",
-        ei_mask: torch.Tensor = None,
-        sparsity_mask: torch.Tensor = None,
-        plasticity_mask: torch.Tensor = None,
-    ):
+    def __init__(self):
         super().__init__()
-        self.input_dim = input_dim
-        self.output_dim = output_dim
-        self.weight_dist = weight
-        self.bias_dist = bias
-        self.weight = self._generate_weight(self.weight_dist)
-        self.bias = self._generate_bias(self.bias_dist)
-        self.ei_mask = ei_mask.T if ei_mask is not None else None
-        self.sparsity_mask = sparsity_mask.T if sparsity_mask is not None else None
-        self.plasticity_mask = (
-            plasticity_mask.T if plasticity_mask is not None else None
-        )
-        # All unique plasticity values in the plasticity mask
-        self.plasticity_scales = (
-            torch.unique(self.plasticity_mask)
-            if self.plasticity_mask is not None
-            else None
-        )
-
-        self._init_trainable()
-        self._check_layer()
-
-    # INITIALIZATION
-    # ======================================================================================
-    @staticmethod
-    def _check_keys(layer_struct):
-        required_keys = ["input_dim", "output_dim"]
-        for key in required_keys:
-            if key not in layer_struct:
-                raise ValueError(f"Key '{key}' is missing in layer_struct")
-
-        valid_keys = ["input_dim", "output_dim", "weight", "bias", "ei_mask", "sparsity_mask", "plasticity_mask"]
-        for key in layer_struct.keys():
-            if key not in valid_keys:
-                raise ValueError(f"Key '{key}' is not a valid key in layer_struct")
-
-    @classmethod
-    def from_dict(cls, layer_struct):
-        """
-        Alternative constructor to initialize LinearLayer from a dictionary.
-        """
-        # Create an instance using the dictionary values
-        cls._check_keys(layer_struct)
-        return cls(
-            input_dim=layer_struct["input_dim"],
-            output_dim=layer_struct["output_dim"],
-            weight=layer_struct.get("weight", "uniform"),
-            bias=layer_struct.get("bias", "uniform"),
-            ei_mask=layer_struct.get("ei_mask"),
-            sparsity_mask=layer_struct.get("sparsity_mask"),
-            plasticity_mask=layer_struct.get("plasticity_mask"),
-        )
-
-    def _check_layer(self):
-        """
-        Check if the layer is initialized properly
-        """
-        # TODO: Implement this
-        pass
-
-    # INIT TRAINABLE
-    # ======================================================================================
-    def _init_trainable(self):
-        # Enfore constraints
-        self._init_constraints()
-        # Convert weight and bias to learnable parameters
-        self.weight = nn.Parameter(
-            self.weight, requires_grad=self.weight_dist is not None
-        )
-        self.bias = nn.Parameter(self.bias, requires_grad=self.bias_dist is not None)
-
-    def _init_constraints(self):
-        """
-        Initialize constraints
-        It will also balance excitatory and inhibitory neurons
-        """
-        if self.sparsity_mask is not None:
-
-            self.weight *= self.sparsity_mask
-        if self.ei_mask is not None:
-            # Apply Dale's law
-            self.weight[self.ei_mask == 1] = torch.clamp(
-                self.weight[self.ei_mask == 1], min=0
-            ) # For excitatory neurons, set negative weights to 0
-            self.weight[self.ei_mask == -1] = torch.clamp(
-                self.weight[self.ei_mask == -1], max=0
-            ) # For inhibitory neurons, set positive weights to 0
-
-            # Balance excitatory and inhibitory neurons weight magnitudes
-            self._balance_excitatory_inhibitory()
-
-    def _generate_bias(self, bias_init):
-        """Generate random bias"""
-        if bias_init == "uniform":
-            # If uniform, let b be uniform in [-sqrt(k), sqrt(k)]
-            sqrt_k = torch.sqrt(torch.tensor(1 / self.input_dim))
-            b = torch.rand(self.output_dim) * sqrt_k
-            b = b * 2 - sqrt_k
-        elif bias_init == "normal":
-            b = torch.randn(self.output_dim) / torch.sqrt(torch.tensor(self.input_dim))
-        elif bias_init == "zero" or bias_init == None:
-            b = torch.zeros(self.output_dim)
-        elif type(bias_init) == np.ndarray:
-            b = torch.from_numpy(bias_init)
-        else:
-            raise NotImplementedError
-        return b.float()
-
-    def _generate_weight(self, weight_init):
-        """Generate random weight"""
-        if weight_init == "uniform":
-            # If uniform, let w be uniform in [-sqrt(k), sqrt(k)]
-            sqrt_k = torch.sqrt(torch.tensor(1 / self.input_dim))
-            w = torch.rand(self.output_dim, self.input_dim) * sqrt_k
-            w = w * 2 - sqrt_k
-        elif weight_init == "normal":
-            w = torch.randn(self.output_dim, self.input_dim) / torch.sqrt(
-                torch.tensor(self.input_dim)
-            )
-        elif weight_init == "zero":
-            w = torch.zeros((self.output_dim, self.input_dim))
-        elif type(weight_init) == np.ndarray:
-            w = torch.from_numpy(weight_init)
-        else:
-            raise NotImplementedError
-        return w.float()
-
