Sunday, March 4, 2018

Porting Keras Models

I implemented an LSTM in Java that can read a trained Keras models in order
to use it in some other Java projects. You can check the repository at [:Github:]

The ipython notebook exports the weights of an LSTM
and also exports some test for a random input sequence and the resulting output.
The Java implementation reads the exported weights and then applies them. All
matrix operations are implemented using jBlas.

  • The numeric helper class implements matrix loading and slicing.
  • Tanh and the sigmoid functions are also in the helper class.
  • The LSTM state is a separate class holding the cell state and the hidden activation.
  • The LSTM holds all the weights and applies them to sequences.

The basic slicing of the weights is implemented using the same weight
coding as Keras [:Github:]

        self.kernel_i = self.kernel[:, :self.units]
        self.kernel_f = self.kernel[:, self.units: self.units * 2]
        self.kernel_c = self.kernel[:, self.units * 2: self.units * 3]
        self.kernel_o = self.kernel[:, self.units * 3:]

        self.recurrent_kernel_i = self.recurrent_kernel[:, :self.units]
        self.recurrent_kernel_f = self.recurrent_kernel[:, self.units: self.units * 2]
        self.recurrent_kernel_c = self.recurrent_kernel[:, self.units * 2: self.units * 3]
        self.recurrent_kernel_o = self.recurrent_kernel[:, self.units * 3:]

        if self.use_bias:
            self.bias_i = self.bias[:self.units]
            self.bias_f = self.bias[self.units: self.units * 2]
            self.bias_c = self.bias[self.units * 2: self.units * 3]
            self.bias_o = self.bias[self.units * 3:]

Tuesday, December 12, 2017

Implementing Gradient Boosted Trees

Implementing Gradient Boosted Trees

In this post I will share my experience on implementing gradient boosted trees as seen in XGBoost in order to get a better understanding of the method. As in previous posts, the code won't be as efficient as the original. Furthermore, I will use scala again. The basic idea behind boosting is to construct an additive model of a collection of simpler models (base models) for classification or regresion. If you are unfamiliar with the general boosting idea plase consider (Hastie: Elements of Statistics Learning) for a great introduction. This post is mainly based on this blog post and these slides. In boosting, the model is constructed iteratively that is, in an iteration $t$, the new output given a datapoint $x$ is: $$ \hat{y}^t = \hat{y}^{(t - 1)} - f_t(x) $$ The idea of gradient boosting is that in each iteration the next model is determined so it minimizes a given loss function $\mathbb{L}$. Specifically the minimization is performed using the first and second order derivatives of the loss function. Each added model can also be seen as a step in the direction of the gradient. In other words, the iterations can be seen as a form of gradient descent. When extending this idea to regression tree base models and when regularizing the objective function of the optimization, we end up with a powerful algorithm that one multiple Kaggle challenges as well as the Xing hosted recommender systems challenge to years in a row. In the next part, I will derive the optimization step used for decision trees with a cross entropy loss and then "massage" in the regularization.

Cross Entropy loss for Binay Classification

For binary classification, the go-to output function is the sigmoid function: $$P(x = 1) = \frac{1}{1 = e^{-x}}$$ Prominent usage examples include Neural Networks and logistic regressions. Given that our output $P(x = 1)$ is $\hat{y}$ and the true label is $y$, we can measure the goodness of our classifier on our dataset using the cross entropy loss: $$ L(y, \hat{y}) = \sum_i -y_i * log(\hat{y_i}) - (1.0 - y_i) * log(1.0 - \hat{y_i})$$ with its first derivative at $g_i = \hat{y_i} - y_i$ and it's second derivative at $h_i = \hat{y_i} * (1.0 - \hat{y_i})$.


One of the ideas implemented in XGBosst is regularisation. Intuitavely we want to penalize large parameters that dominate our result and model complexity. Given a parameter set $\theta$, the L1 regularization is $\Omega(\theta) = \sum_i ||\theta_i||_1$, where $||x||_1$ is the L1 norm or simply the absolute value. In L2 regularization, we switch to $||\theta_i||_2$ where $||x||_2$ is $x^2$. Then for a decision tree, we could measure the complexity as the number of leaf nodes $T$, and the parameters $\theta$ are the output scores of a leaf nodes (we will later use regression trees). For example, we could penalize large trees by $\gamma T$ and large output by $\frac{1}{2}\sum_i \lambda ||\theta_i||_2$. We can control the penalty amount by two parameters $\gamma$ and $\lambda$.

