I want to classify documents (composed of words) into 3 classes (Positive, Negative, Unknown/Neutral). A subset of the document words become the features.
Until now, I have programmed a Naive Bayes Classifier using as a feature selector Information gain and chi-square statistics. Now, I would like to see what happens if I use Odds ratio as a feature selector.
My problem is that I don't know hot to implement Odds-ratio. Should I:
1) Calculate Odds Ratio for every word w, every class:
E.g. for w:
Prob of word as positive Pw,p = #positive docs with w/#docs
Prob of word as negative Pw,n = #negative docs with w/#docs
Prob of word as unknown Pw,u = #unknown docs with w/#docs
OR(Wi,P) = log( Pw,p*(1-Pw,p) / (Pw,n + Pw,u)*(1-(Pw,n + Pw,u)) )
OR(Wi,N) ...
OR(Wi,U) ...
2) How should I decide if I choose or not the word as a feature ?
Thanks in advance...
Since it took me a while to independently wrap my head around all this, let me explain my findings here for the benefit of humanity.
Using the (log) odds ratio is a standard technique for filtering features prior to text classification. It is a 'one-sided metric' [Zheng et al., 2004] in the sense that it only discovers features which are positively correlated with a particular class. As a log-odds-ratio for the probability of seeing a feature 't' given the class 'c', it is defined as:
LOR(t,c) = log [Pr(t|c) / (1 - Pr(t|c))] : [Pr(t|!c) / (1 - Pr(t|!c))]
= log [Pr(t|c) (1 - Pr(t|!c))] / [Pr(t|!c) (1 - Pr(t|c))]
Here I use '!c' to mean a document where the class is not c.
But how do you actually calculate Pr(t|c) and Pr(t|!c)?
One subtlety to note is that feature selection probabilities, in general, are usually defined over a document event model [McCallum & Nigam 1998, Manning et al. 2008], i.e., Pr(t|c) is the probability of seeing term t one or more times in the document given the class of the document is c (in other words, the presence of t given the class c). The maximum likelihood estimate (MLE) of this probability would be the proportion of documents of class c that contain t at least once. [Technically, this is known as a Multivariate Bernoulli event model, and is distinct from a Multinomial event model over words, which would calculate Pr(t|c) using integer word counts - see the McCallum paper or the Manning IR textbook for more details, specifically on how this applies to a Naive Bayes text classifier.]
One key to using LOR effectively is to smooth these conditional probability estimates, since, as #yura noted, rare events are problematic here (e.g., the MLE of Pr(t|!c) could be zero, leading to an infinite LOR). But how do we smooth?
In the literature, Forman reports smoothing the LOR by "adding one to any zero count in the denominator" (Forman, 2003), while Zheng et al (2004) use "ELE [Expected Likelihood Estimation] smoothing" which usually amounts to adding 0.5 to each count.
To smooth in a way that is consistent with probability theory, I follow standard practices in text classification with a Multivariate Bernoulli event model. Essentially, we assume that we have seen each presence count AND each absence count B extra times. So our estimate for Pr(t|c) can be written in terms of #(t,c): the number of times we've seen t and c, and #(t,!c): the number of times we've seen t without c, as follows:
Pr(t|c) = [#(t,c) + B] / [#(t,c) + #(t,!c) + 2B]
= [#(t,c) + B] / [#(c) + 2B]
If B = 0, we have the MLE. If B = 0.5, we have ELE. If B = 1, we have the Laplacian prior. Note this looks different than smoothing for the Multinomial event model, where the Laplacian prior leads you to add |V| in the denominator [McCallum & Nigam, 1998]
You can choose 0.5 or 1 as your smoothing value, depending on which prior work most inspires you, and plug this into the equation for LOR(t,c) above, and score all the features.
Typically, you then decide on how many features you want to use, say N, and then choose the N highest-ranked features based on the score.
In a multi-class setting, people have often used 1 vs All classifiers and thus did feature selection independently for each classifier and thus each positive class with the 1-sided metrics (Forman, 2003). However, if you want to find a unique reduced set of features that works in a multiclass setting, there are some advanced approaches in the literature (e.g. Chapelle & Keerthi, 2008).
