Uncovering the latent space of handwritten digits

10 Days Of Grad: Deep Learning From The First Principles

Day 9: Roaming The Latent Space

Imagine you are a designer and you want a new font: A little bit heavier, with rounder letters, more casual or a little bit more fancy. Could this font be created just by tuning a handful of parameters? Or imagine that you are a fashion designer and you would like to create a new collection as a mix of previous seasons? Or that you are a musician desperately looking for inspiration. How about a new song that mixes your mood and Beethoven's Symphony No 3? It turns out, all this is actually possible. To better illustrate the concept, here is some music interpolation:

Don't forget to check out

The complete project is also available on Github.

The Secret Space

latent - present and capable of emerging or developing but not now visible, obvious, active, or symptomatic

—Webster's Dictionary


A simple autoencoder with latent dimension $L$.

A simple autoencoder with latent dimension $L$.

How do we implement an autoencoder? Let us take a multilayer network from the image above: $784 \rightarrow 400 \rightarrow L \rightarrow 400 \rightarrow 784$. Where the latent space dimension $L$ is some smaller number such as $20$ or maybe even $2$. The $L$-sized latent vector $z$ is often called a bottleneck. The left part from the bottleck is called an encoder $q_{\phi}$ and the part on the right, a decoder $p_{\theta}$. Where $\phi$ and $\theta$ are trainable parameters of encoder and decoder, respectively.

The encoder takes an input (like an image) and generates a compact representation, typically a vector. It is also not a mistake to call it a compressed representation. The decoder takes this compact representation and creates an output as close as possible to the original input. Hence the name, autoencoder. Of course, some information is lost due to the dimensionality reduction. Therefore, the goal of a autoencoder is to find the most relevant features to preserve as much information about the input object as possible.

data AE = AE
  { -- Encoder parameters
    l1 :: Linear,
    l2 :: Linear,
    -- Decoder parameters
    l3 :: Linear,
    l4 :: Linear
  deriving (Generic, Show, Parameterized)

Then, the whole autoencoder network is

ae :: AE -> Tensor -> (Tensor, Tensor)
ae AE {..} =
  linear l1
  -- Encoder
  ~> relu
  ~> linear l2
  ~> relu
  -- Decoder
  ~> linear l3
  ~> relu
  ~> linear l4
  ~> sigmoid

We can also specify the exact dimensions

aeConfig =
    (LinearSpec 784 400)
    (LinearSpec 400 latent_size)
    (LinearSpec latent_size 400)
    (LinearSpec 400 784)

Of course, a smaller $L$ (latent_size), the more information is lost. Therefore, depending on the application we may want to change this value. As a rule of thumb, $L$ contains the smallest number of neurons to enforce the compression. In this article we set $L=2$ so that we can simply reveal our latent space in two dimensions.

Variational autoencoder

The principal difference of variational autoencoders (VAE) from normal autoencoders is in the bottleneck. Instead of a compressed input, it estimates a distribution. In practice, VAE estimates the mean $\mu$ and the standard deviation $\sigma$ -- normal distribution parameters. By sampling from that distribution, a new unseen before object can be generated. Like a new font or a new piece of cloth. Or a face. Or a melody. Isn't that nice?

Variational autoencoder. Arrows signify fully-connected layers and vertical bars are data vectors.

data VAESpec = VAESpec
    -- Encoder trainable parameters (phi)
    fc1 :: LinearSpec,
    fcMu :: LinearSpec,
    fcSigma :: LinearSpec,

    -- Decoder trainable parameters (theta)
    fc5 :: LinearSpec,
    fc6 :: LinearSpec
  deriving (Show, Eq)

myConfig =
    (LinearSpec 784 400)
    (LinearSpec 400 latent_size)
    (LinearSpec 400 latent_size)
    (LinearSpec latent_size 400)
    (LinearSpec 400 784)

data VAE = VAE
  { l1 :: Linear,
    lMu :: Linear,
    lSigma :: Linear,
    l4 :: Linear,
    l5 :: Linear
  deriving (Generic, Show, Parameterized)

It can be useful to have separate encode $q_{\phi}(z|x)$ and decode $p_{\theta}(x|z)$ functions.

encode :: VAE -> Tensor -> (Tensor, Tensor)
encode VAE {..} x0 =
  let enc_ =
        linear l1
         ~> relu

      x1 = enc_ x0
      mu = linear lMu x1
      logSigma = linear lSigma x1
  in (mu, logSigma)

decode :: VAE -> Tensor -> Tensor
decode VAE {..} =
  linear l4
  ~> relu
  ~> linear l5
  ~> sigmoid