Gradient boosted trees

The combined objective using regularization and some loss function is: $$O = L(y, \hat{y}) + \Omega(\theta)$$ Since we are boosting, we define the objective in terms of the predictions in iteration $t$: $$O^t = L(y, \hat{y}^{t - 1} + f(x)) + \Omega(\theta)$$ while $\hat{y}^{t - 1} + f(x)$ follows directly from the boosting formular $\hat{y}^t = \hat{y}^(t - 1) - f_t(x)$. Since we want to define the gradient in order to optimize f(x), we can apply the Taylor expansion to the loss. Remember that the Taylor expansion is defined as $f(x + \delta x) \approx f(x) + f'(x) * \delta x + \frac{1}{2} f''(x) \delta x^2$ So the loss becomes $$O^t = (L(y, \hat{y}^{t - 1}) + g_i * f(x) + \frac{1}{2} * h_i * f(x)^2) + \Omega(\theta))$$ Assuming a decision tree base classifier we can use the example regularization above and the objective becomes: $$O^t = (L(y, \hat{y}^{t - 1}) + g_i * f(x) + \frac{1}{2} * h_i * f(x)^2) + \gamma T \frac{1}{2}\sum_i \lambda * ||\theta_i||_2$$ With a few transformations, we can redefine the loss in a way we can directly optimize the function with the standard CART learning algorithm. First we defined $\mathbb{I}(j == i)$ as an indicator function that returns 1 if example $i$ when pushed trough the decision tree, ends up in leaf node $j$. Then the result of $f(x_i)$ is $w_j$ the leaf node score at node $j$ ig $x_i$ evaluates true. Now we can rearange the objective function towards the leaf nodes as: $$O^t = \sum_j [(\sum_i \mathbb{I}(j == i) * g_i) * w_j + \frac{1}{2} (\sum_i \mathbb{I}(j == i) * h_i + \lambda) * w_j^2] + \gamma T$$ redefining the sums of the gradients to $G_j$ and $H_j$ we get: $$O^t = \sum_j [G_j * w_j + \frac{1}{2} (H_j + lambda) * w_j^2] + \gamma T$$ Now we can update a leaf node using the gradient statistics by setting the derivative of the objective to zero: $$Gj + (H_j + \lambda) = 0$$ and then $w_j = -\frac{G_j}{H_j + \lambda}$. Intuitively, we model the gradient to take given an input in each leaf node. And these gradients are normalized by their second order statistics. So each leaf prediction will push the total function output of the ensemble more towards the wanted result. In order to construct a tree, we can use the same gradients to define a gain function and then learn the trees like a normal decision tree. The formular is the gradient "amplitude" before the split $(G_l + G_h)^2 / (H_l + H_r + \lambda)$ and after the split $G_l^2 / (H_l + \lambda)$, where $G_l$ and $H_l$ are the sum of the gradients in the left node or the right node. Then the gain is simply: $$Gain = \frac{1}{2} [ \frac{G_l^2}{H_l + \lambda} + \frac{G_r^2}{H_r + \lambda} - \frac{(G_l + G_h)^2}{H_l + H_r + \lambda}]$$ Now we can implement these functions:
package gbt

import math._

trait Loss {

  def gradient(truth: Double, prediction: Double): Double

  def hessian(truth: Double, prediction: Double): Double

  def loss(truth: Double, prediction: Double): Double

  def output(x: Double): Double


class Logistic extends Loss {

  private def sigmoid(x: Double): Double = 1.0 / (1.0 + exp(-x))

  override def loss(truth: Double, prediction: Double): Double = {
    val isOne  = -truth * log(sigmoid(prediction))
    val isZero = (1 - truth) * log(1.0 - sigmoid(prediction))
    (isOne - isZero)

  override def gradient(truth: Double, prediction: Double): Double = sigmoid(prediction) - truth

  override def hessian(truth: Double, prediction: Double): Double =
    sigmoid(prediction) * (1.0 - sigmoid(prediction))

  override def output(x: Double) = sigmoid(x)


class Squared extends Loss {

  override def loss(truth: Double, prediction: Double): Double = pow(truth - prediction, 2.0)

