Michael Hahsler

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Association Rule Mining

[1] Michael Hahsler. Grouping association rules using lift. In C. Iyigun, R. Moghaddess, and A. Oztekin, editors, 11th INFORMS Workshop on Data Mining and Decision Analytics (DM-DA 2016), November 2016. [ bib | .pdf ]
Association rule mining is a well established and popular data mining method for finding local dependencies between items in large transaction databases. However, a practical drawback of mining and efficiently using association rules is that the set of rules returned by the mining algorithm is typically too large to be directly used. Clustering association rules into a small number of meaningful groups would be valuable for experts who need to manually inspect the rules, for visualization and as the input for other applications. Interestingly, clustering is not widely used as a standard method to summarize large sets of associations. In fact it performs poorly due to high dimensionality, the inherent extreme data sparseness and the dominant frequent itemset structure reflected in sets of association rules. In this paper, we review association rule clustering and their shortcomings. We then propose a simple approach based on grouping columns in a lift matrix and give an example to illustrate its usefulness.
[2] Michael Hahsler and Radoslaw Karpienko. Visualizing association rules in hierarchical groups. Journal of Business Economics, pages 1--19, May 2016. [ bib | DOI | .pdf ]
Association rule mining is one of the most popular data mining methods. However, mining association rules often results in a very large number of found rules, leaving the analyst with the task to go through all the rules and discover interesting ones. Sifting manually through large sets of rules is time consuming and strenuous. Visualization has a long history of making large amounts of data better accessible using techniques like selecting and zooming. However, most association rule visualization techniques are still falling short when it comes to a large number of rules. In this paper we present an integrated framework for post-processing and visualization of association rules, which allows to intuitively explore and interpret highly complex scenarios. We demonstrate how this framework can be used to analyze large sets of association rules using the R software for statistical computing, and provide examples from the implementation in the R-package arulesViz.
[3] Anurag Nagar, Michael Hahsler, and Hisham Al-Mubaid. Association rule mining of gene ontology annotation terms for SGD. In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, August 2015. [ bib | DOI | .pdf ]
Gene Ontology is one of the largest bioinformatics project that seeks to consolidate knowledge about genes through annotation of terms to three ontologies. In this work, we present a technique to find association relationships in the annotation terms for the Saccharomyces cerevisiae (SGD) genome. We first present a normalization algorithm to ensure that the annotation terms have a similar level of specificity. Association rule mining algorithms are used to find significant and non-trivial association rules in these normalized datasets. Metrics such as support, confidence, and lift can be used to evaluate the strength of found rules. We conducted experiments on the entire SGD annotation dataset and here we present the top 10 strongest rules for each of the three ontologies. We verify the found rules using evidence from the biomedical literature. The presented method has a number of advantages - it relies only on the structure of the gene ontology, has minimal memory and storage requirements, and can be easily scaled for large genomes, such as the human genome. There are many applications of this technique, such as predicting the GO annotations for new genes or those that have not been studied extensively.
[4] Jörg Lässig and Michael Hahsler. Cooperative data analysis in supply chains using selective information disclosure. In Brian Borchers, J. Paul Brooks, and Laura McLay, editors, Operations Research and Computing: Algorithms and Software for Analytics, 14th INFORMS Computing Society Conference (ICS2015). INFORMS, January 2015. [ bib | at the publisher ]
Many modern products (e. g., consumer electronics) consist of hundreds of complex parts sourced from a large number of suppliers. In such a setting, finding the source of certain properties, e. g., the source of defects in the final product, becomes increasingly difficult. Data analysis methods can be used on information shared in modern supply chains. However, some information may be confidential since they touch proprietary production processes or trade secrets. Important principles of confidentiality are data minimization and that each participant has control over how much information is communicated with others, both of which makes data analysis more difficult. In this work, we investigate the effectiveness of strategies for selective information disclosure in order to perform cooperative data analysis in a supply chain. The goal is to minimize information exchange by only exchanging information which is needed for the analysis tasks at hand. The work is motivated by the growing demand for cross company data analysis, while simultaneously addressing confidentiality concerns. As an example, we apply a newly developed protocol with association mining techniques in an empirical simulation study to compare its effectiveness with complete information disclosure. The results show that the predictive performance is comparable while the amount of exchanged information is reduced significantly.
