Often it is useful to train a model once on a large amount of data, and then query the model repeatedly with small amounts of new data. That is, given new information it might make sense to create a new cluster, split an existing cluster, or merge two previously separate clusters.

If the actual clusters and hence their labels change with each new data point it becomes impossible to compare the cluster assignments between such queries. This allows for a very inexpensive operation to compute a predicted cluster for the new data point.

This ensures that HDBSCAN does a little extra computation when fitting the model that can dramatically speed up the prediction queries later. We can plot them in black to see where they happen to fall. If you have a single point be sure to wrap it in a list. The result is a set of labels as you can see.

Many of the points as classified as noise, but several are also assigned to clusters. We can also visualize how this worked, coloring the new data points by the cluster to which they were assigned. It is as simple as that. So now you can get started using HDBSCAN as a streaming clustering service — just be sure to cache your data and retrain your model periodically to avoid drift! Read the Docs v: latest Versions latest stable 0.While articles and blog posts about clustering using numerical variables on the net are abundant, it took me some time to find solutions for categorical data, which is, indeed, less straightforward if you think of it.

Methods for categorical data clustering are still being developed — I will try one or the other in a different post. Nobody wants to do this. Clustering could appear to be useful. So this post is all about sharing what I wish I bumped into when I started with clustering. The clustering process itself contains 3 distinctive steps:. This post is going to be sort of beginner level, covering the basics and implementation in R.

D issimilarity Matrix Arguably, this is the backbone of your clustering. Dissimilarity matrix is a mathematical expression of how different, or distant, the points in a data set are from each other, so you can later group the closest ones together or separate the furthest ones — which is a core idea of clustering.

This is the step where data types differences are important as dissimilarity matrix is based on distances between individual data points. While it is quite easy to imagine distances between numerical data points remember Eucledian distancesas an example?

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In order to calculate a dissimilarity matrix in this case, you would go for something called Gower distance. Done with a dissimilarity matrix. In reality, it is quite likely that you will have to clean the dataset first, perform the necessary transformations from strings to factors and keep an eye on missing values.

In my own case, the dataset contained rows of missing values, which nicely clustered together every time, leading me to assume that I found a treasure until I had a look at the values meh! C lustering Algorithms You could have heard that there is k-means and hierarchical clustering. In this post, I focus on the latter as it is a more exploratory type, and it can be approached differently: you could choose to follow either agglomerative bottom-up or divisive top-down way of clustering.

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Agglomerative clustering will start with n clusters, where n is the number of observations, assuming that each of them is its own separate cluster. Then the algorithm will try to find most similar data points and group them, so they start forming clusters.

In contrast, divisive clustering will go the other way around — assuming all your n data points are one big cluster and dividing most dissimilar ones into separate groups. If you are thinking which one of them to use, it is always worth trying all the options, but in general, agglomerative clustering is better in discovering small clusters, and is used by most software; divisive clustering — in discovering larger clusters.

I personally like having a look at dendrograms — graphical representation of clustering first to decide which method I will stick to. As you will see below, some of dendrograms will be pretty balancedwhile others will look like a mess.

hdbscan categorical data

A ssessing clusters Here, you will decide between different clustering algorithms and a different number of clusters. As it often happens with assessment, there is more than one way possible, complemented by your own judgement. Working with categorical variables, you might end up with non-sense clusters because the combination of their values is limited — they are discrete, so is the number of their combinations. In the end, it all comes to your goal and what you do your analysis for.

Conceptually, when clusters are created, you are interested in distinctive groups of data points, such that the distance between them within clusters or compactness is minimal while the distance between groups separation is as large as possible.

This is intuitively easy to understand: distance between points is a measure of their dissimilarity derived from dissimilarity matrix. Hence, the assessment of clustering is built around evaluation of compactness and separation.But in exchange, you have to tune two other parameters.

The eps parameter is the maximum distance between two data points to be considered in the same neighborhood. The algorithm will determine a number of clusters based on the density of a region. The thinking is that these two parameters are much easier to choose for some clustering problems. Use a new Python session so that memory is clear and you have a clean slate to work with. After running those two statements, you should not see any messages from the interpreter.

The variable iris should contain all the data from the iris. Check what parameters were used by typing the following code into the interpreter:.

Hierarchical Clustering on Categorical Data in R

Note, however, that the figure closely resembles a two-cluster solution: It shows only 17 instances of label — 1.

You can increase the distance parameter eps from the default setting of 0. The distance parameter is the maximum distance an observation is to the nearest cluster. The greater the value for the distance parameter, the fewer clusters are found because clusters eventually merge into other clusters. The —1 labels are scattered around Cluster 1 and Cluster 2 in a few locations:.

The graph only shows a two-dimensional representation of the data. The distance can also be measured in higher dimensions. Its performance was pretty consistent with other clustering algorithms that end up with a two-cluster solution.

Anasse Bari, Ph. Mohamed Chaouchi is a veteran software engineer who has conducted extensive research using data mining methods.

Tommy Jung is a software engineer with expertise in enterprise web applications and analytics.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. The dark mode beta is finally here. Change your preferences any time.

Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. This is a key strength of it, it can easily be applied to various kinds of data, all you need is to define a distance function and thresholds.

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You can prune some of these computations this is where the index comes into playbut essentially you need to compare every object to every other object, so it is in O n log n and not one-pass. One-pass: I believe the original k-means was a one-pass algorithm. The first k objects are your initial means.

For every new object, you choose the closes mean and update it incrementally with the new object.

hdbscan categorical data

As long as you don't do another iteration over your data set, this was "one-pass". The result will be even worse than lloyd-style k-means though.