References:
Zheng, Wu, Srihari, 2004
McCallum & Nigam 1998
Manning, Raghavan & Schütze, 2008
Forman, 2003
Chapelle & Keerthi, 2008
Odd ratio is not good measure for feature selection, because it is only shows what happen when feature present, and nothing when it is not. So it will not work for rare features and almost all features are rare so it not work for almost all features. Example feature with 100% confidence that class is positive which present in 0.0001 is useless for classification. Therefore if you still want to use odd ratio add threshold on frequency of feature, like feature present in 5% of cases. But I would recommend better approach - use Chi or info gain metrics which automatically solve those problems.
Related
I implemented a cosine-theta function, which calculates the relation between two articles. If two articles are very similar then the words should contain quite some overlap. However, a cosine theta score of 0.54 does not mean "related" or "not related". I should end up with a definitive answer which is either 0 for 'not related' or 1 for 'related'.
I know that there are sigmoid and softmax functions, yet I should find the optimal parameters to give to such functions and I do not know if these functions are satisfactory solutions. I was thinking that I have the cosine theta score, I can calculate the percentage of overlap between two sentences two (e.g. the amount of overlapping words divided by the amount of words in the article) and maybe some more interesting things. Then with the data, I could maybe write a function (what type of function I do not know and is part of the question!), after which I can minimize the error via the SciPy library. This means that I should do some sort of supervised learning, and I am willing to label article pairs with labels (0/1) in order to train a network. Is this worth the effort?
# Count words of two strings.
v1, v2 = self.word_count(s1), self.word_count(s2)
# Calculate the intersection of the words in both strings.
v3 = set(v1.keys()) & set(v2.keys())
# Calculate some sort of ratio between the overlap and the
# article length (since 1 overlapping word on 2 words is more important
# then 4 overlapping words on articles of 492 words).
p = min(len(v1), len(v2)) / len(v3)
numerator = sum([v1[w] * v2[w] for w in v3])
w1 = sum([v1[w]**2 for w in v1.keys()])
w2 = sum([v2[w]**2 for w in v2.keys()])
denominator = math.sqrt(w1) * math.sqrt(w2)
# Calculate the cosine similarity
if not denominator:
return 0.0
else:
return (float(numerator) / denominator)
As said, I would like to use variables such as p, and the cosine theta score in order to produce an accurate discrete binary label, either 0 or 1.
As said, I would like to use variables such as p, and the cosine theta score in order to produce an accurate discrete binary label, either 0 or 1.
Here it really comes down to what you mean by accuracy. It is up to you to choose how the overlap affects whether or not two strings are "matching" unless you have a labelled data set. If you have a labelled data set (I.e., a set of pairs of strings along with a 0 or 1 label), then you can train a binary classification algorithm and try to optimise based on that. I would recommend something like a neural net or SVM due to the potentially high dimensional, categorical nature of your problem.
Even the optimisation, however, is a subjective measure. For example, in theory let's pretend you have a model which out of 100 samples only predicts 1 answer (Giving 99 unknowns). Technically if that one answer is correct, that is a model with 100% accuracy, but which has a very low recall. Generally in machine learning you will find a trade off between recall and accuracy.
Some people like to go for certain metrics which combine the two (The most famous of which is the F1 score), but honestly it depends on the application. If I have a marketing campaign with a fixed budget, then I care more about accuracy - I would only want to target consumers who are likely to buy my product. If however, we are looking to test for a deadly disease or markers for bank fraud, then it's feasible for that test to be accurate only 10% of the time - if its recall of true positives is somewhere close to 100%.
Finally, if you have no labelled data, then your best bet is just to define some cut off value which you believe indicates a good match. This is would then be more analogous to a binary clustering problem, and you could use some more abstract measure such as distance to a centroid to test which cluster (Either the "related" or "unrelated" cluster) the point belongs to. Note however that here your features feel like they would be incredibly hard to define.
