Sammon Embedding

Word embedding has been a frequent theme of this blog. But the original embedding has been algorithms that perform a non-linear mapping of higher dimensional data to the lower one. This entry I will talk about one of the most oldest and widely used one: Sammon Embedding, published in 1969. This is an embedding algorithm that preserves the distances between all points. How is it achieved?

Assume there are high dimensional data described by d-dimensional vectors, X_i where i=1, 2, \ldots, N. And they will be mapped into vectors Y_i, with dimensions 2 or 3. Denote the distances to be d_{ij}^{*} = \sqrt{| X_i - X_j|^2} and d_{ij} = \sqrt{| Y_i - Y_j|^2}. In this problem, Y_i are the variables to be learned. The cost function to minimize is

E = \frac{1}{c} \sum_{i<j} \frac{(d_{ij}^{*} - d_{ij})^2}{d_{ij}^{*}},

where c = \sum_{i<j} d_{ij}^{*}. To minimize this, use Newton's method by

Y_{pq} (m+1) = Y_{pq} (m) - \alpha \Delta_{pq} (m),

where \Delta_{pq} (m) = \frac{\partial E(m)}{\partial Y_{pq}(m)} / \left|\frac{\partial^2 E(m)}{\partial Y_{pq} (m)^2} \right|, and \alpha is the learning rate.

To implement it, use Theano package of Python to define the cost function for the sake of optimization, and then implement the learning with numpy. Define the cost function with the outline above:

import theano
import theano.tensor as T

import numerical_gradients as ng

# define variables
mf = T.dscalar('mf')         # magic factor / learning rate

# coordinate variables
Xmatrix = T.dmatrix('Xmatrix')
Ymatrix = T.dmatrix('Ymatrix')

# number of points and dimensions (user specify them)
N, d = Xmatrix.shape
_, td = Ymatrix.shape

# grid indices
n_grid = T.mgrid[0:N, 0:N]
ni = n_grid[0].flatten()
nj = n_grid[1].flatten()

# cost function
c_terms, _ = theano.scan(lambda i, j: T.switch(, j),
                         sequences=[ni, nj])
c = T.sum(c_terms)

s_term, _ = theano.scan(lambda i, j: T.switch(, j),
                        sequences=[ni, nj])
s = T.sum(s_term)

E = s / c

# function compilation and optimization
Efcn = theano.function([Xmatrix, Ymatrix], E)

And implement the update algorithm with the following function:

import numpy

# training
def sammon_embedding(Xmat, initYmat, alpha=0.3, tol=1e-8, maxsteps=500, return_updates=False):
    N, d = Xmat.shape
    NY, td = initYmat.shape
    if N != NY:
        raise ValueError('Number of vectors in Ymat ('+str(NY)+') is not the same as Xmat ('+str(N)+')!')

    # iteration
    Efcn_X = lambda Ymat: Efcn(Xmat, Ymat)
    step = 0
    oldYmat = initYmat
    oldE = Efcn_X(initYmat)
    update_info = {'Ymat': [initYmat], 'cost': [oldE]}
    converged = False
    while (not converged) and step<=maxsteps:
        newYmat = oldYmat - alpha*ng.tensor_gradient(Efcn_X, oldYmat, tol=tol)/ng.tensor_divgrad(Efcn_X, oldYmat, tol=tol)
        newE = Efcn_X(newYmat)
        if np.all(np.abs(newE-oldE)<tol):
            converged = True
        oldYmat = newYmat
        oldE = newE
        step += 1
        if return_updates:
            print 'Step ', step, '\tCost = ', oldE

    # return results
    if return_updates:
        update_info['num_steps'] = step
        return oldYmat, update_info
        return oldYmat

The above code is stored in the file We can test the algorithm with an example. Remember tetrahedron, a three-dimensional object with four points equidistant from one another. We expect the embedding will reflect this by sampling points around these four points. With the code, we implemented it this way:

import argparse

import numpy as np
import matplotlib.pyplot as plt

import sammon as sn

argparser = argparse.ArgumentParser('Embedding points around tetrahedron.')
                       help='file name of the output plot')

args = argparser.parse_args()

tetrahedron_points = [np.array([0., 0., 0.]),
                      np.array([1., 0., 0.]),
                      np.array([np.cos(np.pi/3), np.sin(np.pi/3), 0.]),
                      np.array([0.5, 0.5/np.sqrt(3), np.sqrt(2./3.)])]

sampled_points = np.concatenate([np.random.multivariate_normal(point, np.eye(3)*0.0001, 10)
                                 for point in tetrahedron_points])

init_points = np.concatenate([np.random.multivariate_normal(point[:2], np.eye(2)*0.0001, 10)
                              for point in tetrahedron_points])

embed_points = sn.sammon_embedding(sampled_points, init_points, tol=1e-4)

X, Y = embed_points.transpose()
plt.plot(X, Y, 'x')

It outputs a graph:


There are other such non-linear mapping algorithms, such as t-SNE (t-distributed stochastic neighbor embedding) and Kohonen’s mapping (SOM, self-organizing map).

