Another general question on data science!
Let's say I have a bunch of samples and I have to detect outliers on each sample. My data would be univariate, so I can use simple methods like standard deviation or median absolute deviation.
Now my question is: how would one do any sort of validation to see if results are coherent, especially if looking at them by eye wouldn't be an option because of the size of the data? For example to choose how many standard deviations to use to define outliers. I haven't seen any quantitative method so far. Does it even exist?
Cheers
Interestingly you didn't define the dimension of "size of the data". Which is I think important here. E.g., you can draw a q-q plot for high-dimensional data but not that easy for many data-points.
However, when looking for a general methodology I would attack this problem from a probabilistic perspective. This will never tell you which data point is an outlier, however, it will tell you what is the probability that you have an outlier (in certain areas of your data).
I have to make two assumptions (a) you know the family of distribution your data stems from, e.g., normal or poisson (b) you can estimate the parameters of this family given a data set.
Now you can define the Hypothesis that you data is from this Distribution and the alternative Hypothesis (H0) that the data is not from this distribution. If you draw a random sample from your estimated distribution, this drawn distribution should be on average as likely to come from the distribution as your observed sample. If this is not the case
However, probably more interesting is to find the sub-space which contains the outlier. This can be done with the following empirical procedure. If you now estimate the parameters of your distribution given your by Data. You can compare the estimated distribution with the histogram of the seen data. This gives you for each bin of the histogram a probability that ic contains an outlier. For high dimensional data this can be checked programtically.
Related
Will it be a good idea to exclude the noisy data( which may reduce model accuracy or cause unexpected output for testing dataset) from a dataset to generate the training and validation dataset ?
Assumption: Noisy data is pre-known to us
Any suggestion is deeply appreciated!
It depends on your application. If the noisy data is valid, then definitely include it to find the best model.
However, if the noisy data is invalid, then it should be cleaned out before fitting your model.
Noise is a broad term, you better consider them as inliers or outliers instead.
Most of the outliers detection algorithms specify a threshold and sort the outliers candidates according to some given score. In this case, you can choose to eradicate the most extreme values. Say for example 3xSTD far from the mean (of course that is in case you have a Gaussian-like distributed data set).
So my suggestion is to build your judgement based on two things:
Your business concept and logic about validity vs invalidity. For example: A house size, area or price cannot be a negative number.
Your mathematical / algorithmic logic. For example: Detect extreme values based on some threshold to decide (along with / without point no. 1) whether it is a valid observation or not.
Noisy data doesn't cause a huge problem themselves. The extreme noisy data (i.e. extreme values / outliers) are those you should really concern about!
Such points would adjust the hypothesis of your model while fitting the data. Hence, results might be drastically shifted / incorrect.
Finally, you can look at Pyod open-source Pythonic toolbox which contains a lot of different algorithms implemented off-the-shelf. (You can choose more than one algorithm and create a voting pool to decide the extremeness of the observations).
You can use Multivariate Gaussian Distribution for outlier Detection in python. It is the best method.
I'm interested in a statistical classification problem. Given a feature vector X, I would like to classify X as either "yes" or "no". However, the training data will be fed in real-time based on human input. For instance, if the user sees feature vector X, the user will assign "yes" or "no" based on their expertise.
Rather than doing grid search on parameter space, I would like to more intelligently explore the parameter space based on the previously submitted data. For example, if there is a dense cluster of "no's" in part of the parameter space, it probably doesn't make sense to keep sampling there - it's probably just going to be more "no's".
How can I go about doing this? The C4.5 algorithm seems to be up this alley, but I'm unsure if this is the way to go.
An additional subtlety is that some of the features might be specifying random data. Suppose that the first two attributes in the feature vector specify the mean and variance of a gaussian distribution. The data the user classifies could be significantly different, even if all parameters are held equal.
For example, let's say the algorithm displays a sine wave with gaussian noise added, where the gaussian distribution is specified by the mean and variance in the feature vector. The user is asked "does this graph represent a sine wave?" Two very similar values in mean or variance could still have significantly different graphs.
Is there an algorithm designed to handle such cases?
The setting that you're talking about fits in the broad area of Active Learning. This topic addresses the iterative process of model building, and choosing which training examples to query next in order to optimize model performance. Here, the training cost of each data point is roughly the same, and there are no additional variable rewards in the learning phase.
However, in each iteration, if you have a variable reward which is a function of the data point chosen, you would want to look at Multi-Armed Bandits and Reinforcement Learning.
The other issue that you're talking about is one of finding the right features to represent your data points, and should be handled separately.
I've got a problem where I've potentially got a huge number of features. Essentially a mountain of data points (for discussion let's say it's in the millions of features). I don't know what data points are useful and what are irrelevant to a given outcome (I guess 1% are relevant and 99% are irrelevant).