Then, the complete variational autoencoder will be

vaeForward :: VAE -> Bool -> Tensor -> IO (Tensor, Tensor, Tensor)
vaeForward net@(VAE {..}) _ x0 = do
  let (mu, logSigma) = encode net x0
      sigma = exp (0.5 * logSigma)

  eps <- toLocalModel' <$> randnLikeIO sigma

  let z = (eps `mul` sigma) `add` mu
      reconstruction = decode net z

  return (reconstruction, mu, logSigma)

Pay a special attention to the reparametrization:

$$\varepsilon \sim \mathcal{N}(0,\,1)$$ $$z = \varepsilon \odot \sigma + \mu$$

Where $z$ is our latent vector, noise $\varepsilon$ is sampled from the normal distribution (randnLikeIO1), and $\odot$ is elementwise product. Thanks to this trick, we can backpropagate through a stochastic layer. See this excellent post for more details. There are two differences between variational and ordinary autoencoder training: (1) the reparametrization and (2) the loss function, which we cover below.

VAE Loss Function

The loss function consists of two parts:

$$ \rm{loss} = \mathbb{L}(x, \hat x) + \rm{D}_\rm{KL} \left(q_\phi(z) || p_\theta(z) \right).$$

$\mathbb{L}(x, \hat x)$ is the reconstruction loss. It decreases when the decoded output $\hat x$ is closer to the original input $x$. This is basically the loss of an ordinary autoencoder. For instance, it can be binary cross-entropy loss or L2 loss.

And the second term $\rm{D_{KL}}( \cdot )$ is the Kullback-Leibner divergence. It tells how much the distribution $p_\theta(z)$ is different from the distribution $q_\phi(z)$. Or even more informative is to say that KL divergence tells how much information is lost if the distribution $p_\theta$ is used to represent $q_\phi$. From the original paper,

$$ -\rm{D_{KL}}\left(q_\phi(z) || p_\theta(z) \right) =\frac 1 2 \sum_{j=1}^J \left( 1 + \log(\sigma_j^2) - \mu_j^2 - \sigma_j^2 \right).$$

Therefore, the complete VAE loss is

vaeLoss :: Float -> Tensor -> Tensor -> Tensor -> Tensor -> Tensor
vaeLoss beta recon_x x mu logSigma = reconLoss + asTensor beta * kld
    reconLoss = bceLoss recon_x x
    kld = -0.5 * sumAll (1 + logSigma - pow (2 :: Int) mu - exp logSigma)

We also include the $\beta \ge 0$ term. When $\beta = 0$ the networks is trained as an ordinary autoencoder. When $\beta = 1$, we have a classical VAE. And when $\beta > 1$, we force latent vector representations disentanglement. As we can see from the image below, in case of disentanglement, there are separate latent variables that encode position, rotation, and scale. Whereas entangled variables tend to encode all object properties at the same time. I recommend the excellent article by Higgins et al., which is featuring some insights from neuroscience.

Disentangled vs entangled latent representations. <small>Image source: [Higgins et al. 2016](https://arxiv.org/abs/1606.05579).</small>

Disentangled vs entangled latent representations. Image source: Higgins et al. 2016.

The binary cross-entropy loss is defined as

bceLoss target x =
  -sumAll (x * Torch.log(1e-10 + target) + (1 - x) * Torch.log(1e-10 + 1 - target))

We add a small term $10^{-10}$ to avoid numerical errors due to $\log(0)$.

Visualizing the Latent Space

Here is how our latent space looks for different values of $\beta$.

Test data distributions for different $\beta$ values.

Test data distributions for different $\beta$ values.

And here is how we compute that

main = do
    (trainData, testData) <- initMnist "data"
    net0 <- toLocalModel' <$> sample myConfig

    beta_: _ <- getArgs
    putStrLn $ "beta = " ++ beta_

    let beta = read beta_
        trainMnistStream = V.MNIST { batchSize = 128, mnistData = trainData }
        testMnistStream = V.MNIST { batchSize = 128, mnistData = testData }
        epochs = 20
        cpt = printf "VAE-Aug2022-beta_%s.ht" beta_
        logname = printf "beta_%s.log" beta_

    putStrLn "Starting training..."
    net' <- time $ train beta trainMnistStream epochs net0
    putStrLn "Done"