Continue reading “Sammon Embedding”

Short Text Categorization using Deep Neural Networks and Word-Embedding Models

There are situations that we deal with short text, probably messy, without a lot of training data. In that case, we need external semantic information. Instead of using the conventional bag-of-words (BOW) model, we should employ word-embedding models, such as Word2Vec, GloVe etc.

Suppose we want to perform supervised learning, with three subjects, described by the following Python dictionary:

classdict={'mathematics': ['linear algebra',
           'variational calculus',
           'functional field',
           'real analysis',
           'complex analysis',
           'differential equation',
           'statistical optimization',
           'stochastic calculus',
           'numerical analysis',
           'differential geometry'],
          'physics': ['renormalization',
           'classical mechanics',
           'quantum mechanics',
           'statistical mechanics',
           'functional field',
           'path integral',
           'quantum field theory',
           'condensed matter',
           'particle physics',
           'topological solitons',
           'spontaneous symmetry breaking',
           'atomic molecular and optical physics',
           'quantum chaos'],
          'theology': ['divine providence',
           'Holy Trinity',
           'divine degree',
           'creedal confessionalism',

And we implemented Word2Vec here. To add external information, we use a pre-trained Word2Vec model from Google, downloaded here. We can use it with Python package gensim. To load it, enter

from gensim.models import Word2Vec
wvmodel = Word2Vec.load_word2vec_format('<path-to>/GoogleNews-vectors-negative300.bin.gz', binary=True)

How do we represent a phrase in Word2Vec? How do we do the classification? Here I wrote two classes to do it.


We can represent a sentence by summing the word-embedding representations of each word. The class, inside, is coded as follow:

from collections import defaultdict

import numpy as np
from nltk import word_tokenize
from scipy.spatial.distance import cosine

from utils import ModelNotTrainedException

class SumEmbeddedVecClassifier:
    def __init__(self, wvmodel, classdict, vecsize=300):
        self.wvmodel = wvmodel
        self.classdict = classdict
        self.vecsize = vecsize
        self.trained = False

    def train(self):
        self.addvec = defaultdict(lambda : np.zeros(self.vecsize))
        for classtype in self.classdict:
            for shorttext in self.classdict[classtype]:
                self.addvec[classtype] += self.shorttext_to_embedvec(shorttext)
            self.addvec[classtype] /= np.linalg.norm(self.addvec[classtype])
        self.addvec = dict(self.addvec)
        self.trained = True

    def shorttext_to_embedvec(self, shorttext):
        vec = np.zeros(self.vecsize)
        tokens = word_tokenize(shorttext)
        for token in tokens:
            if token in self.wvmodel:
                vec += self.wvmodel[token]
        norm = np.linalg.norm(vec)
        if norm!=0:
            vec /= np.linalg.norm(vec)
        return vec

    def score(self, shorttext):
        if not self.trained:
            raise ModelNotTrainedException()
        vec = self.shorttext_to_embedvec(shorttext)
        scoredict = {}
        for classtype in self.addvec:
                scoredict[classtype] = 1 - cosine(vec, self.addvec[classtype])
            except ValueError:
                scoredict[classtype] = np.nan
        return scoredict

Here the exception ModelNotTrainedException is just an exception raised if the model has not been trained yet, but scoring function was called by the user. (Codes listed in my Github repository.) The similarity will be calculated by cosine similarity.

Such an implementation is easy to understand and carry out. It is good enough for a lot of application. However, it has the problem that it does not take the relation between words or word order into account.

