Let's suppose we have a highly imbalanced binary classification problem in place.
Now, XGBoost provides us with 2 options to manage class imbalance during training. One is using the parameter scale_pos_weight while the other is using weights parameter of the DMatrix.
For eg -
I can either use - params = {'scale_pos_weight' : some value}
Or I can give class weights while creating the DMatrix like -
xgb = xgb.DMatrix(features, target, weight)
Can somebody please explain me the difference between these 2 cases? And how does the scores differ in both the cases?
The Difference
As explained in the (python) documentation, scale_pos_weight is a float (i.e. single value), which allows you to adjust the classification threshold. I.e. to tune the model's tendency to predict positive or negative values across the entire dataset.
DMatrix's weight argument requires an array-like object and is used to specify a "Weight for each instance". This allows more control over how the classifier makes its predictions, as each weight is used to scale the loss function that is being optimised.
An Example
To make this difference more concrete, imagine we are trying to predict the presence of cats in pictures under two scenarios.
Scenario One
In this scenario, our dataset consists of images either with a cat or with no animal at all. The dataset is imbalanced, with most images having no animal. Here we might use scale_pos_weight to increase the weighting of positive (with cats) images to deal with the imbalance.
In general, we tend to set scale_pos_weight proportionally to the imbalance. For example, if 20% of the images contain a cat, we would set scale_positive_weight to 4. (Of course this hyperparameter should be set empirically, e.g. using cross-validation, but this is a sensible initial/default value.)
Scenario Two
In this scenario, our dataset is again imbalanced with similar proportions of cat vs 'no-cat' images. However, this time it also includes some images with a dog. Potentially, our classifier may tend to mistake dogs for cats, decreasing its performance, with a higher false positive rate. In this instance, we may wish to specify per-sample weights using DMatrix's weight argument. In effect we would attempt to penalise dog-related false positives, which would not be possible with a single factor applied to the overall classification threshold.
Related
When using SKlearn and getting probabilities with the predict_proba(x) function for a binary classification [1, 0] the function returns the probability that the classification falls into each class. example [.8, .34].
Is there a community adopted standard way to reduce this down to a single classification confidence which takes all factors into consideration?
Option 1)
Just take the probability for the classification that was predicted (.8 in this example)
Option 2)
Some mathematical formula or function call which which takes into consideration all of the different probabilities and returns a single number. Such a confidence approach could take into consideration who close the probabilities of the different classes and return a lower confidence if there is not much separation between the different classes.
Theres no standard of of doing it. But what you can do is vary the threshold. What I exactly mean is if you use predict instead it throws out a binary out classifying your dataset, what its doing is taking 0.5 as a threshhold for predicting. Like if the probability of classifying in 1 is >0.5 classify it as 1 and 0 if <=0.5. But this can lead to a bad f1-score in some cases.
So, the approach should be to vary the threshhold and and choose one which yields maximum f1-score or any other metric you want to use as a score function. ROC(Receiver operating characteristic)curves are meant for this purpose only. And infact, the motive behind sklearn for giving out the class probabilities for this only, to let you choose the best threshhold.
A very nice example is predicting whether the patient has cancer or not. So you have to choose your threshhold wisely, if you choose it high you'll might be getting false-negatives a lot or if you choose it low you might get false-positives a lot. So you just choose the threshold according to your needs (as its better to get more false-positives).
Hope it helps!
I am interested in any tips on how to train a set with a very limited positive set and a large negative set.
I have about 40 positive examples (quite lengthy articles about a particular topic), and about 19,000 negative samples (most drawn from the sci-kit learn newsgroups dataset). I also have about 1,000,000 tweets that I could work with.. negative about the topic I am trying to train on. Is the size of the negative set versus the positive going to negatively influence training a classifier?
I would like to use cross-validation in sci-kit learn. Do I need to break this into train / test-dev / test sets? Is know there are some pre-built libraries in sci-kit. Any implementation examples that you recommend or have used previously would be helpful.
Thanks!
The answer to your first question is yes, the amount by which it will affect your results depends on the algorithm. My advive would be to keep an eye on the class-based statistics such as recall and precision (found in classification_report).
For RandomForest() you can look at this thread which discusses
the sample weight parameter. In general sample_weight is what
you're looking for in scikit-learn.
For SVM's have a look at either this example or this
example.
For NB classifiers, this should be handled implicitly by Bayes
rule, however in practice you may see some poor performances.
For you second question it's up for discussion, personally I break my data into a training and test split, perform cross validation on the training set for parameter estimation, retrain on all the training data and then test on my test set. However the amount of data you have may influence the way you split your data (more data means more options).
