This article contains promotional content .(January 2019) |
Developer(s) | Technical University of Dortmund; initially Ludwig Maximilian University of Munich |
---|---|
Stable release | 0.8.0 / 5 October 2022 |
Repository | |
Written in | Java |
Operating system | Microsoft Windows, Linux, Mac OS |
Platform | Java platform |
Type | Data mining |
License | AGPL (since version 0.4.0) |
Website | elki-project |
ELKI (Environment for Developing KDD-Applications Supported by Index-Structures) is a data mining (KDD, knowledge discovery in databases) software framework developed for use in research and teaching. It was originally created by the database systems research unit at the Ludwig Maximilian University of Munich, Germany, led by Professor Hans-Peter Kriegel. The project has continued at the Technical University of Dortmund, Germany. It aims at allowing the development and evaluation of advanced data mining algorithms and their interaction with database index structures.
The ELKI framework is written in Java and built around a modular architecture. Most currently included algorithms perform clustering, outlier detection, [1] and database indexes. The object-oriented architecture allows the combination of arbitrary algorithms, data types, distance functions, indexes, and evaluation measures. The Java just-in-time compiler optimizes all combinations to a similar extent, making benchmarking results more comparable if they share large parts of the code. When developing new algorithms or index structures, the existing components can be easily reused, and the type safety of Java detects many programming errors at compile time.
ELKI is a free tool for analyzing data, mainly focusing on finding patterns and unusual data points without needing labels. It's written in Java and aims to be fast and able to handle big datasets by using special structures. It's made for researchers and students to add their own methods and compare different algorithms easily. [2]
ELKI has been used in data science to cluster sperm whale codas, [3] for phoneme clustering, [4] for anomaly detection in spaceflight operations, [5] for bike sharing redistribution, [6] and traffic prediction. [7]
The university project is developed for use in teaching and research. The source code is written with extensibility and reusability in mind, but is also optimized for performance. The experimental evaluation of algorithms depends on many environmental factors and implementation details can have a large impact on the runtime. [8] ELKI aims at providing a shared codebase with comparable implementations of many algorithms.
As research project, it currently does not offer integration with business intelligence applications or an interface to common database management systems via SQL. The copyleft (AGPL) license may also be a hindrance to an integration in commercial products; nevertheless it can be used to evaluate algorithms prior to developing an own implementation for a commercial product. Furthermore, the application of the algorithms requires knowledge about their usage, parameters, and study of original literature. The audience is students, researchers, data scientists, and software engineers.
ELKI is modeled around a database-inspired core, which uses a vertical data layout that stores data in column groups (similar to column families in NoSQL databases). This database core provides nearest neighbor search, range/radius search, and distance query functionality with index acceleration for a wide range of dissimilarity measures. Algorithms based on such queries (e.g. k-nearest-neighbor algorithm, local outlier factor and DBSCAN) can be implemented easily and benefit from the index acceleration. The database core also provides fast and memory efficient collections for object collections and associative structures such as nearest neighbor lists.
ELKI makes extensive use of Java interfaces, so that it can be extended easily in many places. For example, custom data types, distance functions, index structures, algorithms, input parsers, and output modules can be added and combined without modifying the existing code. This includes the possibility of defining a custom distance function and using existing indexes for acceleration.
ELKI uses a service loader architecture to allow publishing extensions as separate jar files.
ELKI uses optimized collections for performance rather than the standard Java API. [9] For loops for example are written similar to C++ iterators:
for(DBIDIteriter=ids.iter();iter.valid();iter.advance()){relation.get(iter);// E.g., get the referenced objectidcollection.add(iter);// E.g., add the reference to a DBID collection}
In contrast to typical Java iterators (which can only iterate over objects), this conserves memory, because the iterator can internally use primitive values for data storage. The reduced garbage collection improves the runtime. Optimized collections libraries such as GNU Trove3, Koloboke, and fastutil employ similar optimizations. ELKI includes data structures such as object collections and heaps (for, e.g., nearest neighbor search) using such optimizations.
The visualization module uses SVG for scalable graphics output, and Apache Batik for rendering of the user interface as well as lossless export into PostScript and PDF for easy inclusion in scientific publications in LaTeX. Exported files can be edited with SVG editors such as Inkscape. Since cascading style sheets are used, the graphics design can be restyled easily. Unfortunately, Batik is rather slow and memory intensive, so the visualizations are not very scalable to large data sets (for larger data sets, only a subsample of the data is visualized by default).