I do have the data points and the final outcome (a binary result). I'm interested in reducing the feature set so that I can identify the most useful set of data points to collect to train future classification algorithms.
My current data set is huge, and I can't generate as many training examples with the mountain of data as I could if I were to identify the relevant features, cut down how many data points I collect, and increase the number of training examples. I expect that I would get better classifiers with more training examples given fewer feature data points (while maintaining the relevant ones).
What machine learning algorithms should I focus on to, first,
identify the features that are relevant to the outcome?
From some reading I've done it seems like SVM provides weighting per feature that I can use to identify the most highly scored features. Can anyone confirm this? Expand on the explanation? Or should I be thinking along another line?
Feature weights in a linear model (logistic regression, naive Bayes, etc) can be thought of as measures of importance, provided your features are all on the same scale.
Your model can be combined with a regularizer for learning that penalises certain kinds of feature vectors (essentially folding feature selection into the classification problem). L1 regularized logistic regression sounds like it would be perfect for what you want.
Maybe you can use PCA or Maximum entropy algorithm in order to reduce the data set...
You can go for Chi-Square tests or Entropy depending on your data type. Supervized discretization highly reduces the size of your data in a smart way (take a look into Recursive Minimal Entropy Partitioning algorithm proposed by Fayyad & Irani).
If you work in R, the SIS package has a function that will do this for you.
If you want to do things the hard way, what you want to do is feature screening, a massive preliminary dimension reduction before you do feature selection and model selection from a sane-sized set of features. Figuring out what is the sane-size can be tricky, and I don't have a magic answer for that, but you can prioritize what order you'd want to include the features by
1) for each feature, split the data in two groups by the binary response
2) find the Komogorov-Smirnov statistic comparing the two sets
The features with the highest KS statistic are most useful in modeling.
There's a paper "out there" titled "A selctive overview of feature screening for ultrahigh-dimensional data" by Liu, Zhong, and Li, I'm sure a free copy is floating around the web somewhere.
4 years later I'm now halfway through a PhD in this field and I want to add that the definition of a feature is not always simple. In the case that your features are a single column in your dataset, the answers here apply quite well.
However, take the case of an image being processed by a convolutional neural network, for example, a feature is not one pixel of the input, rather it's much more conceptual than that. Here's a nice discussion for the case of images:
https://medium.com/#ageitgey/machine-learning-is-fun-part-3-deep-learning-and-convolutional-neural-networks-f40359318721
I have a collection of documents related to a particular domain and have trained the centroid classifier based on that collection. What I want to do is, I will be feeding the classifier with documents from different domains and want to determine how much they are relevant to the trained domain. I can use the cosine similarity for this to get a numerical value but my question is what is the best way to determine the threshold value?
For this, I can download several documents from different domains and inspect their similarity scores to determine the threshold value. But is this the way to go, does it sound statistically good? What are the other approaches for this?
Actually there is another issue with centroids in sparse vectors. The problem is that they usually are significantly less sparse than the original data. For examples, this increases computation costs. And it can yield vectors that are themselves actually atypical because they have a different sparsity pattern. This effect is similar to using arithmetic means of discrete data: say the mean number of doors in a car is 3.4; yet obviously no car exists that actually has 3.4 doors. So in particular, there will be no car with an euclidean distance of less than 0.4 to the centroid! - so how "central" is the centroid then really?
Sometimes it helps to use medoids instead of centroids, because they actually are proper objects of your data set.
Make sure you control such effects on your data!
A simple method to try would be to employ various machine-learning algorithms - and in particular, tree-based ones - on the distances from your centroids.
As mentioned in another answer(#Anony-Mousse), this won't necessarily provide you with good or usable answers, but it just might. Using a ML framework for this procedure, E.g. WEKA, will also help you with estimating your accuracy in a more rigorous manner.
Here are the steps to take, using WEKA:
Generate a train set by finding a decent amount of documents representing each of your classes (to get valid estimations, I'd recommend at least a few dozens per class)
Calculate the distance from each document to each of your centroids.
Generate a feature vector for each such document, composed of the distances from this document to the centroids. You can either use a single feature - the distance to the nearest centroid; or use all distances, if you'd like to try a more elaborate thresholding scheme. For example, if you chose the simpler method of using a single feature, the vector representing a document with a distance of 0.2 to the nearest centroid, belonging to class A would be: "0.2,A"
Save this set in ARFF or CSV format, load into WEKA, and try classifying, e.g. using a J48 tree.
The results would provide you with an overall accuracy estimation, with a detailed confusion matrix, and - of course - with a specific model, e.g. a tree, you can use for classifying additional documents.
These results can be used to iteratively improve the models and thresholds by collecting additional train documents for problematic classes, either by recreating the centroids or by retraining the thresholds classifier.
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.