If this is longer than the closest distance between any two of the k items, you can swap the new item with one of these two and at least not decrease the closest distance between any two of the new k items. Do so so as to increase this distance as much as possible. Then after running this algorithm, you will retain at least one point from each cluster.

Learn more. Asked 9 years ago. Active 8 years, 2 months ago. Viewed 4k times. And what is a one pass clustering algorithm? Could you provide pseudo code for a one pass clustering algorithm? Active Oldest Votes. Read the first k items and hold them. Compute the distances between them.There are a lot of clustering algorithms to choose from. The standard sklearn clustering suite has thirteen different clustering classes alone. So what clustering algorithms should you be using?

As with every question in data science and machine learning it depends on your data. A number of those thirteen classes in sklearn are specialised for certain tasks such as co-clustering and bi-clustering, or clustering features instead data points.

Obviously an algorithm specializing in text clustering is going to be the right choice for clustering text data, and other algorithms specialize in other specific kinds of data. Thus, if you know enough about your data, you can narrow down on the clustering algorithm that best suits that kind of data, or the sorts of important properties your data has, or the sorts of clustering you need done.

So, what algorithm is good for exploratory data analysis? There are other nice to have features like soft clusters, or overlapping clusters, but the above desiderata is enough to get started with because, oddly enough, very few clustering algorithms can satisfy them all! Next we need some data. So, on to testing ….

Before we try doing the clustering, there are some things to keep in mind as we look at the results.

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K-Means has a few problems however. That leads to the second problem: you need to specify exactly how many clusters you expect. If you know a lot about your data then that is something you might expect to know.

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Finally K-Means is also dependent upon initialization; give it multiple different random starts and you can get multiple different clusterings.

This does not engender much confidence in any individual clustering that may result. K-Means scores very poorly on this point. Best to have many runs and check though. There are few algorithms that can compete with K-Means for performance.

If you have truly huge data then K-Means might be your only option. But enough opinion, how does K-Means perform on our test dataset?I was recently asked to give a lightning talk regarding a clustering algorithm called HDBScan. HDBScan is based on the DBScan algorithm, and like other clustering algorithms it is used to group like data together. I covered three main topics during the talk: advantages of HDBScan, implementation, and how it works. Regular DBScan is amazing at clustering data of varying shapes, but falls short of clustering data of varying density.

You can see that there is one main center cluster and noise on the left and right. After playing with the parameters, below is how DBScan performed. Below is how HDBScan performed.

I was able to get only one cluster, which I was looking for. Unfortunately, no algorithm is perfect and it did put some of the noise into the purple cluster, but it was closer to what I was looking for than regular DBScan. HDScan is a separate library from scikitlearn so you will either have to pip install it or conda install it.

Both algorithms have the minimum number of samples parameter which is the neighbor threshold for a record to become a core point. DBScan has the parameter epsilon, which is the radius those neighbors have to be in for the core to form. HDBScan has the parameter minimum cluster size, which is how big a cluster needs to be in order to form. This is more intuitive than epsilon because you probably have an idea of how big your clusters need to be to make actionable decisions on them.

How It Works. Both algorithms start by finding the core distance of each point, which is the distance between that point and its farthest neighbor defined by the minimum samples parameter. The potential clusters can form a dendogram, and the cutoff point for DBScan on the dendogram is epsilon. HDBScan approaches this differently by throwing out the tiny off shoots, and instead keeping the biggest clusters as defined by the minimum cluster size parameter.

This results in a more condensed dendogram as seen below. Overall, HDBScan seems like a great algorithm.Released: Mar 19, View statistics for this project via Libraries.

Tags cluster, clustering, density, hierarchical. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. In practice this means that HDBSCAN returns a good clustering straight away with little or no parameter tuning — and the primary parameter, minimum cluster size, is intuitive and easy to select.

McInnes L, Healy J. Campello, D. Moulavi, and J. The hdbscan package inherits from sklearn classes, and thus drops in neatly next to other sklearn clusterers with an identical calling API. Significant effort has been put into making the hdbscan implementation as fast as possible.

The hdbscan package comes equipped with visualization tools to help you understand your clustering results. After fitting data the clusterer object has attributes for:. All of which come equipped with methods for plotting and converting to Pandas or NetworkX for further analysis. The clusterer objects also have an attribute providing cluster membership strengths, resulting in optional soft clustering and no further compute expense.

Finally each cluster also receives a persistence score giving the stability of the cluster over the range of distance scales present in the data. This provides a measure of the relative strength of clusters. The result is a vector of score values, one for each data point that was fit.

hdbscan categorical data

Higher scores represent more outlier like objects. Selecting outliers via upper quantiles is often a good approach. The hdbscan package also provides support for the robust single linkage clustering algorithm of Chaudhuri and Dasgupta. The robust single linkage hierarchy is available as an attribute of the robust single linkage clusterer, again with the ability to plot or export the hierarchy, and to extract flat clusterings at a given cut level and gamma value.

The hdbscan library supports both Python 2 and Python 3. However we recommend Python 3 as the better option if it is available to you. For simple issues you can consult the FAQ in the documentation. If your issue is not suitably resolved there, please check the issues on github.

Finally, if no solution is available there feel free to open an issue ; the authors will attempt to respond in a reasonably timely fashion. We welcome contributions in any form! Assistance with documentation, particularly expanding tutorials, is always welcome.

What is a Categorical Variable?

To contribute please fork the project make your changes and submit a pull request. We will do our best to work through any issues with you and get your code merged into the main branch.

If you have used this codebase in a scientific publication and wish to cite it, please use the Journal of Open Source Software article. To reference the high performance algorithm developed in this library please cite our paper in ICDMW proceedings.

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