Version 0.4, presented at the "Symposium on Spatial and Temporal Databases" 2011, which included various methods for spatial outlier detection, [10] won the conference's "best demonstration paper award".
Select included algorithms: [11]
Version 0.1 (July 2008) contained several Algorithms from cluster analysis and anomaly detection, as well as some index structures such as the R*-tree. The focus of the first release was on subspace clustering and correlation clustering algorithms. [12]
Version 0.2 (July 2009) added functionality for time series analysis, in particular distance functions for time series. [13]
Version 0.3 (March 2010) extended the choice of anomaly detection algorithms and visualization modules. [14]
Version 0.4 (September 2011) added algorithms for geo data mining and support for multi-relational database and index structures. [10]
Version 0.5 (April 2012) focuses on the evaluation of cluster analysis results, adding new visualizations and some new algorithms. [15]
Version 0.6 (June 2013) introduces a new 3D adaption of parallel coordinates for data visualization, apart from the usual additions of algorithms and index structures. [16]
Version 0.7 (August 2015) adds support for uncertain data types, and algorithms for the analysis of uncertain data. [17]
Version 0.7.5 (February 2019) adds additional clustering algorithms, anomaly detection algorithms, evaluation measures, and indexing structures. [18]
Version 0.8 (October 2022) adds automatic index creation, garbage collection, and incremental priority search, as well as many more algorithms such as BIRCH. [19]
Data mining is the process of extracting and discovering patterns in large data sets involving methods at the intersection of machine learning, statistics, and database systems. Data mining is an interdisciplinary subfield of computer science and statistics with an overall goal of extracting information from a data set and transforming the information into a comprehensible structure for further use. Data mining is the analysis step of the "knowledge discovery in databases" process, or KDD. Aside from the raw analysis step, it also involves database and data management aspects, data pre-processing, model and inference considerations, interestingness metrics, complexity considerations, post-processing of discovered structures, visualization, and online updating.
In statistics, an outlier is a data point that differs significantly from other observations. An outlier may be due to a variability in the measurement, an indication of novel data, or it may be the result of experimental error; the latter are sometimes excluded from the data set. An outlier can be an indication of exciting possibility, but can also cause serious problems in statistical analyses.
Dimensionality reduction, or dimension reduction, is the transformation of data from a high-dimensional space into a low-dimensional space so that the low-dimensional representation retains some meaningful properties of the original data, ideally close to its intrinsic dimension. Working in high-dimensional spaces can be undesirable for many reasons; raw data are often sparse as a consequence of the curse of dimensionality, and analyzing the data is usually computationally intractable. Dimensionality reduction is common in fields that deal with large numbers of observations and/or large numbers of variables, such as signal processing, speech recognition, neuroinformatics, and bioinformatics.
Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group are more similar to each other than to those in other groups (clusters). It is a main task of exploratory data analysis, and a common technique for statistical data analysis, used in many fields, including pattern recognition, image analysis, information retrieval, bioinformatics, data compression, computer graphics and machine learning.
The curse of dimensionality refers to various phenomena that arise when analyzing and organizing data in high-dimensional spaces that do not occur in low-dimensional settings such as the three-dimensional physical space of everyday experience. The expression was coined by Richard E. Bellman when considering problems in dynamic programming. The curse generally refers to issues that arise when the number of datapoints is small relative to the intrinsic dimension of the data.
R-trees are tree data structures used for spatial access methods, i.e., for indexing multi-dimensional information such as geographical coordinates, rectangles or polygons. The R-tree was proposed by Antonin Guttman in 1984 and has found significant use in both theoretical and applied contexts. A common real-world usage for an R-tree might be to store spatial objects such as restaurant locations or the polygons that typical maps are made of: streets, buildings, outlines of lakes, coastlines, etc. and then find answers quickly to queries such as "Find all museums within 2 km of my current location", "retrieve all road segments within 2 km of my location" or "find the nearest gas station". The R-tree can also accelerate nearest neighbor search for various distance metrics, including great-circle distance.
Parallel Coordinates plots are a common method of visualizing high-dimensional datasets to analyze multivariate data having multiple variables, or attributes.