Convolutional Neural Network

To tackle the problem of word relations, we have to use deeper neural networks. Yoon Kim published a well cited paper regarding this in EMNLP in 2014, titled “Convolutional Neural Networks for Sentence Classification.” The model architecture is as follow: (taken from his paper)


Each word is represented by an embedded vector, but neighboring words are related through the convolutional matrix. And MaxPooling and a dense neural network were implemented afterwards. His paper involves multiple filters with variable window sizes / spatial extent, but for our cases of short phrases, I just use one window of size 2 (similar to dealing with bigram). While Kim implemented using Theano (see his Github repository), I implemented using keras with Theano backend. The codes, inside, are as follow:

import numpy as np
from keras.layers import Convolution1D, MaxPooling1D, Flatten, Dense
from keras.models import Sequential
from nltk import word_tokenize

from utils import ModelNotTrainedException

class CNNEmbeddedVecClassifier:
    def __init__(self,
        self.wvmodel = wvmodel
        self.classdict = classdict
        self.n_gram = n_gram
        self.vecsize = vecsize
        self.nb_filters = nb_filters
        self.maxlen = maxlen
        self.trained = False

    def convert_trainingdata_matrix(self):
        classlabels = self.classdict.keys()
        lblidx_dict = dict(zip(classlabels, range(len(classlabels))))

        # tokenize the words, and determine the word length
        phrases = []
        indices = []
        for label in classlabels:
            for shorttext in self.classdict[label]:
                category_bucket = [0]*len(classlabels)
                category_bucket[lblidx_dict[label]] = 1

        # store embedded vectors
        train_embedvec = np.zeros(shape=(len(phrases), self.maxlen, self.vecsize))
        for i in range(len(phrases)):
            for j in range(min(self.maxlen, len(phrases[i]))):
                train_embedvec[i, j] = self.word_to_embedvec(phrases[i][j])
        indices = np.array(indices,

        return classlabels, train_embedvec, indices

    def train(self):
        # convert classdict to training input vectors
        self.classlabels, train_embedvec, indices = self.convert_trainingdata_matrix()

        # build the deep neural network model
        model = Sequential()
                                input_shape=(self.maxlen, self.vecsize)))
        model.add(Dense(len(self.classlabels), activation='softmax'))
        model.compile(loss='categorical_crossentropy', optimizer='rmsprop')

        # train the model, indices)

        # flag switch
        self.model = model
        self.trained = True

    def word_to_embedvec(self, word):
        return self.wvmodel[word] if word in self.wvmodel else np.zeros(self.vecsize)

    def shorttext_to_matrix(self, shorttext):
        tokens = word_tokenize(shorttext)
        matrix = np.zeros((self.maxlen, self.vecsize))
        for i in range(min(self.maxlen, len(tokens))):
            matrix[i] = self.word_to_embedvec(tokens[i])
        return matrix

    def score(self, shorttext):
        if not self.trained:
            raise ModelNotTrainedException()

        # retrieve vector
        matrix = np.array([self.shorttext_to_matrix(shorttext)])

        # classification using the neural network
        predictions = self.model.predict(matrix)

        # wrangle output result
        scoredict = {}
        for idx, classlabel in zip(range(len(self.classlabels)), self.classlabels):
            scoredict[classlabel] = predictions[0][idx]
        return scoredict

The output is a vector of length equal to the number of class labels, 3 in our example. The elements of the output vector add up to one, indicating its score, and a nature of probability.


A simple cross-validation to the example data set does not tell a difference between the two algorithms:


However, we can test the algorithm with a few examples:

Example 1: “renormalization”

  • Average: {‘mathematics’: 0.54135105096749336, ‘physics’: 0.63665460856632494, ‘theology’: 0.31014049736087901}
  • CNN: {‘mathematics’: 0.093827009201049805, ‘physics’: 0.85451591014862061, ‘theology’: 0.051657050848007202}

As renormalization was a strong word in the training data, it gives an easy result. CNN can distinguish much more clearly.

Example 2: “salvation”

  • Average: {‘mathematics’: 0.14939650156482298, ‘physics’: 0.21692765541184023, ‘theology’: 0.5698233329716329}
  • CNN: {‘mathematics’: 0.012395491823554039, ‘physics’: 0.022725773975253105, ‘theology’: 0.96487873792648315}

“Salvation” is not found in the training data, but it is closely related to “soteriology,” which means the doctrine of salvation. So it correctly identifies it with theology.

Example 3: “coffee”

  • Average: {‘mathematics’: 0.096820211601723272, ‘physics’: 0.081567332119268032, ‘theology’: 0.15962682945135631}
  • CNN: {‘mathematics’: 0.27321341633796692, ‘physics’: 0.1950736939907074, ‘theology’: 0.53171288967132568}

Coffee is not related to all subjects. The first architecture correctly indicates the fact, but CNN, with its probabilistic nature, has to roughly equally distribute it (but not so well.)

The code can be found in my Github repository: stephenhky/PyShortTextCategorization. (This repository has been updated since this article was published. The link shows the version of the code when this appeared online.)

