I am new to python and machine learning. I am trying to cluster my dataset by using the DBSCAN algorithm. But I am stuck with getting correct values for MinPts and eps. I checked several solutions and didn't find a way to choose the values for those parameters. How can I choose those value, better if can explain it briefly.
In the original publication (section 4.2) of DBSCAN the authors proposed a way to determine good values for MinPoints and eps.
They also ran tests that show that you can elimiate the MinPoints parameter for a 2-dimensional dataset by always using MinPoints = 4. Because there results for values greater than 5 are not significantly different than the ones with MinPoints = 4 but they are computationaly more expensive.
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I was reading through all (or most) previously asked questions, but couldn't find an answer to my problem...
I have 13 variables measured on an ordinal scale (thy represent knowledge transfer channels), which I want to cluster (HCA) for a following binary logistic regression analysis (including all 13 variables is not possible due to sample size of N=208). A Factor Analysis seems inappropriate due to the scale level. I am using SPSS (but tried R as well).
Questions:
1: Am I right in using the Chi-Squared measure for count data instead of the (squared) euclidian distance?
2. How can I justify a choice of method? I tried single, complete, Ward and average, but all give different results and I can't find a source to base my decision on.
Thanks a lot in advance!
Answer 1: Since the variables are on ordinal scale, the chi-square test is an appropriate measurement test. Because, "A Chi-square test is designed to analyze categorical data. That means that the data has been counted and divided into categories. It will not work with parametric or continuous data (such as height in inches)." Reference.
Again, ordinal scaled data is essentially count or frequency data you can use regular parametric statistics: mean, standard deviation, etc Or non-parametric tests like ANOVA or Mann-Whitney U test to compare 2 groups or Kruskal–Wallis H test to compare three or more groups.
Answer 2: In a clustering problem, the choice of distance method solely depends upon the type of variables. I recommend you to read these detailed posts 1, 2,3
I have used the ELKI implementation of DBSCAN to identify fire hot spot clusters from a fire data set and the results look quite good. The data set is spatial and the clusters are based on latitude, longitude. Basically, the DBSCAN parameters identify hot spot regions where there is a high concentration of fire points (defined by density). These are the fire hot spot regions.
My question is, after experimenting with several different parameters and finding a pair that gives a reasonable clustering result, how does one validate the clusters?
Is there a suitable formal validation method for my use case? Or is this subjective depending on the application domain?
ELKI contains a number of evaluation functions for clusterings.
Use the -evaluator parameter to enable them, from the evaluation.clustering.internal package.
Some of them will not automatically run because they have quadratic runtime cost - probably more than your clustering algorithm.
I do not trust these measures. They are designed for particular clustering algorithms; and are mostly useful for deciding the k parameter of k-means; not much more than that. If you blindly go by these measures, you end up with useless results most of the time. Also, these measures do not work with noise, with either of the strategies we tried.
The cheapest are the label-based evaluators. These will automatically run, but apparently your data does not have labels (or they are numeric, in which case you need to set the -parser.labelindex parameter accordingly). Personally, I prefer the Adjusted Rand Index to compare the similarity of two clusterings. All of these indexes are sensitive to noise so they don't work too well with DBSCAN, unless your reference has the same concept of noise as DBSCAN.
If you can afford it, a "subjective" evaluation is always best.
You want to solve a problem, not a number. That is the whole point of "data science", being problem oriented and solving the problem, not obsessed with minimizing some random quality number. If the results don't work in reality, you failed.
There are different methods to validate a DBSCAN clustering output. Generally we can distinguish between internal and external indices, depending if you have labeled data available or not. For DBSCAN there is a great internal validation indice called DBCV.
External Indices:
If you have some labeled data, external indices are great and can demonstrate how well the cluster did vs. the labeled data. One example indice is the RAND indice.https://en.wikipedia.org/wiki/Rand_index
Internal Indices:
If you don't have labeled data, then internal indices can be used to give the clustering result a score. In general the indices calculate the distance of points within the cluster and to other clusters and try to give you a score based on the compactness (how close are the points to each other in a cluster?) and
separability (how much distance is between the clusters?).
