i hope everyone is doing well
I need some help with generative models.
So im working on a project where the main task is to build a binary classification model. In the dataset which contains 300000 sample and 100 feature, there is an imbalance between the 2 classes where majority class is too much bigger than the minory class.
To handle this problem, i'm using VAE (variational autoencoders) to solve this problem.
So i started training the VAE on the minority class and then use the decoder part of the VAE to generate new or fake samples that are similars to the minority class then concatenate this new data with training set in order to have a new balanced training set.
My question is : is there anyway to evalutate generative models like vae, like is there a way to know if the data generated is similar to the real one ??
I have read that there is some metrics to evaluate generated data like inception distance and Frechet inception distance but i saw that they have been only used on image data
I wanna know if i can use them too on my dataset ?
Thanks in advance
I believe your data is not image as you say there are 100 features. What I believe that you can check the similarity between the synthesised features and the original features (the ones belong to minority class), and keep only the ones with certain similarity. Cosine similarity index would be useful for this problem.
That would be also very nice to check a scatter plot of the synthesised features with the original ones to see if they are close to each other. tSNE would be useful at this point.
I have trained a neural network and an XGBoost model for the same problem, now I am confused that how should I stack them. Should I just pass the output of the neural network as a parameter to the XGBoost model, or should I take the weighting of their results seperately ? Which would be better ?
This question cannot be clearly answered. I would suggest to check both possibilities and chose the one, that worked best.
Using the output of one model as input to the other model
I guess, you know, what you have to do to use the output of the NN as input to XGBoost. You should just take some time, about how you handle the test and train data (see below). Use the "probabilities" rather than the binary labels for that. Of course, you could also try it vice-versa, so that the NN gets the output of the XGBoost model as an additional input.
Using a Votingclassifier
The other possibility is to use a VotingClassifier using soft-voting. You can use VotingClassifier(voting='soft') for that (to be precise sklearn.ensemble.VotingClassifier). You could also play around with the weights here.
Difference
The big difference is, that with the first possibility the XGBoost model might learn, in what areas the NN is weak and in which it is strong, while with the VotingClassifier the outputs of both models are equally weighted for all samples and it relies on the assumption that the model output a "probability" not so close to 0 / 1 if they are not so confident about the prediciton of the specific input record. But this assumption might not be always true.
Handling of the Train/Testdata
In both cases, you need to think about, how you should handle the train/test data. The train/test data should ideally be split the same way for both models. Otherwise you might introduce some kind of data-leakage problem.
For the VotingClassifier this is no problem, because it can be used as a regular skearn model class. For the first method (output of model 1 is one feature of model 2), you should make sure, you do the train-test-split (or the cross-validation) with exactly the same records. If you don't do that, you would run the risk to validate the output of your second model on a record which was in the training set of model 1 (except for the additonal feature of course) and this clearly could cause a data-leakage problem which results in a score that appears to be better than how the model would actually perform on unseen productive data.
Suppose one makes a neural network using Keras. Do the trained weights depend on the order in which the training data has been fed into the system ? Is it ok to feed data belonging to one category first and then data belonging to another category or should they be random?
As the training will be done in batches, which means optimizing the weights on data chunk by chunk, the main assumption is that the batches of data are somewhat representative of the dataset. To make it representative it is thus better to randomly sample the data.
Bottomline : It will theoritically learn better if you feed randomly the neural network. I strongly advise yo to shuffle your dataset when you feed it in training mode (and there is an option in the .fit() function).
In inference mode, if you only want to make a forward pass on the neural net, then the order doesn't matter at all since you don't change the weights.
I hope this clarifies things a bit for you :-)
Nassim answer is believed to be True for small networks and datasets but recent articles (or e.g. this one) makes us believe that for deeper networks (with more than 4 layers) - not shuffling your data set might be considered as some kind of regularization - as poor minima are expected to be deep but small and good minima are expected to be wide and hard to leave.
In case of inference time - the only way where this might harm your inference process is when you are using a training distribution of your data in a highly coupled manner - e.g. using BatchNormalization or Dropout like in a training phase (this is sometimes used for some kinds of Bayesian Deep Learning).
I am currently trying to use satellite imagery to recognize Apples orchards. And I am facing a small problem in the number of representative data for each class.
In fact my question is :
Is it possible to take randomly some different images in my "not-apples" class at each epoch because I have much more of theses (compared to the "apples" one) and I want to increase the probability my network will classify out an image unrepresentative.
Thanks in advance for your help
That is not possible in Keras. Keras will, by default, shuffle your training data and then train on it in a mini-batch fashion. However, there are still ways to re-balance your dataset.
The imbalanced training data problem that you are facing is pretty common. You have many options available to you; I list a few below:
You can adjust the relative weights of your classes using class_weight keyword of the model.fit() function.
You can "up-sample" your "apples" class or "down-sample" your "non-apples" class to have equal numbers of both classes during training.
You can generate synthetic images of your "apples" class to augment your data set. To this end, the ImageDataGenerator class in Keras can be particularly useful. This Keras tutorial is a good introduction to its usage.
In my experience, I've found #2 and #3 to be most useful. #1 is limited by the fact that the convergence of stochastic gradient descent suffers when using class weights differing by a couple orders of magnitude and smaller batch sizes.
Jason Brownlee has put together a list of tactics for dealing with imbalanced classes that might also be useful to you.
How should I approach a situtation when I try to apply some ML algorithm (classification, to be more specific, SVM in particular) over some high dimensional input, and the results I get are not quite satisfactory?
1, 2 or 3 dimensional data can be visualized, along with the algorithm's results, so you can get the hang of what's going on, and have some idea how to aproach the problem. Once the data is over 3 dimensions, other than intuitively playing around with the parameters I am not really sure how to attack it?
