Merge pull request #107 from basf/master

Release v0.2.1

mambular/__version__.py

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ = "0.1.7"
+__version__ = "0.2.1"

mambular/arch_utils/attention_net_arch_utils.py

@@ -0,0 +1,102 @@
+import torch.nn as nn
+import torch
+
+
+import torch
+import torch.nn as nn
+
+
+class Reshape(nn.Module):
+    def __init__(self, j, dim, method="linear"):
+        super(Reshape, self).__init__()
+        self.j = j
+        self.dim = dim
+        self.method = method
+
+        if self.method == "linear":
+            # Use nn.Linear approach
+            self.layer = nn.Linear(dim, j * dim)
+        elif self.method == "embedding":
+            # Use nn.Embedding approach
+            self.layer = nn.Embedding(dim, j * dim)
+        elif self.method == "conv1d":
+            # Use nn.Conv1d approach
+            self.layer = nn.Conv1d(in_channels=dim, out_channels=j * dim, kernel_size=1)
+        else:
+            raise ValueError(f"Unsupported method '{method}' for reshaping.")
+
+    def forward(self, x):
+        batch_size = x.shape[0]
+
+        if self.method == "linear" or self.method == "embedding":
+            x_reshaped = self.layer(x)  # shape: (batch_size, j * dim)
+            x_reshaped = x_reshaped.view(
+                batch_size, self.j, self.dim
+            )  # shape: (batch_size, j, dim)
+        elif self.method == "conv1d":
+            # For Conv1d, add dummy dimension and reshape
+            x = x.unsqueeze(-1)  # Add dummy dimension for convolution
+            x_reshaped = self.layer(x)  # shape: (batch_size, j * dim, 1)
+            x_reshaped = x_reshaped.squeeze(-1)  # Remove dummy dimension
+            x_reshaped = x_reshaped.view(
+                batch_size, self.j, self.dim
+            )  # shape: (batch_size, j, dim)
+
+        return x_reshaped
+
+
+class AttentionNetBlock(nn.Module):
+    def __init__(
+        self,
+        channels,
+        in_channels,
+        d_model,
+        n_heads,
+        n_layers,
+        dim_feedforward,
+        transformer_activation,
+        output_dim,
+        attn_dropout,
+        layer_norm_eps,
+        norm_first,
+        bias,
+        activation,
+        embedding_activation,
+        norm_f,
+        method,
+    ):
+        super(AttentionNetBlock, self).__init__()
+
+        self.reshape = Reshape(channels, in_channels, method)
+
+        encoder_layer = nn.TransformerEncoderLayer(
+            d_model=d_model,
+            nhead=n_heads,
+            batch_first=True,
+            dim_feedforward=dim_feedforward,
+            dropout=attn_dropout,
+            activation=transformer_activation,
+            layer_norm_eps=layer_norm_eps,
+            norm_first=norm_first,
+            bias=bias,
+        )
+
+        self.encoder = nn.TransformerEncoder(
+            encoder_layer,
+            num_layers=n_layers,
+            norm=norm_f,
+        )
+
+        self.linear = nn.Linear(d_model, output_dim)
+        self.activation = activation
+        self.embedding_activation = embedding_activation
+
+    def forward(self, x):
+        z = self.reshape(x)
+        x = self.embedding_activation(z)
+        x = self.encoder(x)
+        x = z + x
+        x = torch.sum(x, dim=1)
+        x = self.linear(x)
+        x = self.activation(x)
+        return x