I have a few distance functions which return distance between two images , I want to combine these distance into a single distance, using weighted scoring e.g. ax1+bx2+cx3+dx4 etc i want to learn these weights automatically such that my test error is minimised.
For this purpose i have a labeled dataset which has various triplets of images such that (a,b,c) , a has less distance to b than it has to c.
i.e. d(a,b)<d(a,c)
I want to learn such weights so that this ordering of triplets can be as accurate as possible.(i.e. the weighted linear score given is less for a&b and more for a&c).
What sort of machine learning algorithm can be used for the task,and how the desired task can be achieved?
Hopefully I understand your question correctly, but it seems that this could be solved more easily with constrained optimization directly, rather than classical machine learning (the algorithms of which are often implemented via constrained optimization, see e.g. SVMs).
As an example, a possible objective function could be:
argmin_{w} || e ||_2 + lambda || w ||_2
where w is your weight vector (Oh god why is there no latex here), e is the vector of errors (one component per training triplet), lambda is some tunable regularizer constant (could be zero), and your constraints could be:
max{d(I_p,I_r)-d(I_p,I_q),0} <= e_j for jth (p,q,r) in T s.t. d(I_p,I_r) <= d(I_p,I_q)
for the jth constraint, where I_i is image i, T is the training set, and
d(u,v) = sum_{w_i in w} w_i * d_i(u,v)
with d_i being your ith distance function.
Notice that e is measuring how far your chosen weights are from satisfying all the chosen triplets in the training set. If the weights preserve ordering of label j, then d(I_p,I_r)-d(I_p,I_q) < 0 and so e_j = 0. If they don't, then e_j will measure the amount of violation of training label j. Solving the optimization problem would give the best w; i.e. the one with the lowest error.
If you're not familiar with linear/quadratic programming, convex optimization, etc... then start googling :) Many libraries exist for this type of thing.
On the other hand, if you would prefer a machine learning approach, you may be able to adapt some metric learning approaches to your problem.
I've been working a bit with neural networks and I'm interested on implementing a spiking neuron model.
I've read a fair amount of tutorials but most of them seem to be about generating pulses and I haven't found any application of it on a given input train.
Say for example I got input train:
Input[0] = [0,0,0,1,0,0,1,1]
It enters the Izhikevich neuron, does the input multiply a weight or only makes use of the parameters a, b, c and d?
Izhikevich equations are:
v[n+1] = 0.04*v[n]^2 + 5*v[n] + 140 - u[n] + I
u[n+1] = a*(b*v[n] - u[n])
where v[n] is input voltage and u[n] is a general recovery variable.
Are there any texts on implementations of Izhikevich or similar spiking neuron models on a practical problem? I'm trying to understand how information is encoded on this models but it looks different from what's done with standard second generation neurons. The only tutorial I've found where it deals with a spiking train and a set of weights is [1] but I haven't seen the same with Izhikevich.
[1] https://msdn.microsoft.com/en-us/magazine/mt422587.aspx
The plain Izhikevich model by itself, does not include weights.
The two equations you mentioned, model the membrane potential (v[]) over time of a point neuron. To use weights, you could connect two or more of such cells with synapses.
Each synapse could include some sort spike detection mechanism on the source cell (pre-synaptic), and a synaptic current mechanism in the target (post-synaptic) cell side. That synaptic current could then be multiplied by a weight term, and then become part of the I term (in the 1st equation above) for the target cell.
As a very simple example of a two cell network, at every time step, you could check if pre- cell v is above (say) 0 mV. If so, inject (say) 0.01 pA * weightPrePost into the post- cell. weightPrePost would range from 0 to 1, and could be modified in response to things like firing rate, or Hebbian-like spike synchrony like in STDP.
With multiple synaptic currents going into a cell, you could devise various schemes how to sum them. The simplest one would be just a simple sum, more complicated ones could include things like distance and dendrite diameters (e.g. simulated neural morphology).