[5] Michael Hahsler and Sudheer Chelluboina. Visualizing association rules in hierarchical groups. Unpublished. Presented at the 42nd Symposium on the Interface: Statistical, Machine Learning, and Visualization Algorithms (Interface 2011), June 2011. [ bib | .pdf ]
Association rule mining is one of the most popular data mining methods. However, mining association rules often results in a very large number of found rules, leaving the analyst with the task to go through all the rules and discover interesting ones. Sifting manually through large sets of rules is time consuming and strenuous. Visualization has a long history of making large amounts of data better accessible using techniques like selecting and zooming. However, most association rule visualization techniques are still falling short when it comes to a large number of rules. In this paper we present a new interactive visualization technique which lets the user navigate through a hierarchy of groups of association rules. We demonstrate how this new visualization techniques can be used to analyze a large sets of association rules with examples from our implementation in the R-package arulesViz.
[6] Michael Hahsler, Sudheer Chelluboina, Kurt Hornik, and Christian Buchta. The arules R-package ecosystem: Analyzing interesting patterns from large transaction datasets. Journal of Machine Learning Research, 12:1977--1981, 2011. [ bib | at the publisher ]
This paper describes the ecosystem of R add-on packages developed around the infrastructure provided by the package arules. The packages provide comprehensive functionality for analyzing interesting patterns including frequent itemsets, association rules, frequent sequences and for building applications like associative classification. After discussing the ecosystem's design we illustrate the ease of mining and visualizing rules with a short example.
[7] Michael Hahsler, Christian Buchta, and Kurt Hornik. Selective association rule generation. Computational Statistics, 23(2):303--315, April 2008. [ bib | DOI | at the publisher | .pdf ]
Mining association rules is a popular and well researched method for discovering interesting relations between variables in large databases. A practical problem is that at medium to low support values often a large number of frequent itemsets and an even larger number of association rules are found in a database. A widely used approach is to gradually increase minimum support and minimum confidence or to filter the found rules using increasingly strict constraints on additional measures of interestingness until the set of rules found is reduced to a manageable size. In this paper we describe a different approach which is based on the idea to first define a set of “interesting” itemsets (e.g., by a mixture of mining and expert knowledge) and then, in a second step to selectively generate rules for only these itemsets. The main advantage of this approach over increasing thresholds or filtering rules is that the number of rules found is significantly reduced while at the same time it is not necessary to increase the support and confidence thresholds which might lead to missing important information in the database.
[8] Michael Hahsler and Kurt Hornik. Building on the arules infrastructure for analyzing transaction data with R. In R. Decker and H.-J. Lenz, editors, Advances in Data Analysis, Studies in Classification, Data Analysis, and Knowledge Organization, pages 449--456. Springer-Verlag, 2007. [ bib | DOI | .pdf ]
The free and extensible statistical computing environment R with its enormous number of extension packages already provides many state-of-the-art techniques for data analysis. Support for association rule mining, a popular exploratory method which can be used, among other purposes, for uncovering cross-selling opportunities in market baskets, has become available recently with the R extension package arules. After a brief introduction to transaction data and association rules, we present the formal framework implemented in arules and demonstrate how clustering and association rule mining can be applied together using a market basket data set from a typical retailer. This paper shows that implementing a basic infrastructure with formal classes in R provides an extensible basis which can very efficiently be employed for developing new applications (such as clustering transactions) in addition to association rule mining.
[9] Michael Hahsler and Kurt Hornik. New probabilistic interest measures for association rules. Intelligent Data Analysis, 11(5):437--455, 2007. [ bib | at the publisher | .pdf ]
Mining association rules is an important technique for discovering meaningful patterns in transaction databases. Many different measures of interestingness have been proposed for association rules. However, these measures fail to take the probabilistic properties of the mined data into account. In this paper, we start with presenting a simple probabilistic framework for transaction data which can be used to simulate transaction data when no associations are present. We use such data and a real-world database from a grocery outlet to explore the behavior of confidence and lift, two popular interest measures used for rule mining. The results show that confidence is systematically influenced by the frequency of the items in the left hand side of rules and that lift performs poorly to filter random noise in transaction data. Based on the probabilistic framework we develop two new interest measures, hyper-lift and hyper-confidence, which can be used to filter or order mined association rules. The new measures show significantly better performance than lift for applications where spurious rules are problematic.
