I have a bunch of already human-classified documents in some groups.
Is there a modified version of lda which I can use to train a model and then later classify unknown documents with it?
For what it's worth, LDA as a classifier is going to be fairly weak because it's a generative model, and classification is a discriminative problem. There is a variant of LDA called supervised LDA which uses a more discriminative criterion to form the topics (you can get source for this in various places), and there's also a paper with a max margin formulation that I don't know the status of source-code-wise. I would avoid the Labelled LDA formulation unless you're sure that's what you want, because it makes a strong assumption about the correspondence between topics and categories in the classification problem.
However, it's worth pointing out that none of these methods use the topic model directly to do the classification. Instead, they take documents, and instead of using word-based features use the posterior over the topics (the vector that results from inference for the document) as its feature representation before feeding it to a classifier, usually a Linear SVM. This gets you a topic model based dimensionality reduction, followed by a strong discriminative classifier, which is probably what you're after. This pipeline is available
in most languages using popular toolkits.
You can implement supervised LDA with PyMC that uses Metropolis sampler to learn the latent variables in the following graphical model:
The training corpus consists of 10 movie reviews (5 positive and 5 negative) along with the associated star rating for each document. The star rating is known as a response variable which is a quantity of interest associated with each document. The documents and response variables are modeled jointly in order to find latent topics that will best predict the response variables for future unlabeled documents. For more information, check out the original paper.
Consider the following code:
import pymc as pm
import numpy as np
from sklearn.feature_extraction.text import TfidfVectorizer
train_corpus = ["exploitative and largely devoid of the depth or sophistication ",
"simplistic silly and tedious",
"it's so laddish and juvenile only teenage boys could possibly find it funny",
"it shows that some studios firmly believe that people have lost the ability to think",
"our culture is headed down the toilet with the ferocity of a frozen burrito",
"offers that rare combination of entertainment and education",
"the film provides some great insight",
"this is a film well worth seeing",
"a masterpiece four years in the making",
"offers a breath of the fresh air of true sophistication"]
test_corpus = ["this is a really positive review, great film"]
train_response = np.array([3, 1, 3, 2, 1, 5, 4, 4, 5, 5]) - 3
#LDA parameters
num_features = 1000 #vocabulary size
num_topics = 4 #fixed for LDA
tfidf = TfidfVectorizer(max_features = num_features, max_df=0.95, min_df=0, stop_words = 'english')
#generate tf-idf term-document matrix
A_tfidf_sp = tfidf.fit_transform(train_corpus) #size D x V
print "number of docs: %d" %A_tfidf_sp.shape[0]
print "dictionary size: %d" %A_tfidf_sp.shape[1]
#tf-idf dictionary
tfidf_dict = tfidf.get_feature_names()
K = num_topics # number of topics
V = A_tfidf_sp.shape[1] # number of words
D = A_tfidf_sp.shape[0] # number of documents
data = A_tfidf_sp.toarray()
#Supervised LDA Graphical Model
Wd = [len(doc) for doc in data]
alpha = np.ones(K)
beta = np.ones(V)
theta = pm.Container([pm.CompletedDirichlet("theta_%s" % i, pm.Dirichlet("ptheta_%s" % i, theta=alpha)) for i in range(D)])
phi = pm.Container([pm.CompletedDirichlet("phi_%s" % k, pm.Dirichlet("pphi_%s" % k, theta=beta)) for k in range(K)])
z = pm.Container([pm.Categorical('z_%s' % d, p = theta[d], size=Wd[d], value=np.random.randint(K, size=Wd[d])) for d in range(D)])
#pm.deterministic
def zbar(z=z):
zbar_list = []
for i in range(len(z)):
hist, bin_edges = np.histogram(z[i], bins=K)
zbar_list.append(hist / float(np.sum(hist)))
return pm.Container(zbar_list)
eta = pm.Container([pm.Normal("eta_%s" % k, mu=0, tau=1.0/10**2) for k in range(K)])
y_tau = pm.Gamma("tau", alpha=0.1, beta=0.1)
#pm.deterministic
def y_mu(eta=eta, zbar=zbar):
y_mu_list = []
for i in range(len(zbar)):
y_mu_list.append(np.dot(eta, zbar[i]))
return pm.Container(y_mu_list)
#response likelihood
y = pm.Container([pm.Normal("y_%s" % d, mu=y_mu[d], tau=y_tau, value=train_response[d], observed=True) for d in range(D)])
# cannot use p=phi[z[d][i]] here since phi is an ordinary list while z[d][i] is stochastic
w = pm.Container([pm.Categorical("w_%i_%i" % (d,i), p = pm.Lambda('phi_z_%i_%i' % (d,i), lambda z=z[d][i], phi=phi: phi[z]),
value=data[d][i], observed=True) for d in range(D) for i in range(Wd[d])])
model = pm.Model([theta, phi, z, eta, y, w])
mcmc = pm.MCMC(model)
mcmc.sample(iter=1000, burn=100, thin=2)
#visualize topics
phi0_samples = np.squeeze(mcmc.trace('phi_0')[:])
phi1_samples = np.squeeze(mcmc.trace('phi_1')[:])
phi2_samples = np.squeeze(mcmc.trace('phi_2')[:])
phi3_samples = np.squeeze(mcmc.trace('phi_3')[:])
ax = plt.subplot(221)
plt.bar(np.arange(V), phi0_samples[-1,:])
ax = plt.subplot(222)
plt.bar(np.arange(V), phi1_samples[-1,:])
ax = plt.subplot(223)
plt.bar(np.arange(V), phi2_samples[-1,:])
ax = plt.subplot(224)
plt.bar(np.arange(V), phi3_samples[-1,:])
plt.show()
Given the training data (observed words and response variables), we can learn the global topics (beta) and regression coefficients (eta) for predicting the response variable (Y) in addition to topic proportions for each document (theta).