This chapter is a nice introduction to other ways to model synapses: Modelling
Synaptic Transmission
I am using Support Vector Machines for document classification. My feature set for each document is a tf-idf vector. I have M documents with each tf-idf vector of size N.
Giving M * N matrix.
The size of M is just 10 documents and tf-idf vector is 1000 word vector. So my features are much larger than number of documents. Also each word occurs in either 2 or 3 documents. When i am normalizing each feature ( word ) i.e. column normalization in [0,1] with
val_feature_j_row_i = ( val_feature_j_row_i - min_feature_j ) / ( max_feature_j - min_feature_j)
It either gives me 0, 1 of course.
And it gives me bad results. I am using libsvm, with rbf function C = 0.0312, gamma = 0.007815
Any recommendations ?
Should i include more documents ? or other functions like sigmoid or better normalization methods ?
The list of things to consider and correct is quite long, so first of all I would recommend some machine-learning reading before trying to face the problem itself. There are dozens of great books (like ie. Haykin's "Neural Networks and Learning Machines") as well as online courses, which will help you with such basics, like those listed here: http://www.class-central.com/search?q=machine+learning .
Getting back to the problem itself:
10 documents is rows of magnitude to small to get any significant results and/or insights into the problem,
there is no universal method of data preprocessing, you have to analyze it through numerous tests and data analytics,
SVMs are parametrical models, you cannot use a single C and gamma values and expect any reasonable results. You have to check dozens of them to even get a clue "where to search". The most simple method for doing so is so called grid search,
1000 of features is a great number of dimensions, this suggest that using a kernel, which implies infinitely dimensional feature space is quite... redundant - it would be a better idea to first analyze simplier ones, which have smaller chance to overfit (linear or low degree polynomial)
finally is tf*idf a good choice if "each word occurs in 2 or 3 documents"? It can be doubtfull, unless what you actually mean is 20-30% of documents
finally why is simple features squashing
It either gives me 0, 1 of course.
it should result in values in [0,1] interval, not just its limits. So if this is a case you are probably having some error in your implementation.
I have a scenario where I have several thousand instances of data. The data itself is represented as a single integer value. I want to be able to detect when an instance is an extreme outlier.
For example, with the following example data:
a = 10
b = 14
c = 25
d = 467
e = 12
d is clearly an anomaly, and I would want to perform a specific action based on this.
I was tempted to just try an use my knowledge of the particular domain to detect anomalies. For instance, figure out a distance from the mean value that is useful, and check for that, based on heuristics. However, I think it's probably better if I investigate more general, robust anomaly detection techniques, which have some theory behind them.
Since my working knowledge of mathematics is limited, I'm hoping to find a technique which is simple, such as using standard deviation. Hopefully the single-dimensioned nature of the data will make this quite a common problem, but if more information for the scenario is required please leave a comment and I will give more info.
Edit: thought I'd add more information about the data and what I've tried in case it makes one answer more correct than another.
The values are all positive and non-zero. I expect that the values will form a normal distribution. This expectation is based on an intuition of the domain rather than through analysis, if this is not a bad thing to assume, please let me know. In terms of clustering, unless there's also standard algorithms to choose a k-value, I would find it hard to provide this value to a k-Means algorithm.
The action I want to take for an outlier/anomaly is to present it to the user, and recommend that the data point is basically removed from the data set (I won't get in to how they would do that, but it makes sense for my domain), thus it will not be used as input to another function.
So far I have tried three-sigma, and the IQR outlier test on my limited data set. IQR flags values which are not extreme enough, three-sigma points out instances which better fit with my intuition of the domain.
Information on algorithms, techniques or links to resources to learn about this specific scenario are valid and welcome answers.
What is a recommended anomaly detection technique for simple, one-dimensional data?