For DBSCAN, there is one great internal validation indice called DBCV by Moulavi et al. Paper is available here: https://epubs.siam.org/doi/pdf/10.1137/1.9781611973440.96
Python package: https://github.com/christopherjenness/DBCV
I am working on a UCI data set about wine quality. I have applied multiple classifiers and k-nearest neighbor is one of them. I was wondering if there is a way to find the exact value of k for nearest neighbor using 5-fold cross validation. And if yes, how do I apply that? And how can I get the depth of a decision tree using 5-fold CV?
Thanks!
I assume here that you mean the value of k that returns the lowest error in your wine quality model.
I find that a good k can depend on your data. Sparse data might prefer a lower k whereas larger datasets might work well with a larger k. In most of my work, a k between 5 and 10 have been quite good for problems with a large number of cases.
Trial and Error can at times be the best tool here, but it shouldn't take too long to see a trend in the modelling error.
Hope this Helps!
What kind of knowledge/ inference can be made from k means clustering analysis of KDDcup99 dataset?
We ploted some graphs using matlab they looks like this:::
Experiment 1: Plot of dst_host_count vs serror_rate
Experiment 2: Plot of srv_count vs srv_serror_rate
Experiment 3: Plot of count vs serror_rate
I just extracted saome features from kddcup data set and ploted them.....
The main problem am facing is due to lack of domain knowledge I cant determine what inference can be drawn form this graphs another one is if I have chosen wrong axis then what should be the correct chosen feature?
I got very less time to complete this thing so I don't understand the backgrounds very well
Any help telling the interpretation of these graphs would be helpful
What kind of unsupervised learning can be made using this data and plots?
Just to give you some domain knowledge: the KDD cup data set contains information about different aspects of network connections. Each sample contains 'connection duration', 'protocol used', 'source/destination byte size' and many other features that describes one connection connection. Now, some of these connections are malicious. The malicious samples have their unique 'fingerprint' (unique combination of different feature values) that separates them from good ones.
What kind of knowledge/ inference can be made from k means clustering analysis of KDDcup99 dataset?
You can try k-means clustering to initially cluster the normal and bad connections. Also, the bad connections falls into 4 main categories themselves. So, you can try k = 5, where one cluster will capture the good ones and other 4 the 4 malicious ones. Look at the first section of the tasks page for details.
You can also check if some dimensions in your data set have high correlation. If so, then you can use something like PCA to reduce some dimensions. Look at the full list of features. After PCA, your data will have a simpler representation (with less number of dimensions) and might give better performance.
What should be the correct chosen feature?
This is hard to tell. Currently data is very high dimensional, so I don't think trying to visualize 2/3 of the dimensions in a graph will give you a good heuristics on what dimensions to choose. I would suggest
Use all the dimensions for for training and testing the model. This will give you a measure of the best performance.
Then try removing one dimension at a time to see how much the performance is affected. For example, you remove the dimension 'srv_serror_rate' from your data and the model performance comes out to be almost the same. Then you know this dimension is not giving you any important info about the problem at hand.
Repeat step two until you can't find any dimension that can be removed without hurting performance.
First, sorry by the tag as "ANOVA", it is about MANOVA (yet to become a tag...)
From the tutorials I found, all the examples use small matrices, following them would not be feasible for the case of big ones as it is the case of many studies.
I got 2 matrices for my 14 sampling points, 1 for the organisms IDs (4493 IDs) and other to chemical profile (190 variables).
The 2 matrices were correlated by spearman and based on the correlation, split in 4 clusters (k-means regarding the square euclidian clustering values), the IDs on the row and chemical profile on line.
The differences among them are somewhat clear, but to have it in a more robust way I want to perform MANOVA to show the differences between and within the clusters - that is a key factor for the conclusion, of course.
Problem is that, after 8h trying, could not even input the data in a format acceptable to the analysis.
The tutorials I found are designed to very few variables and even when I think I overcame that, the program says that my matrices can't be compared by their difference in length.
Each cluster has its own set of IDs sharing all same set of variables.
What should I do?
Thanks in advance.
Diogo Ogawa
If you have missing values in your data (which practically all data sets seem to contain) you can either remove those observations or you can create a model using those observations. Use the first approach if something about your methodology gives you conviction that there is something different about those observations. Most of the time, it is better to run the model using the missing values. In this case, use the general linear model instead of a balanced ANOVA model. The balanced model will struggle with those missing data.