mambular/arch_utils/attention_utils.py

@@ -0,0 +1,97 @@
+import torch.nn as nn
+import torch
+from rotary_embedding_torch import RotaryEmbedding
+from einops import rearrange
+import torch.nn.functional as F
+import numpy as np
+
+
+class GEGLU(nn.Module):
+    def forward(self, x):
+        x, gates = x.chunk(2, dim=-1)
+        return x * F.gelu(gates)
+
+
+def FeedForward(dim, mult=4, dropout=0.0):
+    return nn.Sequential(
+        nn.LayerNorm(dim),
+        nn.Linear(dim, dim * mult * 2),
+        GEGLU(),
+        nn.Dropout(dropout),
+        nn.Linear(dim * mult, dim),
+    )
+
+
+class Attention(nn.Module):
+    def __init__(self, dim, heads=8, dim_head=64, dropout=0.0, rotary=False):
+        super().__init__()
+        inner_dim = dim_head * heads
+        self.heads = heads
+        self.scale = dim_head**-0.5
+        self.norm = nn.LayerNorm(dim)
+        self.to_qkv = nn.Linear(dim, inner_dim * 3, bias=False)
+        self.to_out = nn.Linear(inner_dim, dim, bias=False)
+        self.dropout = nn.Dropout(dropout)
+        self.rotary = rotary
+        dim = np.int64(dim / 2)
+        self.rotary_embedding = RotaryEmbedding(dim=dim)
+
+    def forward(self, x):
+        h = self.heads
+        x = self.norm(x)
+        q, k, v = self.to_qkv(x).chunk(3, dim=-1)
+        q, k, v = map(lambda t: rearrange(t, "b n (h d) -> b h n d", h=h), (q, k, v))
+        if self.rotary:
+            q = self.rotary_embedding.rotate_queries_or_keys(q)
+            k = self.rotary_embedding.rotate_queries_or_keys(k)
+        q = q * self.scale
+
+        sim = torch.einsum("b h i d, b h j d -> b h i j", q, k)
+
+        attn = sim.softmax(dim=-1)
+        dropped_attn = self.dropout(attn)
+
+        out = torch.einsum("b h i j, b h j d -> b h i d", dropped_attn, v)
+        out = rearrange(out, "b h n d -> b n (h d)", h=h)
+        out = self.to_out(out)
+
+        return out, attn
+
+
+class Transformer(nn.Module):
+    def __init__(
+        self, dim, depth, heads, dim_head, attn_dropout, ff_dropout, rotary=False
+    ):
+        super().__init__()
+        self.layers = nn.ModuleList([])
+
+        for _ in range(depth):
+            self.layers.append(
+                nn.ModuleList(
+                    [
+                        Attention(
+                            dim,
+                            heads=heads,
+                            dim_head=dim_head,
+                            dropout=attn_dropout,
+                            rotary=rotary,
+                        ),
+                        FeedForward(dim, dropout=ff_dropout),
+                    ]
+                )
+            )
+
+    def forward(self, x, return_attn=False):
+        post_softmax_attns = []
+
+        for attn, ff in self.layers:
+            attn_out, post_softmax_attn = attn(x)
+            post_softmax_attns.append(post_softmax_attn)
+
+            x = attn_out + x
+            x = ff(x) + x
+
+        if not return_attn:
+            return x
+
+        return x, torch.stack(post_softmax_attns)