You could probably use Random Forest for your classification problem. There are basically 3 parameters to deal with data imbalance. Class Weight, Samplesize and Cutoff.
Class Weight-The higher the weight a class is given, the more its error rate is decreased.
Samplesize- Oversample the minority class to improve class imbalance while sampling the defects for each tree[not sure if Sci-kit supports this, used to be param in R)
Cutoff- If >x% trees vote for the minority class, classify it as minority class. By default x is 1/2 in Random forest for 2-class problem. You can set it to a lower value for the minority class.
Check out balancing predict error at https://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm
For the 2nd question if you are using Random Forest, you do not need to keep separate train/validation/test set. Random Forest does not choose any parameters based on a validation set, so validation set is un-necessary.
Also during the training of Random Forest, the data for training each individual tree is obtained by sampling by replacement from the training data, thus each training sample is not used for roughly 1/3 of the trees. We can use the votes of these 1/3 trees to predict the out of box probability of the Random forest classification. Thus with OOB accuracy you just need a training set, and not validation or test data to predict performance on unseen data. Check Out of Bag error at https://www.stat.berkeley.edu/~breiman/RandomForests/cc_home.htm for further study.
How should I set my gamma and Cost parameters in libSVM when I am using an imbalanced dataset that consists of 75% 'true' labels and 25% 'false' labels? I'm getting a constant error of having all the predicted labels set on 'True' due to the data imbalance.
If the issue isn't with libSVM, but with my dataset, how should I handle this imbalance from a Theoretical Machine Learning standpoint? *The number of features I'm using is between 4-10 and I have a small set of 250 data points.
Classes imbalance has nothing to do with selection of C and gamma, to deal with this issue you should use the class weighting scheme which is avaliable in for example scikit-learn package (built on libsvm)
Selection of best C and gamma is performed using grid search with cross validation. You should try vast range of values here, for C it is reasonable to choose values between 1 and 10^15 while a simple and good heuristic of gamma range values is to compute pairwise distances between all your data points and select gamma according to the percentiles of this distribution - think about putting in each point a gaussian distribution with variance equal to 1/gamma - if you select such gamma that this distribution overlaps will many points you will get very "smooth" model, while using small variance leads to the overfitting.
Imbalanced data sets can be tackled in various ways. Class balance has no effect on kernel parameters such as gamma for the RBF kernel.
The two most popular approaches are:
Use different misclassification penalties per class, this basically means changing C. Typically the smallest class gets weighed higher, a common approach is npos * wpos = nneg * wneg. LIBSVM allows you to do this using its -wX flags.
Subsample the overrepresented class to obtain an equal amount of positives and negatives and proceed with training as you traditionally would for a balanced set. Take note that you basically ignore a large chunk of data this way, which is intuitively a bad idea.
I know this has been asked some time ago, but I would like to answer it since you might find my answer useful.
As others have mentioned, you might want to consider using different weights for the minority classes or using different misclassification penalties. However, there is a more clever way of dealing with the imbalanced datasets.
You can use the SMOTE (Synthetic Minority Over-sampling Technique) algorithm to generate synthesized data for the minority class. It is a simple algorithm that can deal with some imbalance datasets pretty well.
In each iteration of the algorithm, SMOTE considers two random instances of the minority class and add an artificial example of the same class somewhere in between. The algorithm keeps injecting the dataset with the samples until the two classes become balanced or some other criteria(e.g. add certain number of examples). Below you can find a picture describing what the algorithm does for a simple dataset in 2D feature space.
Associating weight with the minority class is a special case of this algorithm. When you associate weight $w_i$ with instance i, you are basically adding the extra $w_i - 1$ instances on top of the instance i!
What you need to do is to augment your initial dataset with the samples created by this algorithm, and train the SVM with this new dataset. You can also find many implementation online in different languages like Python and Matlab.
There have been other extensions of this algorithm, I can point you to more materials if you want.
To test the classifier you need to split the dataset into test and train, add synthetic instances to the train set (DO NOT ADD ANY TO THE TEST SET), train the model on the train set, and finally test it on the test set. If you consider the generated instances when you are testing you will end up with a biased(and ridiculously higher) accuracy and recall.
I am working on a classification problem, which has different sensors. Each sensor collect a sets of numeric values.
I think its a classification problem and want to use weka as a ML tool for this problem. But I am not sure how to use weka to deal with the input values? And which classifier will best fit for this problem( one instance of a feature is a sets of numeric value)?