[10] Thomas Reutterer, Michael Hahsler, and Kurt Hornik. Data Mining und Marketing am Beispiel der explorativen Warenkorbanalyse. Marketing ZFP, 29(3):165--181, 2007. [ bib | at the publisher ]
Techniken des Data Mining stellen für die Marketingforschung und -praxis eine zunehmend bedeutsamere Bereicherung des herkömmlichen Methodenarsenals dar. Mit dem Einsatz solcher primär datengetriebener Analysewerkzeuge wird das Ziel verfolgt, marketingrelevante Informationen ”intelligent” aus großen Datenbanken (sog. Data Warehouses) zu extrahieren und für die weitere Entscheidungsvorbereitung in geeigneter Form aufzubereiten. Im vorliegenden Beitrag werden Berührungspunkte zwischen Data Mining und Marketing diskutiert und der konkrete Einsatz ausgewählter Data-Mining-Methoden am Beispiel der explorativen Warenkorb- bzw. Sortimentsverbundanalyse für einen Transaktionsdatensatz aus dem Lebensmitteleinzelhandel demonstriert. Zur Anwendung gelangen dabei Techniken aus dem Bereich der klassischen Affinitätsanalyse, ein K-Medoid-Verfahren der Clusteranalyse sowie Werkzeuge zur Generierung und anschließenden Beurteilung von Assoziationsregeln zwischen im Sortiment enthaltenen Warengruppen. Die Vorgehensweise wird dabei anhand des mit der Statistik-Software R frei verfügbaren Erweiterungspakets arules illustriert.
[11] Michael Hahsler. A model-based frequency constraint for mining associations from transaction data. Data Mining and Knowledge Discovery, 13(2):137--166, September 2006. [ bib | DOI | at the publisher | .pdf ]
Mining frequent itemsets is a popular method for finding associated items in databases. For this method, support, the co-occurrence frequency of the items which form an association, is used as the primary indicator of the associations's significance. A single user-specified support threshold is used to decided if associations should be further investigated. Support has some known problems with rare items, favors shorter itemsets and sometimes produces misleading associations. In this paper we develop a novel model-based frequency constraint as an alternative to a single, user-specified minimum support. The constraint utilizes knowledge of the process generating transaction data by applying a simple stochastic mixture model (the NB model) which allows for transaction data's typically highly skewed item frequency distribution. A user-specified precision threshold is used together with the model to find local frequency thresholds for groups of itemsets. Based on the constraint we develop the notion of NB-frequent itemsets and adapt a mining algorithm to find all NB-frequent itemsets in a database. In experiments with publicly available transaction databases we show that the new constraint provides improvements over a single minimum support threshold and that the precision threshold is more robust and easier to set and interpret by the user.
[12] Michael Hahsler, Kurt Hornik, and Thomas Reutterer. Warenkorbanalyse mit Hilfe der Statistik-Software R. In Peter Schnedlitz, Renate Buber, Thomas Reutterer, Arnold Schuh, and Christoph Teller, editors, Innovationen in Marketing, pages 144--163. Linde-Verlag, 2006. [ bib | at the publisher | .pdf ]
Die Warenkorb- oder Sortimentsverbundanalyse bezeichnet eine Reihe von Methoden zur Untersuchung der bei einem Einkauf gemeinsam nachgefragten Produkte oder Kategorien aus einem Handelssortiment. In diesem Beitrag wird die explorative Warenkorbanalyse näher beleuchtet, welche eine Verdichtung und kompakte Darstellung der in (zumeist sehr umfangreichen) Transaktionsdaten des Einzelhandels auffindbaren Verbundbeziehungen beabsichtigt. Mit einer enormen Anzahl an verfügbaren Erweiterungspaketen bietet sich die frei verfügbare Statistik-Software R als ideale Basis für die Durchführung solcher Warenkorbanalysen an. Die im Erweiterungspaket arules vorhandene Infrastruktur für Transaktionsdaten stellt eine flexible Basis für die Warenkorbanalyse bereit. Unterstützt wird die effiziente Darstellung, Bearbeitung und Analyse von Warenkorbdaten mitsamt beliebigen Zusatzinformationen zu Produkten (zum Beispiel Sortimentshierarchie) und zu Transaktionen (zum Beispiel Umsatz oder Deckungsbeitrag). Das Paket ist nahtlos in R integriert und ermöglicht dadurch die direkte Anwendung von bereits vorhandenen modernsten Verfahren für Sampling, Clusterbildung und Visualisierung von Warenkorbdaten. Zusätzlich sind in arules gängige Algorithmen zum Auffinden von Assoziationsregeln und die notwendigen Datenstrukturen zur Analyse von Mustern vorhanden. Eine Auswahl der wichtigsten Funktionen wird anhand eines realen Transaktionsdatensatzes aus dem Lebensmitteleinzelhandel demonstriert.