  override def gradient(truth: Double, prediction: Double): Double = 2.0 * (prediction - truth)

  override def hessian(truth: Double, prediction: Double): Double = 2.0

  override def output(x: Double): Double = x


object LossUtils {

  def score(gradients: Vector[Double], hessians: Vector[Double], lambda: Double): Double = {
    val G = gradients.sum
    val H = hessians.sum 
    - G / (H + lambda)

  def gain(
    gradients: Vector[Double],
    hessians: Vector[Double],
    left: Vector[Int],
    right: Vector[Int],
    lambda: Double,
    gamma: Double
  ): Double = {
    val GL = => gradients(i)).sum
    val HL = => hessians(i)).sum
    val GR = => gradients(i)).sum
    val HR = => hessians(i)).sum 
    0.5 * (
      (pow(GL, 2) / (HL + lambda)) + (pow(GR, 2) / (HR + lambda)) - (pow(GL + GR, 2) / (HL + HR + lambda))
    ) - gamma

The full code can be found on github

Wednesday, November 29, 2017

Refactoring My Previous Deep Learning Library Ideas

Refactoring My Previous Deep Learning Library Ideas

in some previous posts I looked at how I could implement a simple deep learning library to gain a better understanding on the inner workings of: Auto Differentiation, Weight Sharing and a good Back Propagation implementation from the deep learning book.

In this post I will present my ideas on a refactored version. The main point is that the graph representation I implemented in the first two posts made it easier to build the computation graph, 
but the code to run back propagation, especially with weight sharing was quite messy. So this refactored version first creates a computation tree as before, only that the actual computations are decoupled from the tree. The tree later is translated into the instructions and parent / child relationships used in the book version of the back propagation algorithm. 

Now in the first step we write model setup code. For example, a neural network for mnist classification:

As in tensorflow I define placeholders, variables and computation nodes, along with their name.
Furthermore, the variables get a shape and an initialisation method. In the background this method constructs a computation tree rooted at a5 using the following DSL.

Each node, keeps track of the name, an instruction name and a shape, if needed.
We can then convert this tree into a neural network ready to be used in the back propagation code from original post. We build four maps keeping:
  1. Mapping from node names to computations (like add, multiply, ...)
  2. Mapping from node names to their parents node names
  3. Mapping from node names to their child node names
  4. Mapping from node names that are weights to matrices.
All computations such as add or multiply implement the forward pass through the variable 
as well as the backward pass.

Using a class I called TensorStore that maps from names to matrices, I implemented the forward and the backward pass as follows:

The code can be found along the other versions on github. An example for the spiral dataset as well as the mnist data set is attached.

Of course the code is not at all up to the popular libraries in terms of speed or functionality so for me it is more an ongoing investigation on how these libraries are implemented and what I can reproduce. :). On Mnist the given network achieves between 96 and 98 % accuracy depending on the starting condition.

Sunday, September 10, 2017

Variational Fashion Encoder

Variational Fashion Encoder

In this experiment I want to try out Variational Auto Encoders, an unsupervised feature learning algorithm on a new fashion classification dataset from Zalando. Since I wanted to play around with both more, I will build a generic Variational Auto Encoder and then learn it on the new fashion-mnist dataset.
Code can be found on github

Variational Auto Encoder

The bottom part of the model is embedding the input X into a mean and variance vector.
The mean and variance represent the parameters of a gaussian that is trained to be close to a standard normal distribution N(0, I).The decoder network is trying to reconstruct the input from a sample from said distribution. The encoder as well as the decoder network can have multiple layers in my case 3 each.

The loss function is a combination of the Kullback-Leibler divergence between the distribution from the encoder network and a standard normal distribution, basically centering the latent space around 0 with standard deviation 1. This can be seen as a form of regularisation. Furthermore, the decoder
does not reconstruct directly from the encoder output but from a sample of the distribution in the latent space.

Fashion Reconstruction

The images in the fashion dataset are 28 pixels by 28 pixels, in the same way as the MNIST dataset.
The fashion data consists of 10 - classes of cloths: 
  1. tshirt
  2. trouser
  3. pullover
  4. dress
  5. coat
  6. sandal
  7. shirt
  8. sneaker
  9. bag
  10. ankle boo
After training for 5 epochs on the training set, I plotted the reconstructions from the Variational Auto Encoder.