In statistics, the k-nearest neighbors algorithm (k-NN) is a non-parametric supervised learning method. It was first developed by Evelyn Fix and Joseph Hodges in 1951, and later expanded by Thomas Cover. Most often, it is used for classification, as a k-NN classifier, the output of which is a class membership. An object is classified by a plurality vote of its neighbors, with the object being assigned to the class most common among its k nearest neighbors (k is a positive integer, typically small). If k = 1, then the object is simply assigned to the class of that single nearest neighbor.
k-means clustering is a method of vector quantization, originally from signal processing, that aims to partition n observations into k clusters in which each observation belongs to the cluster with the nearest mean, serving as a prototype of the cluster. This results in a partitioning of the data space into Voronoi cells. k-means clustering minimizes within-cluster variances, but not regular Euclidean distances, which would be the more difficult Weber problem: the mean optimizes squared errors, whereas only the geometric median minimizes Euclidean distances. For instance, better Euclidean solutions can be found using k-medians and k-medoids.
Waikato Environment for Knowledge Analysis (Weka) is a collection of machine learning and data analysis free software licensed under the GNU General Public License. It was developed at the University of Waikato, New Zealand and is the companion software to the book "Data Mining: Practical Machine Learning Tools and Techniques".
In data analysis, anomaly detection is generally understood to be the identification of rare items, events or observations which deviate significantly from the majority of the data and do not conform to a well defined notion of normal behavior. Such examples may arouse suspicions of being generated by a different mechanism, or appear inconsistent with the remainder of that set of data.
Oracle Data Mining (ODM) is an option of Oracle Database Enterprise Edition. It contains several data mining and data analysis algorithms for classification, prediction, regression, associations, feature selection, anomaly detection, feature extraction, and specialized analytics. It provides means for the creation, management and operational deployment of data mining models inside the database environment.
Density-based spatial clustering of applications with noise (DBSCAN) is a data clustering algorithm proposed by Martin Ester, Hans-Peter Kriegel, Jörg Sander, and Xiaowei Xu in 1996. It is a density-based clustering non-parametric algorithm: given a set of points in some space, it groups together points that are closely packed, and marks as outliers points that lie alone in low-density regions . DBSCAN is one of the most commonly used and cited clustering algorithms.
Ordering points to identify the clustering structure (OPTICS) is an algorithm for finding density-based clusters in spatial data. It was presented by Mihael Ankerst, Markus M. Breunig, Hans-Peter Kriegel and Jörg Sander. Its basic idea is similar to DBSCAN, but it addresses one of DBSCAN's major weaknesses: the problem of detecting meaningful clusters in data of varying density. To do so, the points of the database are (linearly) ordered such that spatially closest points become neighbors in the ordering. Additionally, a special distance is stored for each point that represents the density that must be accepted for a cluster so that both points belong to the same cluster. This is represented as a dendrogram.
Clustering high-dimensional data is the cluster analysis of data with anywhere from a few dozen to many thousands of dimensions. Such high-dimensional spaces of data are often encountered in areas such as medicine, where DNA microarray technology can produce many measurements at once, and the clustering of text documents, where, if a word-frequency vector is used, the number of dimensions equals the size of the vocabulary.
In anomaly detection, the local outlier factor (LOF) is an algorithm proposed by Markus M. Breunig, Hans-Peter Kriegel, Raymond T. Ng and Jörg Sander in 2000 for finding anomalous data points by measuring the local deviation of a given data point with respect to its neighbours.
Hans-Peter Kriegel is a German computer scientist and professor at the Ludwig Maximilian University of Munich and leading the Database Systems Group in the Department of Computer Science. He was previously professor at the University of Würzburg and the University of Bremen after habilitation at the Technical University of Dortmund and doctorate from Karlsruhe Institute of Technology.
The following outline is provided as an overview of, and topical guide to, machine learning:
Arthur Zimek is a professor in data mining, data science and machine learning at the University of Southern Denmark in Odense, Denmark.
Isolation Forest is an algorithm for data anomaly detection using binary trees. It was developed by Fei Tony Liu in 2008. It has a linear time complexity and a low memory use, which works well for high-volume data. It is based on the assumption that because anomalies are few and different from other data, they can be isolated using few partitions. Like decision tree algorithms, it does not perform density estimation. Unlike decision tree algorithms, it uses only path length to output an anomaly score, and does not use leaf node statistics of class distribution or target value.
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