For example, I have three sensors A ,B, C. Can I define 5 collected data from all sensors,as one instance? Such as, One instance of A is {1,2,3,4,5,6,7}, and one instance of B is{3,434,534,213,55,4,7). C{424,24,24,13,24,5,6}.
Thanks a lot for your time on reviewing my question.
Commonly the first classifier to try is Naive Bayes (you can find it under "Bayes" directory in Weka) because it's fast, parameter less and the classification accuracy is hard to beat whenever the training sample is small.
Random Forest (you can find it under "Tree" directory in Weka) is another pleasant classifier since it process almost any data. Just run it and see whether it gives better results. It can be just necessary to increase the number of trees from the default 10 to some higher value. Since you have 7 attributes 100 trees should be enough.
Then I would try k-NN (you can find it under "Lazy" directory in Weka and it's called "IBk") because it commonly ranks amount the best single classifiers for a wide range of datasets. The only issues with k-nn are that it scales badly for large datasets (> 1GB) and it needs to fine tune k, the number of neighbors. This value is by default set to 1 but with increasing number of training samples it's commonly better to set it up to some higher integer value in range from 2 to 60.
And finally for some datasets where both, Naive Bayes and k-nn performs poorly, it's best to use SVM (under "Functions", it's called "Lib SVM"). However, it can be hassle to set up all the parameters of the SVM to get competitive results. Hence I leave it to the end when I already know what classification accuracies to expect. This classifier may not be the most convenient if you have more than two classes to classify.
I want to double check some concepts I am uncertain of regarding the training set for classifier learning. When we select records for our training data, do we select an equal number of records per class, summing to N or should it be randomly picking N number of records (regardless of class)?
Intuitively I was thinking of the former but thought of the prior class probabilities would then be equal and not be really helpful?
It depends on the distribution of your classes and the determination can only be made with domain knowledge of problem at hand.
You can ask the following questions:
Are there any two classes that are very similar and does the learner have enough information to distinguish between them?
Is there a large difference in the prior probabilities of each class?
If so, you should probably redistribute the classes.
In my experience, there is no harm in redistributing the classes, but it's not always necessary.
It really depends on the distribution of your classes. In the case of fraud or intrusion detection, the distribution of the prediction class can be less than 1%.
In this case you must distribute the classes evenly in the training set if you want the classifier to learn differences between each class. Otherwise, it will produce a classifier that correctly classifies over 99% of the cases without ever correctly identifying a fraud case, which is the whole point of creating a classifier to begin with.
Once you have a set of evenly distributed classes you can use any technique, such as k-fold, to perform the actual training.
Another example where class distributions need to be adjusted, but not necessarily in an equal number of records for each, is the case of determining upper-case letters of the alphabet from their shapes.
If you take a distribution of letters commonly used in the English language to train the classifier, there will be almost no cases, if any, of the letter Q. On the other hand, the letter O is very common. If you don't redistribute the classes to allow for the same number of Q's and O's, the classifier doesn't have enough information to ever distinguish a Q. You need to feed it enough information (i.e. more Qs) so it can determine that Q and O are indeed different letters.
The preferred approach is to use K-Fold Cross validation for picking up learning and testing data.
Quote from wikipedia:
K-fold cross-validation
In K-fold cross-validation, the
original sample is randomly
partitioned into K subsamples. Of the
K subsamples, a single subsample is
retained as the validation data for
testing the model, and the remaining K
− 1 subsamples are used as training
data. The cross-validation process is
then repeated K times (the folds),
with each of the K subsamples used
exactly once as the validation data.
The K results from the folds then can
be averaged (or otherwise combined) to
produce a single estimation. The
advantage of this method over repeated
random sub-sampling is that all
observations are used for both
training and validation, and each
observation is used for validation
exactly once. 10-fold cross-validation
is commonly used.
In stratified K-fold cross-validation,
the folds are selected so that the
mean response value is approximately
equal in all the folds. In the case of
a dichotomous classification, this
means that each fold contains roughly
the same proportions of the two types
of class labels.
You should always take the common approach in order to have comparable results with other scientific data.
I built an implementation of a Bayesian classifier to determine if a sample is NSFW (Not safe for work) by examining the occurrence of words in examples. When training a classifier for NSFW detection I've tried making it so that each class in the training sets has the same number of examples. This didn't work out as well as I had planned being that one of the classes had many more words per example than the other class.
Since I was computing the likelihood of NSFW based on these words I found that balancing out the classes based on their actual size (in MB) worked. I tried 10-cross fold validation for both approaches (balancing by number of examples and size of classes) and found that balancing by the size of the data worked well.