-    def _balance_excitatory_inhibitory(self):
-        """Balance excitatory and inhibitory weights"""
-        scale_mat = torch.ones_like(self.weight)
-        ext_sum = self.weight[self.sparsity_mask == 1].sum()
-        inh_sum = self.weight[self.sparsity_mask == -1].sum()
-        if ext_sum == 0 or inh_sum == 0:
-            # Automatically stop balancing if one of the sums is 0
-            # devide by 10 to avoid recurrent explosion/decay
-            self.weight /= 10
-        else:
-            if ext_sum > abs(inh_sum):
-                _scale = abs(inh_sum).item() / ext_sum.item()
-                scale_mat[self.sparsity_mask == 1] = _scale
-            elif ext_sum < abs(inh_sum):
-                _scale = ext_sum.item() / abs(inh_sum).item()
-                scale_mat[self.sparsity_mask == -1] = _scale
-            # Apply scaling
-            self.weight *= scale_mat
-
-    # TRAINING
-    # ======================================================================================
-    def to(self, device):
-        """Move the network to the device (cpu/gpu)"""
-        super().to(device)
-        if self.sparsity_mask is not None:
-            self.sparsity_mask = self.sparsity_mask.to(device)
-        if self.ei_mask is not None:
-            self.ei_mask = self.ei_mask.to(device)
-        if self.bias.requires_grad:
-            self.bias = self.bias.to(device)
-        return self
-
-    def forward(self, x):
-        """
-        Forwardly update network
-
-        Inputs:
-            - x: input, shape: (batch_size, input_dim)
-
-        Returns:
-            - state: shape: (batch_size, hidden_size)
-        """
-        return x.float() @ self.weight.T + self.bias
-
-    def apply_plasticity(self):
-        """
-        Apply plasticity mask to the weight gradient
-        """
-        with torch.no_grad():
-            # assume the plasticity mask are all valid and being checked in ctrnn class
-            for scale in self.plasticity_scales:
-                if self.weight.grad is not None:
-                    self.weight.grad[self.plasticity_mask == scale] *= scale
-                else:
-                    raise RuntimeError(
-                        "Weight gradient is None, possibly because the forward loop is non-differentiable"
-                    )
-
-    def freeze(self):
-        """Freeze the layer"""
-        self.weight.requires_grad = False
-        self.bias.requires_grad = False
-
-    def unfreeze(self):
-        """Unfreeze the layer"""
-        self.weight.requires_grad = True
-        self.bias.requires_grad = True
-
-    # CONSTRAINTS
-    # ======================================================================================
-    def enforce_constraints(self):
-        """
-        Enforce constraints
-
-        The constraints are:
-            - sparsity_mask: mask for sparse connectivity
-            - ei_mask: mask for Dale's law
-        """
-        if self.sparsity_mask is not None:
-            self._enforce_sparsity()
-        if self.ei_mask is not None:
-            self._enforce_ei()
-
-    def _enforce_sparsity(self):
-        """Enforce sparsity"""
-        w = self.weight.detach().clone() * self.sparsity_mask
-        self.weight.data.copy_(torch.nn.Parameter(w))
-
-    def _enforce_ei(self):
-        """Enforce Dale's law"""
-        w = self.weight.detach().clone()
-        w[self.ei_mask == 1] = torch.clamp(w[self.ei_mask == 1], min=0)
-        w[self.ei_mask == -1] = torch.clamp(w[self.ei_mask == -1], max=0)
-        self.weight.data.copy_(torch.nn.Parameter(w))
-
-    # HELPER FUNCTIONS
-    # ======================================================================================
-    def set_weight(self, weight):
-        """Set the value of weight"""
-        assert (
-            weight.shape == self.weight.shape
-        ), f"Weight shape mismatch, expected {self.weight.shape}, got {weight.shape}"
-        with torch.no_grad():
-            self.weight.copy_(weight)
-
-    def plot_layer(self):
-        """Plot the weights matrix and distribution of each layer"""
-        weight = (
-            self.weight.cpu()
-            if self.weight.device != torch.device("cpu")
-            else self.weight
-        )
-        utils.plot_connectivity_matrix_dist(
-            weight.detach().numpy(),
-            f"Weight",
-            False,
-            self.sparsity_mask is not None,
-        )
 
     def get_specs(self):
-        """Print the specs of each layer"""
-        return {
-            "input_dim": self.input_dim,
-            "output_dim": self.output_dim,
-            "weight_learnable": self.weight.requires_grad,
-            "weight_min": self.weight.min().item(),
-            "weight_max": self.weight.max().item(),
-            "bias_learnable": self.bias.requires_grad,
-            "bias_min": self.bias.min().item(),
-            "bias_max": self.bias.max().item(),
-            "sparsity": (
-                self.sparsity_mask.sum() / self.sparsity_mask.numel()
-                if self.sparsity_mask is not None
-                else 1
-            )
-        }
+        pass
 
     def print_layer(self):
         """
         Print the specs of the layer
         """
-        utils.print_dict("Layer Specs", self.get_specs())
+        utils.print_dict(f"{self.__class__.__name__} layer", self.get_specs())