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Martin Ester

Bio: Martin Ester is an academic researcher from Simon Fraser University. The author has contributed to research in topics: Cluster analysis & Recommender system. The author has an hindex of 59, co-authored 212 publications receiving 45928 citations. Previous affiliations of Martin Ester include University of British Columbia & Ludwig Maximilian University of Munich.


Papers
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Proceedings Article
02 Aug 1996
TL;DR: In this paper, a density-based notion of clusters is proposed to discover clusters of arbitrary shape, which can be used for class identification in large spatial databases and is shown to be more efficient than the well-known algorithm CLAR-ANS.
Abstract: Clustering algorithms are attractive for the task of class identification in spatial databases. However, the application to large spatial databases rises the following requirements for clustering algorithms: minimal requirements of domain knowledge to determine the input parameters, discovery of clusters with arbitrary shape and good efficiency on large databases. The well-known clustering algorithms offer no solution to the combination of these requirements. In this paper, we present the new clustering algorithm DBSCAN relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape. DBSCAN requires only one input parameter and supports the user in determining an appropriate value for it. We performed an experimental evaluation of the effectiveness and efficiency of DBSCAN using synthetic data and real data of the SEQUOIA 2000 benchmark. The results of our experiments demonstrate that (1) DBSCAN is significantly more effective in discovering clusters of arbitrary shape than the well-known algorithm CLAR-ANS, and that (2) DBSCAN outperforms CLARANS by a factor of more than 100 in terms of efficiency.

17,056 citations

Proceedings Article
01 Jan 1996
TL;DR: DBSCAN, a new clustering algorithm relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape, is presented which requires only one input parameter and supports the user in determining an appropriate value for it.
Abstract: Clustering algorithms are attractive for the task of class identification in spatial databases. However, the application to large spatial databases rises the following requirements for clustering algorithms: minimal requirements of domain knowledge to determine the input parameters, discovery of clusters with arbitrary shape and good efficiency on large databases. The well-known clustering algorithms offer no solution to the combination of these requirements. In this paper, we present the new clustering algorithm DBSCAN relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape. DBSCAN requires only one input parameter and supports the user in determining an appropriate value for it. We performed an experimental evaluation of the effectiveness and efficiency of DBSCAN using synthetic data and real data of the SEQUOIA 2000 benchmark. The results of our experiments demonstrate that (1) DBSCAN is significantly more effective in discovering clusters of arbitrary shape than the well-known algorithm CLARANS, and that (2) DBSCAN outperforms CLARANS by a factor of more than 100 in terms of efficiency.

14,297 citations

Journal ArticleDOI
TL;DR: This work developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories, and evaluated the most accurate SCL predictors using 5-fold cross validation plus an independent proteomics analysis.
Abstract: Motivation: PSORTb has remained the most precise bacterial protein subcellular localization (SCL) predictor since it was first made available in 2003. However, the recall needs to be improved and no accurate SCL predictors yet make predictions for archaea, nor differentiate important localization subcategories, such as proteins targeted to a host cell or bacterial hyperstructures/organelles. Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program. Results: We developed PSORTb version 3.0 with improved recall, higher proteome-scale prediction coverage, and new refined localization subcategories. It is the first SCL predictor specifically geared for all prokaryotes, including archaea and bacteria with atypical membrane/cell wall topologies. It features an improved standalone program, with a new batch results delivery system complementing its web interface. We evaluated the most accurate SCL predictors using 5-fold cross validation plus we performed an independent proteomics analysis, showing that PSORTb 3.0 is the most accurate but can benefit from being complemented by Proteome Analyst predictions. Availability: http://www.psort.org/psortb (download open source software or use the web interface). Contact: psort-mail@sfu.ca Supplementary Information:Supplementary data are availableat Bioinformatics online.

1,954 citations

Proceedings ArticleDOI
26 Sep 2010
TL;DR: A model-based approach for recommendation in social networks, employing matrix factorization techniques and incorporating the mechanism of trust propagation into the model demonstrates that modeling trust propagation leads to a substantial increase in recommendation accuracy, in particular for cold start users.
Abstract: Recommender systems are becoming tools of choice to select the online information relevant to a given user Collaborative filtering is the most popular approach to building recommender systems and has been successfully employed in many applications With the advent of online social networks, the social network based approach to recommendation has emerged This approach assumes a social network among users and makes recommendations for a user based on the ratings of the users that have direct or indirect social relations with the given user As one of their major benefits, social network based approaches have been shown to reduce the problems with cold start users In this paper, we explore a model-based approach for recommendation in social networks, employing matrix factorization techniques Advancing previous work, we incorporate the mechanism of trust propagation into the model Trust propagation has been shown to be a crucial phenomenon in the social sciences, in social network analysis and in trust-based recommendation We have conducted experiments on two real life data sets, the public domain Epinionscom dataset and a much larger dataset that we have recently crawled from Flixstercom Our experiments demonstrate that modeling trust propagation leads to a substantial increase in recommendation accuracy, in particular for cold start users

1,468 citations

Journal ArticleDOI
TL;DR: The generalized algorithm DBSCAN can cluster point objects as well as spatially extended objects according to both, their spatial and their nonspatial attributes, and four applications using 2D points (astronomy, 3D points,biology, 5D points and 2D polygons) are presented, demonstrating the applicability of GDBSCAN to real-world problems.
Abstract: The clustering algorithm DBSCAN relies on a density-based notion of clusters and is designed to discover clusters of arbitrary shape as well as to distinguish noise. In this paper, we generalize this algorithm in two important directions. The generalized algorithm—called GDBSCAN—can cluster point objects as well as spatially extended objects according to both, their spatial and their nonspatial attributes. In addition, four applications using 2D points (astronomy), 3D points (biology), 5D points (earth science) and 2D polygons (geography) are presented, demonstrating the applicability of GDBSCAN to real-world problems.

