Is it possible to apply RandomForests to very small datasets?
I have a dataset with many variables but only 25 observation each. Random forests produce reasonable results with low OOB errors (10-25%).
Is there any rule of thumb regarding the minimum number of observations to use?
In fact one of the response variable is unbalanced, and if I'm going to subsample it I will end up with an even smaller number of observations.
Thanks in advance
Absolutely RF can be used on these type of datasets (i.e. p>n). In fact they use RF in fields like genomics where the number of fields >= 20000 and there are only a very small number of rows - say 10-12. The entire problem is figuring out which of the 20k variables would make up a parsimonious marker (i.e. feature selection is the entire problem).
I don't have any ROTs about minimum size other than if your model doesn't work well on a held back sample (or Hold-One-Back cross validation might work well in your case) well then you should try something else.
Hope this helps
Related
I am dealing with a repeating pattern in time series data. My goal is to classify every pattern as 1, and anything that does not follow the pattern as 0. The pattern repeats itself between every two peaks as shown below in the image.
The patterns are not necessarily fixed in sample size but stay within approximate sample size, let's say 500samples +-10%. The heights of the peaks can change. The random signal (I called it random, but basically it means not following pattern shape) can also change in value.
The data is from a sensor. Patterns are when the device is working smoothly. If the device is malfunctioning, then I will not see the patterns and will get something similar to the class 0 I have shown in the image.
What I have done so far is building a logistic regression model. Here are my steps for data preparation:
Grab data between every two consecutive peaks, resample it to a fixed size of 100 samples, scale data to [0-1]. This is class 1.
Repeated step 1 on data between valley and called it class 0.
I generated some noise, and repeated step 1 on chunk of 500 samples to build extra class 0 data.
Bottom figure shows my predictions on the test dataset. Prediction on the noise chunk is not great. I am worried in the real data I may get even more false positives. Any idea on how I can improve my predictions? Any better approach when there is no class 0 data available?
I have seen similar question here. My understanding of Hidden Markov Model is limited but I believe it's used to predict future data. My goal is to classify a sliding window of 500 sample throughout my data.
I have some proposals, that you could try out.
First, I think in this field often recurrent neural networks are used (e.g. LSTMs). But I also heard that some people also work with tree based method like light gbm (I think Aileen Nielsen uses this approach).
So if you don't want to dive into neural networks, which is probably not necessary, because your signals seem to be distinguishable relative easily, you can give light gbm (or other tree ensamble methods) a chance.
If you know the maximum length of a positive sample, you can define the length of your "sliding sample-window" that becomes your input vector (so each sample in the sliding window becomes one input feature), then I would add an extra attribute with the number of samples when the last peak occured (outside/before the sample window). Then you can check in how many steps you let your window slide over the data. This also depends on the memory you have available for this.
But maybe it would be wise then to skip some of the windows between a change between positive and negative, because the states might not be classifiable unambiguously.
In case memory becomes an issue, neural networks could be the better choice, because for training they do not need all training data available at once, so you can generate your input data in batches. With tree based methods this possible does not exist or only in a very limited way.
I'm not sure of what you are trying to achieve.
If you want to characterize what is a peak or not - which is an after the facts classification - then you can use a simple rule to define peaks such as signal(t) - average(signal, t-N to t) > T, with T a certain threshold and N a number of data points to look backwards to.
This would qualify what is a peak (class 1) and what is not (class 0), hence does a classification of patterns.
If your goal is to predict that a peak is going to happen few time units before the peak (on time t), using say data from t-n1 to t-n2 as features, then logistic regression might not necessarily be the best choice.
To find the right model you have to start with visualizing the features you have from t-n1 to t-n2 for every peak(t) and see if there is any pattern you can find. And it can be anything:
was there a peak in in the n3 days before t ?
is there a trend ?
was there an outlier (transform your data into exponential)
in order to compare these patterns, think of normalizing them so that the n2-n1 data points go from 0 to 1 for example.
If you find a pattern visually then you will know what kind of model is likely to work, on which features.
If you don't then it's likely that the white noise you added will be as good. so you might not find a good prediction model.
However, your bottom graph is not so bad; you have only 2 major false positives out of >15 predictions. This hints at better feature engineering.
The whole point of using an SVM is that the algorithm will be able to decide whether an input is true or false etc etc.
I am trying to use an SVM for predictive maintenance to predict how likely a system is to overheat.
For my example, the range is 0-102°C and if the temperature reaches 80°C or above it's classed as a failure.
My inputs are arrays of 30 doubles(the last 30 readings).
I am making some sample inputs to train the SVM and I was wondering if it is good practice to pass in very specific data to train it - eg passing in arrays 80°C, 81°C ... 102°C so that the model will automatically associate these values with failure. You could do an array of 30 x 79°C as well and set that to pass.
This seems like a complete way of doing it, although if you input arrays like that - would it not be the same as hardcoding a switch statement to trigger when the temperature reads 80->102°C.
Would it be a good idea to pass in these "hardcoded" style arrays or should I stick to more random inputs?
If there is a finite set of possibilities I would really recommend using Naïve Bayes, as that method would fit this problem perfectly. However if you are forced to use an SVM, I would say that would be rather difficult. For starters the main idea with an SVM is to use it for classification, and the amount of scenarios does not really matter. The input is however seldom discrete, so I guess there usually are infinite scenarios. However, an SVM implemented normally would only give you a classification, unless you have 100 classes one for 1% another one for 2%, this wouldn't really solve problem.
The conclusion is that this could work, but it would not be considered "best practice". You can imagine your 30 dimensional vector space divided into 100 small sub spaces, and each datapoint, a 30x1 vector is a point in that vectorspace so that the probability is decided by which of the 100 subsets its in. However, having a 100 classes and not very clean or insufficient data, will lead to very bad, hard performing models.