mambular/arch_utils/embedding_layer.py

@@ -0,0 +1,163 @@
+import torch
+import torch.nn as nn
+
+
+class EmbeddingLayer(nn.Module):
+    def __init__(
+        self,
+        num_feature_info,
+        cat_feature_info,
+        d_model,
+        embedding_activation=nn.Identity(),
+        layer_norm_after_embedding=False,
+        use_cls=False,
+        cls_position=0,
+        cat_encoding="int",
+    ):
+        """
+        Embedding layer that handles numerical and categorical embeddings.
+
+        Parameters
+        ----------
+        num_feature_info : dict
+            Dictionary where keys are numerical feature names and values are their respective input dimensions.
+        cat_feature_info : dict
+            Dictionary where keys are categorical feature names and values are the number of categories for each feature.
+        d_model : int
+            Dimensionality of the embeddings.
+        embedding_activation : nn.Module, optional
+            Activation function to apply after embedding. Default is `nn.Identity()`.
+        layer_norm_after_embedding : bool, optional
+            If True, applies layer normalization after embeddings. Default is `False`.
+        use_cls : bool, optional
+            If True, includes a class token in the embeddings. Default is `False`.
+        cls_position : int, optional
+            Position to place the class token, either at the start (0) or end (1) of the sequence. Default is `0`.
+
+        Methods
+        -------
+        forward(num_features=None, cat_features=None)
+            Defines the forward pass of the model.
+        """
+        super(EmbeddingLayer, self).__init__()
+
+        self.d_model = d_model
+        self.embedding_activation = embedding_activation
+        self.layer_norm_after_embedding = layer_norm_after_embedding
+        self.use_cls = use_cls
+        self.cls_position = cls_position
+
+        self.num_embeddings = nn.ModuleList(
+            [
+                nn.Sequential(
+                    nn.Linear(input_shape, d_model, bias=False),
+                    self.embedding_activation,
+                )
+                for feature_name, input_shape in num_feature_info.items()
+            ]
+        )
+
+        self.cat_embeddings = nn.ModuleList()
+        for feature_name, num_categories in cat_feature_info.items():
+            if cat_encoding == "int":
+                self.cat_embeddings.append(
+                    nn.Sequential(
+                        nn.Embedding(num_categories + 1, d_model),
+                        self.embedding_activation,
+                    )
+                )
+            elif cat_encoding == "one-hot":
+                self.cat_embeddings.append(
+                    nn.Sequential(
+                        OneHotEncoding(num_categories),
+                        nn.Linear(num_categories, d_model, bias=False),
+                        self.embedding_activation,
+                    )
+                )
+
+        if self.use_cls:
+            self.cls_token = nn.Parameter(torch.zeros(1, 1, d_model))
+        if layer_norm_after_embedding:
+            self.embedding_norm = nn.LayerNorm(d_model)
+
+        self.seq_len = len(self.num_embeddings) + len(self.cat_embeddings)
+
+    def forward(self, num_features=None, cat_features=None):
+        """
+        Defines the forward pass of the model.
+
+        Parameters
+        ----------
+        num_features : Tensor, optional
+            Tensor containing the numerical features.
+        cat_features : Tensor, optional
+            Tensor containing the categorical features.
+
+        Returns
+        -------
+        Tensor
+            The output embeddings of the model.
+
+        Raises
+        ------
+        ValueError
+            If no features are provided to the model.
+        """
+        if self.use_cls:
+            batch_size = (
+                cat_features[0].size(0)
+                if cat_features != []
+                else num_features[0].size(0)
+            )
+            cls_tokens = self.cls_token.expand(batch_size, -1, -1)
+
+        if self.cat_embeddings and cat_features is not None:
+            cat_embeddings = [
+                emb(cat_features[i]) for i, emb in enumerate(self.cat_embeddings)
+            ]
+            cat_embeddings = torch.stack(cat_embeddings, dim=1)
+            cat_embeddings = torch.squeeze(cat_embeddings, dim=2)
+            if self.layer_norm_after_embedding:
+                cat_embeddings = self.embedding_norm(cat_embeddings)
+        else:
+            cat_embeddings = None
+
+        if self.num_embeddings and num_features is not None:
+            num_embeddings = [
+                emb(num_features[i]) for i, emb in enumerate(self.num_embeddings)
+            ]
+            num_embeddings = torch.stack(num_embeddings, dim=1)
+            if self.layer_norm_after_embedding:
+                num_embeddings = self.embedding_norm(num_embeddings)
+        else:
+            num_embeddings = None
+
+        if cat_embeddings is not None and num_embeddings is not None:
+            x = torch.cat([cat_embeddings, num_embeddings], dim=1)
+        elif cat_embeddings is not None:
+            x = cat_embeddings
+        elif num_embeddings is not None:
+            x = num_embeddings
+        else:
+            raise ValueError("No features provided to the model.")
+
+        if self.use_cls:
+            if self.cls_position == 0:
+                x = torch.cat([cls_tokens, x], dim=1)
+            elif self.cls_position == 1:
+                x = torch.cat([x, cls_tokens], dim=1)
+            else:
+                raise ValueError(
+                    "Invalid cls_position value. It should be either 0 or 1."
+                )
+
+        return x
+
+
+class OneHotEncoding(nn.Module):
+    def __init__(self, num_categories):
+        super(OneHotEncoding, self).__init__()
+        self.num_categories = num_categories
+
+    def forward(self, x):
+        return torch.nn.functional.one_hot(x, num_classes=self.num_categories).float()