1,339 citations


Cited by
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Journal ArticleDOI
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Abstract: Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ~10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: [email protected]

43,862 citations

Book
08 Sep 2000
TL;DR: This book presents dozens of algorithms and implementation examples, all in pseudo-code and suitable for use in real-world, large-scale data mining projects, and provides a comprehensive, practical look at the concepts and techniques you need to get the most out of real business data.
Abstract: The increasing volume of data in modern business and science calls for more complex and sophisticated tools. Although advances in data mining technology have made extensive data collection much easier, it's still always evolving and there is a constant need for new techniques and tools that can help us transform this data into useful information and knowledge. Since the previous edition's publication, great advances have been made in the field of data mining. Not only does the third of edition of Data Mining: Concepts and Techniques continue the tradition of equipping you with an understanding and application of the theory and practice of discovering patterns hidden in large data sets, it also focuses on new, important topics in the field: data warehouses and data cube technology, mining stream, mining social networks, and mining spatial, multimedia and other complex data. Each chapter is a stand-alone guide to a critical topic, presenting proven algorithms and sound implementations ready to be used directly or with strategic modification against live data. This is the resource you need if you want to apply today's most powerful data mining techniques to meet real business challenges. * Presents dozens of algorithms and implementation examples, all in pseudo-code and suitable for use in real-world, large-scale data mining projects. * Addresses advanced topics such as mining object-relational databases, spatial databases, multimedia databases, time-series databases, text databases, the World Wide Web, and applications in several fields. *Provides a comprehensive, practical look at the concepts and techniques you need to get the most out of real business data

23,600 citations

Book
25 Oct 1999
TL;DR: This highly anticipated third edition of the most acclaimed work on data mining and machine learning will teach you everything you need to know about preparing inputs, interpreting outputs, evaluating results, and the algorithmic methods at the heart of successful data mining.
Abstract: Data Mining: Practical Machine Learning Tools and Techniques offers a thorough grounding in machine learning concepts as well as practical advice on applying machine learning tools and techniques in real-world data mining situations. This highly anticipated third edition of the most acclaimed work on data mining and machine learning will teach you everything you need to know about preparing inputs, interpreting outputs, evaluating results, and the algorithmic methods at the heart of successful data mining. Thorough updates reflect the technical changes and modernizations that have taken place in the field since the last edition, including new material on Data Transformations, Ensemble Learning, Massive Data Sets, Multi-instance Learning, plus a new version of the popular Weka machine learning software developed by the authors. Witten, Frank, and Hall include both tried-and-true techniques of today as well as methods at the leading edge of contemporary research. *Provides a thorough grounding in machine learning concepts as well as practical advice on applying the tools and techniques to your data mining projects *Offers concrete tips and techniques for performance improvement that work by transforming the input or output in machine learning methods *Includes downloadable Weka software toolkit, a collection of machine learning algorithms for data mining tasks-in an updated, interactive interface. Algorithms in toolkit cover: data pre-processing, classification, regression, clustering, association rules, visualization

20,196 citations

Proceedings Article
02 Aug 1996
TL;DR: In this paper, a density-based notion of clusters is proposed to discover clusters of arbitrary shape, which can be used for class identification in large spatial databases and is shown to be more efficient than the well-known algorithm CLAR-ANS.
Abstract: Clustering algorithms are attractive for the task of class identification in spatial databases. However, the application to large spatial databases rises the following requirements for clustering algorithms: minimal requirements of domain knowledge to determine the input parameters, discovery of clusters with arbitrary shape and good efficiency on large databases. The well-known clustering algorithms offer no solution to the combination of these requirements. In this paper, we present the new clustering algorithm DBSCAN relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape. DBSCAN requires only one input parameter and supports the user in determining an appropriate value for it. We performed an experimental evaluation of the effectiveness and efficiency of DBSCAN using synthetic data and real data of the SEQUOIA 2000 benchmark. The results of our experiments demonstrate that (1) DBSCAN is significantly more effective in discovering clusters of arbitrary shape than the well-known algorithm CLAR-ANS, and that (2) DBSCAN outperforms CLARANS by a factor of more than 100 in terms of efficiency.

17,056 citations

Proceedings Article
01 Jan 1996
TL;DR: DBSCAN, a new clustering algorithm relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape, is presented which requires only one input parameter and supports the user in determining an appropriate value for it.
Abstract: Clustering algorithms are attractive for the task of class identification in spatial databases. However, the application to large spatial databases rises the following requirements for clustering algorithms: minimal requirements of domain knowledge to determine the input parameters, discovery of clusters with arbitrary shape and good efficiency on large databases. The well-known clustering algorithms offer no solution to the combination of these requirements. In this paper, we present the new clustering algorithm DBSCAN relying on a density-based notion of clusters which is designed to discover clusters of arbitrary shape. DBSCAN requires only one input parameter and supports the user in determining an appropriate value for it. We performed an experimental evaluation of the effectiveness and efficiency of DBSCAN using synthetic data and real data of the SEQUOIA 2000 benchmark. The results of our experiments demonstrate that (1) DBSCAN is significantly more effective in discovering clusters of arbitrary shape than the well-known algorithm CLARANS, and that (2) DBSCAN outperforms CLARANS by a factor of more than 100 in terms of efficiency.

14,297 citations