In order to make predictions of Y given the learned beta and eta, we can define a new model where we do not observe Y and use the previously learned beta and eta to obtain the following result:
Here we predicted a positive review (approx 2 given review rating range of -2 to 2) for the test corpus consisting of one sentence: "this is a really positive review, great film" as shown by the mode of the posterior histogram on the right.
See ipython notebook for a complete implementation.
Yes you can try the Labelled LDA in the stanford parser at
http://nlp.stanford.edu/software/tmt/tmt-0.4/
Related
from reading the articles and papers ,I understood that GNN is used for
Node level Prediction
Link prediction and
graph level prediction
but i am very much confused about GNN's input type
I have a list of questions
what is the input type of GNN ? Graphs or numerical data
If GNN takes graphs as input then how it is generated ?
Second edit:
By reading another paper i found that GNN takes graphs as input
1
Now i had only one question how graph is generated from the input ?
Reference:
Jie Zhou a,1, Ganqu Cui a,1, Shengding Hu a, Zhengyan Zhang a, Cheng Yang b, Zhiyuan Liu a,*,
Lifeng Wang c, Changcheng Li c, Maosong Sun a Graph neural networks: A review of methods and applications "Graph neural networks: A review of methods and applications" AI Open
The input of GNN include objects of different dimensions e.g. properties matrix dimension is [n_nodes, n_node_features], adjacency matrix dimension is [n_nodes, n_nodes] depending of the type of graph-neural-networks.
Spektral is a nice library with good examples of different types of GNN. The examples of how to load the data are also provided.
Here is the example of GNN model created using tensorflow and1
class GIN0(Model):
def __init__(self, channels, n_layers):
super().__init__()
self.conv1 = GINConv(channels, epsilon=0, mlp_hidden=[channels, channels])
self.convs = []
for _ in range(1, n_layers):
self.convs.append(
GINConv(channels, epsilon=0, mlp_hidden=[channels, channels])
)
self.pool = GlobalAvgPool()
self.dense1 = Dense(channels, activation="relu")
self.dropout = Dropout(0.5)
self.dense2 = Dense(channels, activation="relu")
def call(self, inputs):
x, a, i = inputs
x = self.conv1([x, a])
for conv in self.convs:
x = conv([x, a])
x = self.pool([x, i])
x = self.dense1(x)
x = self.dropout(x)
return self.dense2(x)
You can also look at this question for a more complete example of GNN application.
I've been implementing VAE and IWAE models on the caltech silhouettes dataset and am having an issue where the VAE outperforms IWAE by a modest margin (test LL ~120 for VAE, ~133 for IWAE!). I don't believe this should be the case, according to both theory and experiments produced here.
I'm hoping someone can find some issue in how I'm implementing that's causing this to be the case.