    -- Saving the trained model
    save' net' cpt

    -- Restoring the model
    net <- load' cpt

    -- Test data distribution in the latent space
    putStrLn $ "Saving test dataset distribution to " ++ logname
    _ <- testLatentSpace logname testMnistStream net


testLatentSpace :: FilePath -> V.MNIST IO -> VAE -> IO ()
testLatentSpace fn testStream net = do
      runContT (streamFromMap (datasetOpts 2) testStream) $ recordPoints fn net. fst

recordPoints :: FilePath -> VAE -> ListT IO (Tensor, Tensor) -> IO ()
recordPoints logname net = P.foldM step begin done. enumerateData
    step :: () -> ((Tensor, Tensor), Int) -> IO ()
    step () args = do
      let ((input, labels), i) = toLocalModel' args
          (encMu, _) = encode net input
          batchSize = head $ shape encMu

      let s = toStr $ Torch.cat (Dim 1) [reshape [-1, 1] labels, encMu]
      appendFile logname s

      return ()

    done () = pure ()
    begin = pure ()

toStr :: Tensor -> String
toStr dec =
    let a = asValue dec :: [[Float]]
        b = map (unwords. map show) a
     in unlines b

Now, let's take a walk around our latent space to get an idea how it looks like inside.

main = do
    net <- load' "VAE-Aug2022-beta_1.ht"

    let xs = [-3,-2.7..3::Float]

        -- 2D latent space as a Cartesian product
        zs = [ [x,y] | x<-xs, y<-xs ]

        decoded = Torch.cat (Dim 0) $
                    map (decode net. toLocalModel'. asTensor. (:[])) zs

    writeFile "latent_space_2D.txt" (toStr decoded)
Some examples from 2D latent space.

Some examples from 2D latent space.

Pretty neat! We see gradual transitions between different digits. Note that these digits are actually generated by VAE.

ConvNet VAE

While we have built a simple variational autoencoder based on MLP (multilayer perceptron), nothing prevents us from using other architectures. In fact, let's build a convolutional VAE!

data VAESpec = VAESpec
    -- Encoder trainable parameters
    conv1 :: Conv2dSpec,
    conv2 :: Conv2dSpec,
    conv3 :: Conv2dSpec,
    fcMu :: LinearSpec,
    fcSigma :: LinearSpec,

    -- Decoder trainable parameters
    fc :: LinearSpec,
    deconv1 :: ConvTranspose2dSpec,
    deconv2 :: ConvTranspose2dSpec,
    deconv3 :: ConvTranspose2dSpec
  deriving (Show, Eq)

myConfig =
    (Conv2dSpec 1 32 4 4)    -- 1 -> 32 channels; 4 x 4 kernel
    (Conv2dSpec 32 64 4 4)   -- 32 -> 64 channels; 4 x 4 kernel
    (Conv2dSpec 64 128 3 3)  -- 64 -> 128 channels; 3 x 3 kernel
    (LinearSpec (2 * 2 * 128) latent_size)
    (LinearSpec (2 * 2 * 128) latent_size)
    (LinearSpec latent_size 1024)
    (ConvTranspose2dSpec 1024 256 4 4)
    (ConvTranspose2dSpec 256 128 6 6)
    (ConvTranspose2dSpec 128 1 6 6)

data VAE = VAE
  { c1 :: Conv2d,
    c2 :: Conv2d,
    c3 :: Conv2d,
    lMu :: Linear,
    lSigma :: Linear,
    l :: Linear,
    t1 :: ConvTranspose2d,
    t2 :: ConvTranspose2d,
    t3 :: ConvTranspose2d
  deriving (Generic, Show, Parameterized)

instance Randomizable VAESpec VAE where
  sample VAESpec {..} =
      <$> sample conv1
      <*> sample conv2
      <*> sample conv3
      <*> sample fcMu
      <*> sample fcSigma
      <*> sample fc
      <*> sample deconv1
      <*> sample deconv2
      <*> sample deconv3

encode :: VAE -> Tensor -> (Tensor, Tensor)
encode VAE {..} x0 =
  let enc_ =
          -- Reshape vectors [batch_size x 784]
          -- into grayscale images of [batch_size x 1 x 28 x 28]
          reshape [-1, 1, 28, 28]
          -- Stride 2, padding 0
          ~> conv2dForward c1 (2, 2) (0, 0)
          ~> relu
          ~> conv2dForward c2 (2, 2) (0, 0)
          ~> relu
          ~> conv2dForward c3 (2, 2) (0, 0)
          ~> relu
          ~> flatten (Dim 1) (Dim (-1))

      x1 = enc_ x0
      mu = linear lMu x1
      logSigma = linear lSigma x1
   in (mu, logSigma)

decode :: VAE -> Tensor -> Tensor
decode VAE {..} =
         linear l
         ~> relu
         ~> reshape [-1, 1024, 1, 1]
         -- Stride 2, padding 0
         ~> convTranspose2dForward t1 (2, 2) (0, 0)
         ~> relu
         ~> convTranspose2dForward t2 (2, 2) (0, 0)
         ~> relu
         ~> convTranspose2dForward t3 (2, 2) (0, 0)
         ~> sigmoid
         ~> reshape [-1, 784]  -- Reshape back

And that is all we need.

