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ELKI: Running DBSCAN on custom Objects in Java

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问题 I'm trying to use ELKI from within JAVA to run DBSCAN. For testing I used a FileBasedDatabaseConnection. Now I would like to run DBSCAN with my custom Objects as parameters. My objects have the following structure: public class MyObject { private Long id; private Float param1; private Float param2; // ... and more parameters as well as getters and setters } I'd like to run DBSCAN within ELKI using a List<MyObject> as database, but only some of the parameters should be taken into account (e.g.

Running clustering algorithms in ELKI

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问题 I need to run a k-medoids clustering algorithm by using ELKI programmatically. I have a similarity matrix that I wish to input to the algorithm. Is there any code snippet available for how to run ELKI algorithms? I basically need to know how to create Database and Relation objects, create a custom distance function, and read the algorithm output. Unfortunately the ELKI tutorial (http://elki.dbs.ifi.lmu.de/wiki/Tutorial) focuses on the GUI version and on implementing new algorithms, and trying

Using ELKI on custom objects and making sense of results

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问题 I am trying to use ELKI's SLINK implementation of hierarchical clustering in my program. I have a set of objects (of my own type) that need to be clustered. For that, I convert them to feature vectors before clustering. This is how I currently got it to run and produce some result (code is in Scala): val clusterer = new SLINK(CosineDistanceFunction.STATIC, 3) val connection = new ArrayAdapterDatabaseConnection(featureVectors) val database = new StaticArrayDatabase(connection, null) database

How to compile ELKI project with Maven

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问题 I have been working on this issue since yesterday. The latest ELKI has a glitch and the developer fixed it on GitHub. However, I have to re-compile the project to use it. I have installed latest Java JDK and Maven. However, the build command always terminates with an error: Error: Could not find or load main class de.lmu.ifi.dbs.elki.application.internal.DocumentParameters This is the project: https://github.com/elki-project/elki. I am running this command: mvn -DskipTests -Dmaven.javadoc

Running OPTICS algorithm on ELKI

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问题 I'm normally an R user (a beginning R user, but I'm starting to get the hang of it). However, I have heard positive things about ELKI--in particular, its speed. I came across this old post "How to group nearby latitude and longitude locations stored in SQL" and the answer posted by Anony-Mousse is similar to what I'd like to do. I would like to be able to replicate each step he has done up to the KML file he has shared on Google Drive. I've downloaded ELKI and am able to run the mini-GUI,

Clustering algorithm with different epsilons on different axes

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问题 I am looking for a clustering algorithm such a s DBSCAN do deal with 3d data, in which is possible to set different epsilons depending on the axis. So for instance an epsilon of 10m on the x-y plan, and an epsilon 0.2m on the z axis. Essentially, I am looking for large but flat clusters. Note: I am an archaeologist, the algorithm will be used to look for potential correlations between objects scattered in large surfaces, but in narrow vertical layers 回答1: Solution 1: Scale your data set to

Clustering string data with ELKI

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问题 I need to cluster a large number of strings using ELKI based on the Edit Distance / Levenshtein Distance. Since the data set is too large, I'd like to avoid file based precomputed distance matrices. How can I (a) load string data in ELKI from a file (only "Labels")? (b) implement a distance function accessing the labels (extend AbstractDBIDDistanceFunction, but how to get the labels?) Some code snippets or example input files would be helpful. 回答1: It's actually pretty straightforward: A )

How can I use the index-structures in ELKI?

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问题 These are quotes form http://elki.dbs.ifi.lmu.de/ : "Essentially, we bind the abstract distance query to a database, and then get a nearest neighbor search for this distance. At this point, ELKI will automatically choose the most appropriate kNN query class. If there exist an appropriate index for our distance function (not every index can accelerate every distance!), it will automatically be used here." "The getKNNForDBID method may boil down to a slow linear scan, but when the database has

ELKI DBSCAN R* tree index

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In MiniGUi, I can see db.index . How do I set it to tree.spatial.rstarvariants.rstar.RStartTreeFactory via Java code? I have implemented: params.addParameter(AbstractDatabase.Parameterizer.INDEX_ID,tree.spatial.rstarvariants.rstar.RStarTreeFactory); For the second parameter of addParameter() function tree.spatial...RStarTreeFactory class not found // Setup parameters: ListParameterization params = new ListParameterization(); params.addParameter( FileBasedDatabaseConnection.Parameterizer.INPUT_ID, fileLocation); params.addParameter(AbstractDatabase.Parameterizer.INDEX_ID, RStarTreeFactory.class

Unable to load java class from w3c

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问题 I am trying to do OPTICS-clustering with ELKI (http://elki.dbs.ifi.lmu.de/). I try do run the clustering with the provided gui, but then I get this exception: Error in starting visualizer window. java.lang.NoClassDefFoundError: org/w3c/dom/svg/SVGSVGElement at de.lmu.ifi.dbs.elki.visualization.gui.ResultWindow.<init>(Unknown Source) at de.lmu.ifi.dbs.elki.visualization.gui.ResultVisualizer$1.run(Unknown Source) at [...] Caused by: java.lang.ClassNotFoundException: org.w3c.dom.svg