[13] Michael Hahsler, Kurt Hornik, and Thomas Reutterer. Implications of probabilistic data modeling for mining association rules. In M. Spiliopoulou, R. Kruse, C. Borgelt, A. Nürnberger, and W. Gaul, editors, From Data and Information Analysis to Knowledge Engineering, Studies in Classification, Data Analysis, and Knowledge Organization, pages 598--605. Springer-Verlag, 2006. [ bib | at the publisher | .pdf ]
Mining association rules is an important technique for discovering meaningful patterns in transaction databases. In the current literature, the properties of algorithms to mine association rules are discussed in great detail. We present a simple probabilistic framework for transaction data which can be used to simulate transaction data when no associations are present. We use such data and a real-world grocery database to explore the behavior of confidence and lift, two popular interest measures used for rule mining. The results show that confidence is systematically influenced by the frequency of the items in the left-hand-side of rules and that lift performs poorly to filter random noise in transaction data. The probabilistic data modeling approach presented in this paper not only is a valuable framework to analyze interest measures but also provides a starting point for further research to develop new interest measures which are based on statistical tests and geared towards the specific properties of transaction data.
[14] Michael Hahsler, Bettina Grün, and Kurt Hornik. arules -- A computational environment for mining association rules and frequent item sets. Journal of Statistical Software, 14(15):1--25, October 2005. [ bib | DOI | at the publisher ]
Mining frequent itemsets and association rules is a popular and well researched approach for discovering interesting relationships between variables in large databases. The R package arules presented in this paper provides a basic infrastructure for creating and manipulating input data sets and for analyzing the resulting itemsets and rules. The package also includes interfaces to two fast mining algorithms, the popular C implementations of Apriori and Eclat by Christian Borgelt. These algorithms can be used to mine frequent itemsets, maximal frequent itemsets, closed frequent itemsets and association rules.
[15] Andreas Geyer-Schulz and Michael Hahsler. Comparing two recommender algorithms with the help of recommendations by peers. In O.R. Zaiane, J. Srivastava, M. Spiliopoulou, and B. Masand, editors, WEBKDD 2002 - Mining Web Data for Discovering Usage Patterns and Profiles 4th International Workshop, Edmonton, Canada, July 2002, Revised Papers, Lecture Notes in Computer Science LNAI 2703, pages 137--158. Springer-Verlag, 2003. (Revised version of the WEBKDD 2002 paper “Evaluation of Recommender Algorithms for an Internet Information Broker based on Simple Association Rules and on the Repeat-Buying Theory”). [ bib | at the publisher | .pdf ]
Since more and more Web sites, especially sites of retailers, offer automatic recommendation services using Web usage mining, evaluation of recommender algorithms has become increasingly important. In this paper we present a framework for the evaluation of different aspects of recommender systems based on the process of discovering knowledge in databases introduced by Fayyad et al. and we summarize research already done in this area. One aspect identified in the presented evaluation framework is widely neglected when dealing with recommender algorithms. This aspect is to evaluate how useful patterns extracted by recommender algorithms are to support the social process of recommending products to others, a process normally driven by recommendations by peers or experts. To fill this gap for recommender algorithms based on frequent itemsets extracted from usage data we evaluate the usefulness of two algorithms. The first recommender algorithm uses association rules, and the other algorithm is based on the repeat-buying theory known from marketing research. We use 6 months of usage data from an educational Internet information broker and compare useful recommendations identified by users from the target group of the broker (peers) with the recommendations produced by the algorithms. The results of the evaluation presented in this paper suggest that frequent itemsets from usage histories match the concept of useful recommendations expressed by peers with satisfactory accuracy (higher than 70%) and precision (between 60% and 90%). Also the evaluation suggests that both algorithms studied in the paper perform similar on real-world data if they are tuned properly.