As one can see the reconstructions work quite well indicating the latent space learned is useful.

Tuesday, August 1, 2017

Investigating Non Linear Optimization in Python

I recently skimmed through some class videos by Tucker Balch, Professor at Georgia Tech called "Machine Learning For Trading". One interesting part was portfolio optimisation.
That is, if you want to invest some amount of money, how do you distribute it
over a selection of assets in a way minimising risk while at the same time
being able to earn money through your investment. A portfolio is basically an allocation of the money into different options or in other words, the percentage of the total amount of money allocated to an option. Anyways, in the class as well as the course book the optimisation is performed using a
python method for constrained non-linear optimisation.  The algorithm used to crunch these problems is called Sequential Least Squares Programming, which is implement using a fortran wrapper.
The original algorithm can be found in the ACM Algorithms catalog (Algorithm 733)
written by D. Kraft. The code is automatically translated using the fortran to python (f2py)

Sunday, July 23, 2017

Black Box Variational Inference and PyFlux

I found an interesting paper on black box variational inference. Variational inference is an
approximate inference algorithm for factored probabilistic models (such as bayesian networks).

In probabilistic inference, we are normally interested in the posterior density of a latent variable
given all our data. The basic idea is to turn the inference problem into an optimisation problem.
That is, we build an approximate probability distribution that is differentiable with respect to it 's parameters. We then find the parameter set that minimises the difference between the true posterior and the approximate distribution.

The problem is that in order to do this for a new model, we still have to do a lot of manual derivations
and work through a lot of math before we can actually use this algorithm. This new paper
however, shows an algorithm that is easier to use given a new model. In my opinion,
one of the successes in deep learning is auto differentiation, where we do not
have to develop all gradients on our own but let the computer do it (as described in earlier posts).
One library that implements this inference method for complex time series is called pyFlux [2].

The proposed algorithm [1] works as follows. First, we sample the latent variables in our model
from the approximate distribution. We then use the samples to compute a gradient
for each parameter that minimises the Kullback-Leibler divergence or more specifically the Expectational Lower Bound (ELBO).

Reproduced from original paper [1]
The z[s] are samples from the latent space. Each z[s] includes a values for each of the latent variables. These samples are used to build the gradient.
The value of the Robbins - Monroe Sequence, is modelling an adaptive learning rate schedule
to guarantee convergence. The gradient has multiple components, including the joint probability of the original distribution, the log of the approximate distribution and the derivative of the approximate distribution. For a lot of cases, these values are easy to compute. First note that when using the samples, all variables in the original joint distribution are observed. For a Bayesian network that means that the joint distribution is simply the product of all variables:

In the paper and in the pyFlux library, the approximate distribution is implemented as a mean field.
Which means that the variables in our model are all independent. This makes the sampling and evaluation of the model very easy. Each variable can be sampled individually and the conditional distribution is simply the product of all the variables. Finally, the pyFlux library implements each variable in the approximate distribution as a one dimensional gaussian. Putting all that together,
the final gradient becomes:

Where the lambda parameters will be the mean and variance of each of the gaussians used
with the gradients:


[1] Ranganath, Gerrish, Blei: "Black Box Variational Inference", AISTATS 2014, 2014
[2] PyFlux

Friday, May 26, 2017

A Generic Sequence Alignment Algorithm

In this post I will describe how a general sequence alignment could be implemented in Scala.
For readers that don't know what sequence alignment is, I recommend reading my
post on building a gesture recogniser under Dynamic Time Warping distance (DTW).

Sequence alignment is often used in several contexts including speech recognition,
gesture recognition, approximate string matching, typing correction, biological
sequence alignment and time series classification and even stereo vision.
All these algorithms are based on a technique called dynamic programming and the algorithms
are all very similar. However, in literature this alignment technique is often found under different names (Dynamic Time Warping, Levensthein Distance, Needleman-Wunsch).

I will first formulate my idea of a general alignment algorithm with a scala implementation and afterwards describe an implementation of the three above algorithms.