The network I'm using to approximate q and p is the same as that detailed in the appendix of the paper above. The calculation part of the model is below:
data_k_vec = data.repeat_interleave(K,0) # Generate K samples (in my case K=50 is producing this behavior)
mu, log_std = model.encode(data_k_vec)
z = model.reparameterize(mu, log_std) # z = mu + torch.exp(log_std)*epsilon (epsilon ~ N(0,1))
decoded = model.decode(z) # this is the sigmoid output of the model
log_prior_z = torch.sum(-0.5 * z ** 2, 1)-.5*z.shape[1]*T.log(torch.tensor(2*np.pi))
log_q_z = compute_log_probability_gaussian(z, mu, log_std) # Definitions below
log_p_x = compute_log_probability_bernoulli(decoded,data_k_vec)
if model_type == 'iwae':
log_w_matrix = (log_prior_z + log_p_x - log_q_z).view(-1, K)
elif model_type =='vae':
log_w_matrix = (log_prior_z + log_p_x - log_q_z).view(-1, 1)*1/K
log_w_minus_max = log_w_matrix - torch.max(log_w_matrix, 1, keepdim=True)[0]
ws_matrix = torch.exp(log_w_minus_max)
ws_norm = ws_matrix / torch.sum(ws_matrix, 1, keepdim=True)
ws_sum_per_datapoint = torch.sum(log_w_matrix * ws_norm, 1)
loss = -torch.sum(ws_sum_per_datapoint) # value of loss that gets returned to training function. loss.backward() will get called on this value
Here are the likelihood functions. I had to fuss with the bernoulli LL in order to not get nan during training
def compute_log_probability_gaussian(obs, mu, logstd, axis=1):
return torch.sum(-0.5 * ((obs-mu) / torch.exp(logstd)) ** 2 - logstd, axis)-.5*obs.shape[1]*T.log(torch.tensor(2*np.pi))
def compute_log_probability_bernoulli(theta, obs, axis=1): # Add 1e-18 to avoid nan appearances in training
return torch.sum(obs*torch.log(theta+1e-18) + (1-obs)*torch.log(1-theta+1e-18), axis)
In this code there's a "shortcut" being used in that the row-wise importance weights are being calculated in the model_type=='iwae' case for the K=50 samples in each row, while in the model_type=='vae' case the importance weights are being calculated for the single value left in each row, so that it just ends up calculating a weight of 1. Maybe this is the issue?
Any and all help is huge - I thought that addressing the nan issue would permanently get me out of the weeds but now I have this new problem.
EDIT:
Should add that the training scheme is the same as that in the paper linked above. That is, for each of i=0....7 rounds train for 2**i epochs with a learning rate of 1e-4 * 10**(-i/7)
The K-sample importance weighted ELBO is
$$ \textrm{IW-ELBO}(x,K) = \log \sum_{k=1}^K \frac{p(x \vert z_k) p(z_k)}{q(z_k;x)}$$
For the IWAE there are K samples originating from each datapoint x, so you want to have the same latent statistics mu_z, Sigma_z obtained through the amortized inference network, but sample multiple z K times for each x.
So its computationally wasteful to compute the forward pass for data_k_vec = data.repeat_interleave(K,0), you should compute the forward pass once for each original datapoint, then repeat the statistics output by the inference network for sampling:
mu = torch.repeat_interleave(mu,K,0)
log_std = torch.repeat_interleave(log_std,K,0)
Then sample z_k. And now repeat your datapoints data_k_vec = data.repeat_interleave(K,0), and use the resulting tensor to efficiently evaluate the conditional p(x |z_k) for each importance sample z_k.
Note you may also want to use the logsumexp operation when calculating the IW-ELBO for numerical stability. I can't quite figure out what's going on with the log_w_matrix calculation in your post, but this is what I would do:
log_pz = ...
log_qzCx = ....
log_pxCz = ...
log_iw = log_pxCz + log_pz - log_qzCx
log_iw = log_iw.reshape(-1, K)
iwelbo = torch.logsumexp(log_iw, dim=1) - np.log(K)
EDIT: Actually after thinking about it a bit and using the score function identity, you can interpret the IWAE gradient as an importance weighted estimate of the standard single-sample gradient, so the method in the OP for calculation of the importance weights is equivalent (if a bit wasteful), provided you place a stop_gradient operator around the normalized importance weights, which you call w_norm. So I the main problem is the absence of this stop_gradient operator.
I have just started using the Naive Bayes for text classification. I have coded it from the pseudo code snapshot attached.
I have two classes i.e. positive and negative. I have total of 2000 samples(IMDB Movie Reviews) out of which 1800 (900 positive, 900 negative) are used to train the classifier whereas 200 (100 negative, 100 positive) are used to test the system.
It marks the positive class documents but failed for classifying negative class documents propely. All documents belonging from negative classes are misclassified into positive class and thereby give accuracy of 50%.
If i documents from each class individually like first test all document belonging from negative classes and then from positive test samples then it give me accuracy of 100% but when i feed it mixed test samples it fails and classify all in one class (in my case positive).
Is there any mistake i am doing or is unavailable in this algorithm ?