[16] Andreas Geyer-Schulz and Michael Hahsler. Evaluation of recommender algorithms for an internet information broker based on simple association rules and on the repeat-buying theory. In Brij Masand, Myra Spiliopoulou, Jaideep Srivastava, and Osmar R. Zaiane, editors, Fourth WEBKDD Workshop: Web Mining for Usage Patterns & User Profiles, pages 100--114, Edmonton, Canada, July 2002. [ bib | .pdf ]
Association rules are a widely used technique to generate recommendations in commercial and research recommender systems. Since more and more Web sites, especially of retailers, offer automatic recommender services using Web usage mining, evaluation of recommender algorithms becomes increasingly important. In this paper we first present a framework for the evaluation of different aspects of recommender systems based on the process of discovering knowledge in databases of Fayyad et al. and then we focus on the comparison of the performance of two recommender algorithms based on frequent itemsets. The first recommender algorithm uses association rules, and the other recommender algorithm is based on the repeat-buying theory known from marketing research. For the evaluation we concentrated on how well the patterns extracted from usage data match the concept of useful recommendations of users. We use 6 month of usage data from an educational Internet information broker and compare useful recommendations identified by users from the target group of the broker with the results of the recommender algorithms. The results of the evaluation presented in this paper suggest that frequent itemsets from purchase histories match the concept of useful recommendations expressed by users with satisfactory accuracy (higher than 70%) and precision (between 60% and 90%). Also the evaluation suggests that both algorithms studied in the paper perform similar on real-world data if they are tuned properly.

Bioinformatics and Healthcare

[1] Zahra Gharibi, Mehmet Ayvaci, Michael Hahsler, Tracy Giacoma, Robert S. Gaston, and Bekir Tanriover. Cost-effectiveness of antibody-based induction therapy in deceased donor kidney transplantation in the united states. Transplantation, 2016. [ bib | DOI | at the publisher ]
Induction therapy in deceased donor kidney transplantation is costly, with wide discrepancy in utilization and a limited evidence base, particularly regarding cost-effectiveness. METHODS: We linked the United States Renal Data System data set to Medicare claims to estimate cumulative costs, graft survival, and incremental cost-effectiveness ratio (ICER - cost per additional year of graft survival) within 3 years of transplantation in 19 450 deceased donor kidney transplantation recipients with Medicare as primary payer from 2000 to 2008. We divided the study cohort into high-risk (age > 60 years, panel-reactive antibody > 20%, African American race, Kidney Donor Profile Index > 50%, cold ischemia time > 24 hours) and low-risk (not having any risk factors, comprising approximately 15% of the cohort). After the elimination of dominated options, we estimated expected ICER among induction categories: no-induction, alemtuzumab, rabbit antithymocyte globulin (r-ATG), and interleukin-2 receptor-antagonist. RESULTS: No-induction was the least effective and most costly option in both risk groups. Depletional antibodies (r-ATG and alemtuzumab) were more cost-effective across all willingness-to-pay thresholds in the low-risk group. For the high-risk group and its subcategories, the ICER was very sensitive to the graft survival; overall both depletional antibodies were more cost-effective, mainly for higher willingness to pay threshold (US $100 000 and US $150 000). Rabbit ATG appears to achieve excellent cost-effectiveness acceptability curves (80% of the recipients) in both risk groups at US $50 000 threshold (except age > 60 years). In addition, only r-ATG was associated with graft survival benefit over no-induction category (hazard ratio, 0.91; 95% confidence interval, 0.84-0.99) in a multivariable Cox regression analysis. CONCLUSIONS: Antibody-based induction appears to offer substantial advantages in both cost and outcome compared with no-induction. Overall, depletional induction (preferably r-ATG) appears to offer the greatest benefits.
[2] Anurag Nagar, Michael Hahsler, and Hisham Al-Mubaid. Association rule mining of gene ontology annotation terms for SGD. In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, August 2015. [ bib | DOI | .pdf ]
Gene Ontology is one of the largest bioinformatics project that seeks to consolidate knowledge about genes through annotation of terms to three ontologies. In this work, we present a technique to find association relationships in the annotation terms for the Saccharomyces cerevisiae (SGD) genome. We first present a normalization algorithm to ensure that the annotation terms have a similar level of specificity. Association rule mining algorithms are used to find significant and non-trivial association rules in these normalized datasets. Metrics such as support, confidence, and lift can be used to evaluate the strength of found rules. We conducted experiments on the entire SGD annotation dataset and here we present the top 10 strongest rules for each of the three ontologies. We verify the found rules using evidence from the biomedical literature. The presented method has a number of advantages - it relies only on the structure of the gene ontology, has minimal memory and storage requirements, and can be easily scaled for large genomes, such as the human genome. There are many applications of this technique, such as predicting the GO annotations for new genes or those that have not been studied extensively.