Here is the latent space for $\beta=1$ (normal VAE) using our CNN architecture:


To better illustrate how parameter $\beta$ encourages disentanglement between latent representations, let us first increase the latent dimension to $L=10$. For $\beta=1$ and $\beta=4$ we perform scan along each individual $z$ coordinate.

Indeed, the latent space under $\beta=4$ looks more disentangled compared to $\beta=1$. We can see e.g. that $z_1$ is the parameter that defines how "light" or how "bold" is the digit, whereas $z_2$ controls how wide is the digit. Whereas such individual components for $\beta=1$ are hard to identify. For instance when $\beta=1$, $z_4$ controls not only how "bold" is the digit, but also its shape.

For more details, see this notebook.

Find the complete project and associated data on Github. For suggestions about the content feel free to open a new issue.


Variational autoencoder is a great tool in modern deep learning. Manipulating the latent space allows us not only to "interpolate" between different images or other objects, but also to perform inpainting (adding details to incomplete images) or even zero shot learning. The last one is crucial for the so-called artificial general intelligence.

The loss function is important for VAE training. If your VAE does not work as expected, the odds are that the loss function is not implemented correctly. Also check if the random noise $\varepsilon$ is drawn from the normal distribution.


 title   = "Roaming The Latent Space",
 author  = "Penkovsky, Bogdan",
 journal = "penkovsky.com",
 year    = "2022",
 month   = "August",
 url     = "https://penkovsky.com/neural-networks/day9/"

Learn More

A Technical Sidenote

Compared to the previous day, the trainLoop is slightly modified: First, we rescale the images between 0 and 1. Second, we include our new loss function in the step function.

    step :: Optimizer o => (VAE, o) -> ((Tensor, Tensor), Int) -> IO (VAE, o)
    step (model, opt) args = do
      let ((x, _), iter) = toLocalModel' args
          -- Rescale pixel values [0, 255] -> [0, 1.0].
          -- This is important as the sigmoid activation in decoder can
          -- reach values only between 0 and 1.
          x' = x / 255.0
      (recon_x, mu, logSigma) <- vaeForward model False x'
      let loss = vaeLoss beta recon_x x' mu logSigma
      -- Print loss every 100 batches
      when (iter `mod` 100 == 0) $ do
          $ printf "Batch: %d | Loss: %.2f" iter (asValue loss :: Float)
      runStep model opt loss lr

The train function now uses Adam optimizer from Torch.Optim.CppOptim, which tends to be faster compared to mkAdam we used previously. This is not very different from mkAdam-based training, except that the learning rate is specified as Cpp.adamLr parameter and not as a trainLoop parameter (ignored when passed to runStep).

train :: Float -> V.MNIST IO -> Int -> VAE -> IO VAE
train beta trainMnist epochs net0 = do
    optimizer <- Cpp.initOptimizer adamOpt net0

    (net', _) <- foldLoop (net0, optimizer) epochs $ \(net', optState) _ ->
      runContT (streamFromMap dsetOpt trainMnist)
      $ trainLoop beta (net', optState) 0.0 . fst

    return net'
    dsetOpt = datasetOpts workers
    workers = 2
    -- Adam optimizer parameters
    adamOpt =
          { Cpp.adamLr = learningRate,
            Cpp.adamBetas = (0.9, 0.999),
            Cpp.adamEps = 1e-8,
            Cpp.adamWeightDecay = 0,
            Cpp.adamAmsgrad = False
          } ::
learningRate :: Double
learningRate = 1e-3

I used a compiled version instead of a notebook since the network training worked much faster (the bottleneck was in training data mini-batches loading). Also I have trained networks with Torch.Optim.CppOptim. It is slightly faster compared to mkAdam.

I was also wondering why I get large values out of the encoder. It turns out that this is because relu function is unbounded. You may want to replace relu with Torch.tanh and visualize the latent space again.

  1. We use sigma as an argument to randnLikeIO so that the resulting random tensor has the same shape as sigma. ^
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