Cleanup impute

.gitignore

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+Working_Code/data
+Working_Code/.pybiomart.sqlite
+Working_Code/GenAI/kaggle.json
+.DS_Store

Working_Code/GenAI/VAE_RNASeq.py

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+import torch
+import torch.nn as nn
+from torch.utils.tensorboard import SummaryWriter
+writer = SummaryWriter('runs/lgbm')
+
+
+def idx2onehot(idx, n):
+
+    assert torch.max(idx).item() < n
+    if idx.dim() == 1:
+        idx = idx.unsqueeze(1)
+
+    onehot = torch.zeros(idx.size(0), n)
+    onehot.scatter_(1, idx, 1)
+
+    return onehot
+
+
+class VAE(nn.Module):
+    def __init__(self, encoder_layer_sizes, latent_size, decoder_layer_sizes,
+                 conditional=False, num_labels=0):
+
+        super().__init__()
+
+        if conditional:
+            assert num_labels > 0
+
+        assert type(encoder_layer_sizes) == list
+        assert type(latent_size) == int
+        assert type(decoder_layer_sizes) == list
+
+        self.latent_size = latent_size
+        self.num_labels = num_labels
+
+        self.encoder = Encoder(
+            encoder_layer_sizes, latent_size, conditional, num_labels)
+        self.decoder = Decoder(
+            decoder_layer_sizes, latent_size, conditional, num_labels)
+
+    def forward(self, x, c=None):
+        view_size = 1000
+        if x.dim() > 2:
+            x = x.view(-1, view_size)
+
+        batch_size = x.size(0)
+
+        means, log_var = self.encoder.forward(x, c)
+
+        std = torch.exp(0.5 * log_var)
+        eps = torch.randn([batch_size, self.latent_size])
+        z = eps * std + means
+
+        recon_x = self.decoder.forward(z, c)
+
+        return recon_x, means, log_var, z
+
+    def inference(self, n=0, c=None):
+        if n == 0:
+            n = self.num_labels
+        batch_size = n
+        z = torch.randn([batch_size, self.latent_size])
+
+        recon_x = self.decoder.forward(z, c)
+
+        return recon_x
+
+    def embedding(self, x, c=None):
+        view_size = 1000
+        #if x.dim() > 2:
+        #    x = x.view(-1, view_size)
+
+        batch_size = x.size(0)
+
+        means, log_var = self.encoder.forward(x, c)
+        std = torch.exp(0.5 * log_var)
+        eps = torch.randn([1, self.latent_size])
+        z = eps * std + means
+
+        return z
+
+
+class Encoder(nn.Module):
+    def __init__(self, layer_sizes, latent_size, conditional, num_labels):
+
+        super().__init__()
+
+        self.conditional = conditional
+        if self.conditional:
+            layer_sizes[0] += num_labels
+
+        self.MLP = nn.Sequential()
+
+        for i, (in_size, out_size) in enumerate(zip(layer_sizes[:-1], layer_sizes[1:])):
+            self.MLP.add_module(
+                name="L{:d}".format(i), module=nn.Linear(in_size, out_size))
+            self.MLP.add_module(name="A{:d}".format(i), module=nn.ReLU())
+
+        self.linear_means = nn.Linear(layer_sizes[-1], latent_size)
+        self.linear_log_var = nn.Linear(layer_sizes[-1], latent_size)
+
+    def forward(self, x, c=None):
+
+        if self.conditional:
+            c = idx2onehot(c, n=self.num_labels)
+            x = torch.cat((x, c), dim=-1)
+
+        x = self.MLP(x)
+
+        means = self.linear_means(x)
+        log_vars = self.linear_log_var(x)
+
+        return means, log_vars
+
+
+class Decoder(nn.Module):
+    def __init__(self, layer_sizes, latent_size, conditional, num_labels):
+
+        super().__init__()
+
+        self.MLP = nn.Sequential()
+        self.num_labels = num_labels
+
+        self.conditional = conditional
+        if self.conditional:
+            input_size = latent_size + num_labels
+        else:
+            input_size = latent_size
+
+        for i, (in_size, out_size) in enumerate(zip([input_size]+layer_sizes[:-1], layer_sizes)):
+            self.MLP.add_module(
+                name="L{:d}".format(i), module=nn.Linear(in_size, out_size))
+            if i+1 < len(layer_sizes):
+                self.MLP.add_module(name="A{:d}".format(i), module=nn.ReLU())
+            else:
+                self.MLP.add_module(name="sigmoid", module=nn.Sigmoid())
+
+    def forward(self, z, c):
+
+        if self.conditional:
+            c = idx2onehot(c, n=self.num_labels)
+            z = torch.cat((z, c), dim=-1)
+
+        x = self.MLP(z)
+
+        return x