Cheers :)
i am fairly new with statitistic.
I made an experiment and used the two way ANOVA with repeated measures. The calculation was done in SPSS. In most papers I have seen, the f-value and the degree of freedom were reported as well. is it normal to report those values as well? if so, which values do i take from the spss output.
how do I interpret these values? what do they mean?
when does the f-value support a significant result and when not?
what are good values for the f-value and the degree of freedom.
in some article is also read about the critical f-values, how do I get this value?
most articles describe how to calculate those values but do not explain their meaning for the experiment.
some clarification in these issues is greatly appreciated.
My English is not very good, but I will try to answer your question.
The main purpose of ANOVA is that we want statistical proof that the measured groups have the same mean or not. So we make a null hypothesis and an alternative hypothesis, then we use a test statistics on the data. You can use ANOVA if the groups has the same variance (squared standard deviation).
You need to test this. This is a hyptest too, the nullhyp. is the groups have the same variance, the anternative hyp. is they dont.
You need to make decision from the Sig. value, if the value is higher than 0,05, we usually accept the nullhyp. If the variances are equal, we can use ANOVA. (I assume that the data is following the Normal distribution.) The nullhyp. is that the groups have equal means, the alternative hyp is that we have at least 1 group with a different mean. You can make your decision from the Sig. value, as I said before, if the value higher than 0.05 we accept the nullhyp. The F-critical value is not important if you are calculating on a computer. You can make an accepting interval from the lower and the upper F-critical, and if the F-value is in the interval you accept the nullhyp, but I only used this method in statistics class. You don't need the F-value and the df in the report, because they don't explain anything on their own.
How can I test/check whether a given kernel (example: RBF/ polynomial) does really separate my data?
I would like to know if there is a method (not plotting the data of course) which can allow me to check if a given data set (labeled with two classes) can be separated in high dimensional space?
In short - no, there is no general way. However, for some kernels you can easily say that... everything is separable. This property, proved in many forms (among other by Schoenberg) says for example that if your kernel is of form K(x,y) = f(||x-y||^2) and f is:
ifinitely differentible
completely monotonic (which more or less means that if you take derivatives, then the first one is negative, next positive, next negative, ... )
positive
then it will always be able to separate every binary labeled, consistent dataset (there are no two points of the exact same label). Actually it says even more - that you can exactly interpolate, meaning, that even if it is a regression problem - you will get zero error. So in particular multi-class, multi-label problems also will be linearly solvable (there exists linear/multi-linear model which gives you a correct interpolation).
However, if the above properties do not hold, it does not mean that your data cannot be perfectly separated. This is only "one way" proof.
In particular, this class of kernels include RBF kernel, thus it will always be able to separate any training set (this is why it overfits so easily!)
So what about in the other way? Here you have to first fix hyperparameters of the kernel and then you can also answer it through optimization - solve hard-margin SVM problem (C=inf) and it will find a solution iff data is separable.
I'm implementing an one-versus-rest classifier to discriminate between neural data corresponding (1) to moving a computer cursor up and (2) to moving it in any of the other seven cardinal directions or no movement. I'm using an SVM classifier with an RBF kernel (created by LIBSVM), and I did a grid search to find the best possible gamma and cost parameters for my classifier. I have tried using training data with 338 elements from each of the two classes (undersampling my large "rest" class) and have used 338 elements from my first class and 7218 from my second one with a weighted SVM.
I have also used feature selection to bring the number of features I'm using down from 130 to 10. I tried using the ten "best" features and the ten "worst" features when training my classifier. I have also used the entire feature set.
Unfortunately, my results are not very good, and moreover, I cannot find an explanation why. I tested with 37759 data points, where 1687 of them came from the "one" (i.e. "up") class and the remaining 36072 came from the "rest" class. In all cases, my classifier is 95% accurate BUT the values that are predicted correctly all fall into the "rest" class (i.e. all my data points are predicted as "rest" and all the values that are incorrectly predicted fall in the "one"/"up" class). When I tried testing with 338 data points from each class (the same ones I used for training), I found that the number of support vectors was 666, which is ten less than the number of data points. In this case, the percent accuracy is only 71%, which is unusual since my training and testing data are the exact same.
Do you have any idea what could be going wrong? If you have any suggestions, please let me know.
Thanks!
Test dataset being same as training data implies your training accuracy was 71%. There is nothing wrong about it as the data was possibly not well separable by the kernel you used.
However, one point of concern is the number of support vectors being high suggests probable overfitting .
Not sure if this amounts to an answer - it would probably be hard to give one without actually seeing the data - but here are some ideas regarding the issue you describe:
In general, SVM tries to find a hyperplane that would best separate your classes. However, since you have opted for 1vs1 classification, you have no choice but to mix all negative cases together (your 'rest' class). This might make the 'best' separation much less fit to solve your problem. I'm guessing that this might be a major issue here.
To verify if that's the case, I suggest trying to use only one other cardinal direction as the negative set, and see if that improves results. In case it does, you can train 7 classifiers, one for each direction. Another option might be to use the multiclass option of libSVM, or a tool like SVMLight, which is able to classify one against many.
One caveat of most SVM implementations is their inability to support big differences between the positive and negative sets, even with weighting. From my experience, weighting factors of over 4-5 are problematic in many cases. On the other hand, since your variety in the negative side is large, taking equal sizes might also be less than optimal. Thus, I'd suggest using something like 338 positive examples, and around 1000-1200 random negative examples, with weighting.
A little off your question, I would have considered also other types of classification. To start with, I'd suggest thinking about knn.
Hope it helps :)