Are training sample too less and classifier performance will increase upon increase training samples?
I have tested same samples with weka and rapid miner both are giving much better accuracy. I know that i have made a mistake but what is that i can't grab it ?Its the most simple one in understanding but accuracy result was totally unexpected and driving me crazy.Here is my code algorithm pseudo code. I have generating document vector using tf-idf for term weighting and document vector is used for calculations.
TrainMultinomialNB(C, D)
1. V = ExtractVocabulary(D)
2. N = CountDocs(D)
3. For each c E C
4. Do Nc = CountDocsInClass (D, c)
5. Prior[c] = Nc/N
6. Textc = ConcatenateTextOfAllDocsInClass (D,c)
7. For each t E V
8. Do Tct = CountTokensOfTerm(textc, t)
9. For each t E V
10. Do condprob[t][c] = (Tct + 1) /(Sum(Tct) + |V|)
11. Return V, prior, condprob
ApplyMultinomialNB(C, V, prior, condprob, d)
1. W = ExtractTokensFromDoc (V, d)
2. For each c E C
3. Do score [c] = log (prior)
4. For each t E W
5. Do score [c] + = log (condprob[t][c])
6. Return argmax(cEC) score [c]
I am trying to teach my SVM algorithm using data of clicks and conversion by people who see the banners. The main problem is that the clicks is around 0.2% of all data so it's big disproportion in it. When I use simple SVM in testing phase it always predict only "view" class and never "click" or "conversion". In average it gives 99.8% right answers (because of disproportion), but it gives 0% right prediction if you check "click" or "conversion" ones. How can you tune the SVM algorithm (or select another one) to take into consideration the disproportion?
The most basic approach here is to use so called "class weighting scheme" - in classical SVM formulation there is a C parameter used to control the missclassification count. It can be changed into C1 and C2 parameters used for class 1 and 2 respectively. The most common choice of C1 and C2 for a given C is to put
C1 = C / n1
C2 = C / n2
where n1 and n2 are sizes of class 1 and 2 respectively. So you "punish" SVM for missclassifing the less frequent class much harder then for missclassification the most common one.
Many existing libraries (like libSVM) supports this mechanism with class_weight parameters.
Example using python and sklearn
print __doc__
import numpy as np
import pylab as pl
from sklearn import svm
# we create 40 separable points
rng = np.random.RandomState(0)
n_samples_1 = 1000
n_samples_2 = 100
X = np.r_[1.5 * rng.randn(n_samples_1, 2),
0.5 * rng.randn(n_samples_2, 2) + [2, 2]]
y = [0] * (n_samples_1) + [1] * (n_samples_2)
# fit the model and get the separating hyperplane
clf = svm.SVC(kernel='linear', C=1.0)
clf.fit(X, y)
w = clf.coef_[0]
a = -w[0] / w[1]
xx = np.linspace(-5, 5)
yy = a * xx - clf.intercept_[0] / w[1]
# get the separating hyperplane using weighted classes
wclf = svm.SVC(kernel='linear', class_weight={1: 10})
wclf.fit(X, y)
ww = wclf.coef_[0]
wa = -ww[0] / ww[1]
wyy = wa * xx - wclf.intercept_[0] / ww[1]
# plot separating hyperplanes and samples
h0 = pl.plot(xx, yy, 'k-', label='no weights')
h1 = pl.plot(xx, wyy, 'k--', label='with weights')
pl.scatter(X[:, 0], X[:, 1], c=y, cmap=pl.cm.Paired)
pl.legend()
pl.axis('tight')
pl.show()
In particular, in sklearn you can simply turn on the automatic weighting by setting class_weight='auto'.
This paper describes a variety of techniques. One simple (but very bad method for SVM) is just replicating the minority class(s) until you have a balance:
http://www.ele.uri.edu/faculty/he/PDFfiles/ImbalancedLearning.pdf
In every book and example always they show only binary classification (two classes) and new vector can belong to any one class.
Here the problem is I have 4 classes(c1, c2, c3, c4). I've training data for 4 classes.
For new vector the output should be like
C1 80% (the winner)
c2 10%
c3 6%
c4 4%
How to do this? I'm planning to use libsvm (because it most popular). I don't know much about it. If any of you guys used it previously please tell me specific commands I'm supposed to use.
LibSVM uses the one-against-one approach for multi-class learning problems. From the FAQ:
Q: What method does libsvm use for multi-class SVM ? Why don't you use the "1-against-the rest" method ?