Continue reading “Short Text Categorization using Deep Neural Networks and Word-Embedding Models”

Word Embedding Algorithms

Embedding has been hot in recent years partly due to the success of Word2Vec, (see demo in my previous entry) although the idea has been around in academia for more than a decade. The idea is to transform a vector of integers into continuous, or embedded, representations. Keras, a Python package that implements neural network models (including the ANN, RNN, CNN etc.) by wrapping Theano or TensorFlow, implemented it, as shown in the example below (which converts a vector of 200 features into a continuous vector of 10):

from keras.layers import Embedding
from keras.models import Sequential

# define and compile the embedding model
model = Sequential()
model.add(Embedding(200, 10, input_length=1))
model.compile('rmsprop', 'mse')  # optimizer: rmsprop; loss function: mean-squared error

We can then convert any features from 0 to 199 into vectors of 20, as shown below:

import numpy as np

model.predict(np.array([10, 90, 151]))

It outputs:

array([[[ 0.02915354,  0.03084954, -0.04160764, -0.01752155, -0.00056815,
         -0.02512387, -0.02073313, -0.01154278, -0.00389587, -0.04596512]],

       [[ 0.02981793, -0.02618774,  0.04137352, -0.04249889,  0.00456919,
          0.04393572,  0.04139435,  0.04415271,  0.02636364, -0.04997493]],

       [[ 0.00947296, -0.01643104, -0.03241419, -0.01145032,  0.03437041,
          0.00386361, -0.03124221, -0.03837727, -0.04804075, -0.01442516]]])

Of course, one must not omit a similar algorithm called GloVe, developed by the Stanford NLP group. Their codes have been wrapped in both Python (package called glove) and R (library called text2vec).

Besides Word2Vec, there are other word embedding algorithms that try to complement Word2Vec, although many of them are more computationally costly. Previously, I introduced LDA2Vec in my previous entry, an algorithm that combines the locality of words and their global distribution in the corpus. And in fact, word embedding algorithms with a similar ideas are also invented by other scientists, as I have introduced in another entry.

However, there are word embedding algorithms coming out. Since most English words carry more than a single sense, different senses of a word might be best represented by different embedded vectors. Incorporating word sense disambiguation, a method called sense2vec has been introduced by Trask, Michalak, and Liu. (arXiv:1511.06388). Matthew Honnibal wrote a nice blog entry demonstrating its use.

There are also other related work, such as wang2vec that is more sensitive to word orders.

Big Bang Theory (Season 2, Episode 5): Euclid Alternative

DMV staff: Application?
Sheldon: I’m actually more or a theorist.

Note: feature image taken from Big Bang Theory (CBS).

Continue reading “Word Embedding Algorithms”

Talking Not So Deep About Deep Learning


On October 14, 2015, I attended the regular meeting of the DCNLP meetup group, a group on natural language processing (NLP) in Washington, DC area. The talk was titled “Deep Learning for Question Answering“, spoken by Mr. Mohit Iyyer, a Ph.D. student in Department of Computer Science, University of Maryland (my alma mater!). He is a very good speaker.

I have no experience on deep learning at all although I did write a blog post remotely related. I even didn’t start training my first neural network until the next day after the talk. However, Mr. Iyyer explained what recurrent neural network (RNN), recursive neural network, and deep averaging network (DAN) are. This helped me a lot in order to understanding more about the principles of the famous word2vec model (which is something I am going to write about soon!). You can refer to his slides for more details. There are really a lot of talents in College Park, like another expert, Joe Yue Hei Ng, who is exploiting deep learning a lot as well.

The applications are awesome: with external knowledge to factual question answering, reasoning-based question answering, and visual question answering, with increasing order of challenging levels.

Mr. Iyyer and the participants discussed a lot about different packages. Mr. Iyyer uses Theano, a Python package for deep learning, which is good for model building and other analytical work. Some prefer Caffe. Some people, who are Java developers, also use deeplearning4j.

Stetsons Famous Bar & Grill (photo from Yelp)

This meetup was a sacred one too, because it is the last time it was held in Stetsons Famous Bar & Grill at U Street, which is going to permanently close on Halloween this year. The group is eagerly looking for a new venue for the upcoming meetup. This meeting was a crowded one. I sincerely thank the organizers, Charlie Greenbacker and Liz Merkhofer, for hosting all these meetings, and Chris Phipps (a linguist from IBM Watson) for recording.


Continue reading “Talking Not So Deep About Deep Learning”

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