Given two sequences X = [x1 .. xi .. xN] and Y = [y .. yj .. yM], we use the following
recursion to find the alignment score S(x, y). At each position i in sequence X and position j in sequence Y we look backwards at the matching score in X only, in Y only and in X and Y simultaneously resulting in the following recursion:

The rank function scores the alignment at position i and j based on the previous alignment scores and
the current elements. The rank function is the main component that changes in all three algorithms.
Looking back in X direction is also called an insertion, in Y direction a deletion and for both it is
called a match so the ranking function becomes:

Furthermore we will also implement a generic initialisation function that starts our recursion.
Ok now the Scala code:

class Alignment[A](
  init: (Int, Int) => Double,
  rank: (Double, Double, Double, A, A) => Double
) {

  def score(x: Array[A], y: Array[A]): Double = {  
    val n  = x.size
    val m  = y.size
    val dp = Array.ofDim[Double](n + 1, m + 1)
    for(i <- 0 until n + 1) dp(i)(0) = init(i, 0)
    for(j <- 0 until m + 1) dp(0)(j) = init(0, j)

    for(i <- 1 until n + 1) {
      for(j <- 1 until m + 1) {
        dp(i)(j) = rank(
          dp(i - 1)(j),     // insertion
          dp(i - 1)(j - 1), // match
          dp(i)(j - 1),     // deletion 
          x(i - 1),         // current sample in x 
          y(j - 1)          // current sample in y



The alignment class has a type parameter specifying the type of the elements in the sequences we want to align and takes the initialising function and the ranking function as input. Now DTW and the Edit distance are just specialisations with a different type parameter and scoring function:

  class DTW extends Alignment[Double](
    init = (i: Int, j: Int) => if(i == 0 && j == 0) 0.0 else Double.PositiveInfinity,
    rank = (insert: Double, matching: Double, delete: Double, x: Double, y: Double) =>
      if(insert < matching && insert < delete) insert + math.pow(x - y, 2)
      else if (delete < insert && delete < matching) delete + math.pow(x - y, 2)
      else matching + math.pow(x - y, 2)

DTW is defined over doubles and is initialising the recursion with 0.0 at position (0,0) and all others to infinity. The ranking adds the euclidian distance to the insertion, deletion and match and then takes the minimum. It is easy to see how this can be generalised to multivariate sequences. The type parameter becomes Seq[Double] and the euclidean distance is implemented for vectors. One can also use kernels instead or the cosine similarity. The next function is the edit distance for discrete sequence elements (here characters):

  class Levensthein extends Alignment[Char](
    init = (i: Int, j: Int) => if(i == 0 && j == 0) 0.0 else if(i == 0) j else i,
    rank = (insert: Double, matching: Double, delete: Double, x: Char, y: Char) =>
      if(insert < matching && insert < delete) insert + 1
      else if (delete < insert && delete < matching) delete + 1
      else matching + (if(x == y) 0.0 else 1.0)

The function is initialised as the index at the borders and the function again takes the minimum of insertion, deletion and match. Insertions and deletions count as an error so we add 1. A match can also be a substitution so we add 1 to the error if the characters do not match. The last algorithm is the Needleman-Wunsch algorithm. Instead of minimising the distance we are maximising a score. The similarity between two symbols can be defined and the 'gap' penalty is not 1 as in the edit distance but given.

  final val Sim = Map(
    ('a', 'a') -> 10,
    ('a', 'g') -> -1,
    ('g', 'a') -> -1,
    ('a', 'c') -> -3,
    ('c', 'a') -> -3,
    ('a', 't') -> -4,
    ('t', 'a') -> -4,
    ('g', 'g') ->  7,
    ('g', 'c') -> -5,
    ('c', 'g') -> -5,
    ('g', 't') -> -3,
    ('t', 'g') -> -3,
    ('c', 'c') ->  9,
    ('c', 't') ->  0,
    ('t', 'c') ->  0,
    ('t', 't') ->  8

  final val Gap = -5
  class NeedlemanWunsch extends Alignment[Char](
    init = (i: Int, j: Int) => if(i == 0 && j == 0) 0.0 else if(i == 0) j * Gap else i * Gap,
    rank = (insert: Double, matching: Double, delete: Double, x: Char, y: Char) =>
      if(insert > matching && insert > delete) insert + Gap
      else if (delete > insert && delete > matching) delete + Gap
      else matching + Sim(x, y)

If one needs the actual alignment, we can backtrack the alignment process in all above cases. The code can be found here [GitHub]