What do you do to the data? My answer: nothing. SVMs are designed to handle high-dimensional data. I'm working on a research problem right now that involves supervised classification using SVMs. Along with finding sources on the Internet, I did my own experiments on the impact of dimensionality reduction prior to classification. Preprocessing the features using PCA/LDA did not significantly increase classification accuracy of the SVM.
To me, this totally makes sense from the way SVMs work. Let x be an m-dimensional feature vector. Let y = Ax where y is in R^n and x is in R^m for n < m, i.e., y is x projected onto a space of lower dimension. If the classes Y1 and Y2 are linearly separable in R^n, then the corresponding classes X1 and X2 are linearly separable in R^m. Therefore, the original subspaces should be "at least" as separable as their projections onto lower dimensions, i.e., PCA should not help, in theory.
Here is one discussion that debates the use of PCA before SVM: link
What you can do is change your SVM parameters. For example, with libsvm link, the parameters C and gamma are crucially important to classification success. The libsvm faq, particularly this entry link, contains more helpful tips. Among them:
Scale your features before classification.
Try to obtain balanced classes. If impossible, then penalize one class more than the other. See more references on SVM imbalance.
Check the SVM parameters. Try many combinations to arrive at the best one.
Use the RBF kernel first. It almost always works best (computationally speaking).
Almost forgot... before testing, cross validate!
EDIT: Let me just add this "data point." I recently did another large-scale experiment using the SVM with PCA preprocessing on four exclusive data sets. PCA did not improve the classification results for any choice of reduced dimensionality. The original data with simple diagonal scaling (for each feature, subtract mean and divide by standard deviation) performed better. I'm not making any broad conclusion -- just sharing this one experiment. Maybe on different data, PCA can help.
Some suggestions:
Project data (just for visualization) to a lower-dimensional space (using PCA or MDS or whatever makes sense for your data)
Try to understand why learning fails. Do you think it overfits? Do you think you have enough data? Is it possible there isn't enough information in your features to solve the task you are trying to solve? There are ways to answer each of these questions without visualizing the data.
Also, if you tell us what the task is and what your SVM output is, there may be more specific suggestions people could make.
You can try reducing the dimensionality of the problem by PCA or the similar technique. Beware that PCA has two important points. (1) It assumes that the data it is applied to is normally distributed and (2) the resulting data looses its natural meaning (resulting in a blackbox). If you can live with that, try it.
Another option is to try several parameter selection algorithms. Since SVM's were already mentioned here, you might try the approach of Chang and Li (Feature Ranking Using Linear SVM) in which they used linear SVM to pre-select "interesting features" and then used RBF - based SVM on the selected features. If you are familiar with Orange, a python data mining library, you will be able to code this method in less than an hour. Note that this is a greedy approach which, due to its "greediness" might fail in cases where the input variables are highly correlated. In that case, and if you cannot solve this problem with PCA (see above), you might want to go to heuristic methods, which try to select best possible combinations of predictors. The main pitfall of this kind of approaches is the high potential of overfitting. Make sure you have a bunch "virgin" data that was not seen during the entire process of model building. Test your model on that data only once, after you are sure that the model is ready. If you fail, don't use this data once more to validate another model, you will have to find a new data set. Otherwise you won't be sure that you didn't overfit once more.
List of selected papers on parameter selection:
Feature selection for high-dimensional genomic microarray data
Oh, and one more thing about SVM. SVM is a black box. You better figure out what is the mechanism that generate the data and model the mechanism and not the data. On the other hand, if this would be possible, most probably you wouldn't be here asking this question (and I wouldn't be so bitter about overfitting).
List of selected papers on parameter selection
Feature selection for high-dimensional genomic microarray data
Wrappers for feature subset selection
Parameter selection in particle swarm optimization
I worked in the laboratory that developed this Stochastic method to determine, in silico, the drug like character of molecules
I would approach the problem as follows:
What do you mean by "the results I get are not quite satisfactory"?
If the classification rate on the training data is unsatisfactory, it implies that either
You have outliers in your training data (data that is misclassified). In this case you can try algorithms such as RANSAC to deal with it.
Your model(SVM in this case) is not well suited for this problem. This can be diagnozed by trying other models (adaboost etc.) or adding more parameters to your current model.
The representation of the data is not well suited for your classification task. In this case preprocessing the data with feature selection or dimensionality reduction techniques would help
If the classification rate on the test data is unsatisfactory, it implies that your model overfits the data:
Either your model is too complex(too many parameters) and it needs to be constrained further,
Or you trained it on a training set which is too small and you need more data
Of course it may be a mixture of the above elements. These are all "blind" methods to attack the problem. In order to gain more insight into the problem you may use visualization methods by projecting the data into lower dimensions or look for models which are suited better to the problem domain as you understand it (for example if you know the data is normally distributed you can use GMMs to model the data ...)
If I'm not wrong, you are trying to see which parameters to the SVM gives you the best result. Your problem is model/curve fitting.
I worked on a similar problem couple of years ago. There are tons of libraries and algos to do the same. I used Newton-Raphson's algorithm and a variation of genetic algorithm to fit the curve.
Generate/guess/get the result you are hoping for, through real world experiment (or if you are doing simple classification, just do it yourself). Compare this with the output of your SVM. The algos I mentioned earlier reiterates this process till the result of your model(SVM in this case) somewhat matches the expected values (note that this process would take some time based your problem/data size.. it took about 2 months for me on a 140 node beowulf cluster).
If you choose to go with Newton-Raphson's, this might be a good place to start.