Check out the three-sigma rule:
mu = mean of the data
std = standard deviation of the data
IF abs(x-mu) > 3*std THEN x is outlier
An alternative method is the IQR outlier test:
Q25 = 25th_percentile
Q75 = 75th_percentile
IQR = Q75 - Q25 // inter-quartile range
IF (x < Q25 - 1.5*IQR) OR (Q75 + 1.5*IQR < x) THEN x is a mild outlier
IF (x < Q25 - 3.0*IQR) OR (Q75 + 3.0*IQR < x) THEN x is an extreme outlier
this test is usually employed by Box plots (indicated by the whiskers):
EDIT:
For your case (simple 1D univariate data), I think my first answer is well suited.
That however isn't applicable to multivariate data.
#smaclell suggested using K-means to find the outliers. Beside the fact that it is mainly a clustering algorithm (not really an outlier detection technique), the problem with k-means is that it requires knowing in advance a good value for the number of clusters K.
A better suited technique is the DBSCAN: a density-based clustering algorithm. Basically it grows regions with sufficiently high density into clusters which will be maximal set of density-connected points.
DBSCAN requires two parameters: epsilon and minPoints. It starts with an arbitrary point that has not been visited. It then finds all the neighbor points within distance epsilon of the starting point.
If the number of neighbors is greater than or equal to minPoints, a cluster is formed. The starting point and its neighbors are added to this cluster and the starting point is marked as visited. The algorithm then repeats the evaluation process for all the neighbors recursively.
If the number of neighbors is less than minPoints, the point is marked as noise.
If a cluster is fully expanded (all points within reach are visited) then the algorithm proceeds to iterate through the remaining unvisited points until they are depleted.
Finally the set of all points marked as noise are considered outliers.
There are a variety of clustering techniques you could use to try to identify central tendencies within your data. One such algorithm we used heavily in my pattern recognition course was K-Means. This would allow you to identify whether there are more than one related sets of data, such as a bimodal distribution. This does require you having some knowledge of how many clusters to expect but is fairly efficient and easy to implement.
After you have the means you could then try to find out if any point is far from any of the means. You can define 'far' however you want but I would recommend the suggestions by #Amro as a good starting point.
For a more in-depth discussion of clustering algorithms refer to the wikipedia entry on clustering.
This is an old topic but still it lacks some information.
Evidently, this can be seen as a case of univariate outlier detection. The approaches presented above have several pros and cons. Here are some weak spots:
Detection of outliers with the mean and sigma has the obvious disadvantage of dependence of mean and sigma on the outliers themselves.
The case of the small sample limit (see question for example) is not adequately covered by, 3 sigma, K-Means, IQR etc.
And I could go on... However the statistical literature offers a simple metric: the median absolute deviation. (Medians are insensitive to outliers)
Details can be found here: https://www.sciencedirect.com/book/9780128047330/introduction-to-robust-estimation-and-hypothesis-testing
I think this problem can be solved in a few lines of python code like this:
import numpy as np
import scipy.stats as sts
x = np.array([10, 14, 25, 467, 12]) # your values
np.abs(x - np.median(x))/(sts.median_abs_deviation(x)/0.6745) #MAD criterion
Subsequently you reject values above a certain threshold (97.5 percentile of the distribution of data), in case of an assumed normal distribution the threshold is 2.24. Here it translates to:
array([ 0.6745 , 0. , 1.854875, 76.387125, 0.33725 ])
or the 467 entry being rejected.
Of course, one could argue, that the MAD (as presented) also assumes a normal dist. Therefore, why is it that argument 2 above (small sample) does not apply here? The answer is that MAD has a very high breakdown point. It is easy to choose different threshold points from different distributions and come to the same conclusion: 467 is the outlier.
Both three-sigma rule and IQR test are often used, and there are a couple of simple algorithms to detect anomalies.
The three-sigma rule is correct
mu = mean of the data
std = standard deviation of the data
IF abs(x-mu) > 3*std THEN x is outlier
The IQR test should be:
Q25 = 25th_percentile
Q75 = 75th_percentile
IQR = Q75 - Q25 // inter-quartile range
If x > Q75 + 1.5 * IQR or x < Q25 - 1.5 * IQR THEN x is a mild outlier
If x > Q75 + 3.0 * IQR or x < Q25 – 3.0 * IQR THEN x is a extreme outlier