It is one-against-one. We chose it after doing the following comparison: C.-W. Hsu and C.-J. Lin. A comparison of methods for multi-class support vector machines, IEEE Transactions on Neural Networks, 13(2002), 415-425.
"1-against-the rest" is a good method whose performance is comparable to "1-against-1." We do the latter simply because its training time is shorter.
Commonly used methods are One vs. Rest and One vs. One.
In the first method you get n classifiers and the resulting class will have the highest score.
In the second method the resulting class is obtained by majority votes of all classifiers.
AFAIR, libsvm supports both strategies of multiclass classification.
You can always reduce a multi-class classification problem to a binary problem by choosing random partititions of the set of classes, recursively. This is not necessarily any less effective or efficient than learning all at once, since the sub-learning problems require less examples since the partitioning problem is smaller. (It may require at most a constant order time more, e.g. twice as long). It may also lead to more accurate learning.
I'm not necessarily recommending this, but it is one answer to your question, and is a general technique that can be applied to any binary learning algorithm.
Use the SVM Multiclass library. Find it at the SVM page by Thorsten Joachims
It does not have a specific switch (command) for multi-class prediction. it automatically handles multi-class prediction if your training dataset contains more than two classes.
Nothing special compared with binary prediction. see the following example for 3-class prediction based on SVM.
install.packages("e1071")
library("e1071")
data(iris)
attach(iris)
## classification mode
# default with factor response:
model <- svm(Species ~ ., data = iris)
# alternatively the traditional interface:
x <- subset(iris, select = -Species)
y <- Species
model <- svm(x, y)
print(model)
summary(model)
# test with train data
pred <- predict(model, x)
# (same as:)
pred <- fitted(model)
# Check accuracy:
table(pred, y)
# compute decision values and probabilities:
pred <- predict(model, x, decision.values = TRUE)
attr(pred, "decision.values")[1:4,]
# visualize (classes by color, SV by crosses):
plot(cmdscale(dist(iris[,-5])),
col = as.integer(iris[,5]),
pch = c("o","+")[1:150 %in% model$index + 1])
data=load('E:\dataset\scene_categories\all_dataset.mat');
meas = data.all_dataset;
species = data.dataset_label;
[g gn] = grp2idx(species); %# nominal class to numeric
%# split training/testing sets
[trainIdx testIdx] = crossvalind('HoldOut', species, 1/10);
%# 1-vs-1 pairwise models
num_labels = length(gn);
clear gn;
num_classifiers = num_labels*(num_labels-1)/2;
pairwise = zeros(num_classifiers ,2);
row_end = 0;
for i=1:num_labels - 1
row_start = row_end + 1;
row_end = row_start + num_labels - i -1;
pairwise(row_start : row_end, 1) = i;
count = 0;
for j = i+1 : num_labels
pairwise( row_start + count , 2) = j;
count = count + 1;
end
end
clear row_start row_end count i j num_labels num_classifiers;
svmModel = cell(size(pairwise,1),1); %# store binary-classifers
predTest = zeros(sum(testIdx),numel(svmModel)); %# store binary predictions
%# classify using one-against-one approach, SVM with 3rd degree poly kernel
for k=1:numel(svmModel)
%# get only training instances belonging to this pair
idx = trainIdx & any( bsxfun(#eq, g, pairwise(k,:)) , 2 );
%# train
svmModel{k} = svmtrain(meas(idx,:), g(idx), ...
'Autoscale',true, 'Showplot',false, 'Method','QP', ...
'BoxConstraint',2e-1, 'Kernel_Function','rbf', 'RBF_Sigma',1);
%# test
predTest(:,k) = svmclassify(svmModel{k}, meas(testIdx,:));
end
pred = mode(predTest,2); %# voting: clasify as the class receiving most votes
%# performance
cmat = confusionmat(g(testIdx),pred);
acc = 100*sum(diag(cmat))./sum(cmat(:));
fprintf('SVM (1-against-1):\naccuracy = %.2f%%\n', acc);
fprintf('Confusion Matrix:\n'), disp(cmat)
For multi class classification using SVM;
It is NOT (one vs one) and NOT (one vs REST).
Instead learn a two-class classifier where the feature vector is (x, y) where x is data and y is the correct label associated with the data.
The training gap is the Difference between the value for the correct class and the value of the nearest other class.
At Inference choose the "y" that has the maximum
value of (x,y).
y = arg_max(y') W.(x,y') [W is the weight vector and (x,y) is the feature Vector]
Please Visit link:
https://nlp.stanford.edu/IR-book/html/htmledition/multiclass-svms-1.html#:~:text=It%20is%20also%20a%20simple,the%20label%20of%20structural%20SVMs%20.