[3] Jake Drew and Michael Hahsler. Practical applications of locality sensitive hashing for unstructured data. In Proceedings of the 2014 CMG Conference: Performance and Capacity. CMG, November 2014. [ bib | .pdf ]
Working with large amounts of unstructured data (e.g., text documents) has become important for many business, engineering and scientific applications. The purpose of this article is to demonstrate how the practical Data Scientist can implement a Locality Sensitive Hashing system from start to finish in order to drastically reduce the time required to perform a similarity search in high dimensional space (e.g., created by the terms in the vector space model for documents). Locality Sensitive Hashing dramatically reduces the amount of data required for storage and comparison by applying probabilistic dimensionality reduction. In this paper we concentrate on the implementation of min-wise independent permutations (MinHashing) which provides an efficient way to determine an accurate approximation of the Jaccard similarity coefficient between sets (e.g., sets of terms in documents).
[4] Jake Drew and Michael Hahsler. Strand: Fast sequence comparison using mapreduce and locality sensitive hashing. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Health Informatics (BCB 2014). ACM, September 2014. [ bib | DOI | .pdf ]
The Super Threaded Reference-Free Alignment-Free N-sequence Decoder (Strand) is a highly parallel technique for the learning and classification of gene sequence data into any number of associated categories or gene sequence taxonomies. Current methods, including the state-of-the-art sequence classification method RDP, balance performance by using a shorter word length. Strand in contrast uses a much longer word length, and does so efficiently by implementing a Divide and Conquer algorithm leveraging MapReduce style processing and locality sensitive hashing. Strand is able to learn gene sequence taxonomies and classify new sequences approximately 20 times faster than the RDP classifier while still achieving comparable accuracy results. This paper compares the accuracy and performance characteristics of Strand against RDP using 16S rRNA sequence data from the RDP training dataset and the Greengenes sequence repository.
[5] Anurag Nagar and Michael Hahsler. Genomic sequence fragment identification using quasi-alignment. In Proceedings of the ACM BCB Conference 2013, Washington D.C., September 2013. [ bib | DOI | .pdf ]
Identification of organisms using their genetic sequences is a popular problem in molecular biology and is used in fields such as metagenomics, molecular phylogenetics and DNA Barcoding. These applications depend on searching large sequence databases for individual matching sequences (e.g., with BLAST) and comparing sequences using multiple sequence alignment (e.g., via Clustal), both of which are computationally expensive and require extensive server resources. We propose a novel method for sequence comparison, analysis, and classification which avoids the need to align sequences at the base level or search a database for similarity. Instead, our method uses alignment-free methods to find probabilistic quasi-alignments for longer (typically 100 base pairs) segments. Clustering is then used to create com- pact models that can be used to analyze a set of sequences and to score and classify unknown sequences against these models. In this paper we expand prior work in two ways. We show how quasi-alignments can be expanded into larger quasi-aligned sections and we develop a method to classify short sequence fragments. The latter is especially useful when working with Next-Generation Sequencing (NGS) techniques that generate output in the form of relatively short reads. We have conducted extensive experiments using fragments from bacterial 16S rRNA sequences obtained from the Greengenes project and our results show that the new quasi-alignment based approach can provide excellent results as well as overcome some of the restrictions of by the widely used Ribosomal Database Project (RDP) classifier.
[6] Anurag Nagar and Michael Hahsler. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC Bioinformatics, 14(Suppl. 11), 2013. [ bib | DOI | at the publisher ]
Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment, which has a polynomial run time in terms of the number of sequences. Often significant computational resources are required. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments can be used for a variety of tasks such as species characterization and identification, phylogenetic analysis, functional analysis of sequences and, as in this paper, for discovering conserved regions. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with know hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time linear in the number of sequences, whereas existing multiple sequence alignment methods (such as Clustal) need a superlinear polynomial run time. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.
[7] Anurag Nagar and Michael Hahsler. A novel quasi-alignment-based method for discovering conserved regions in genetic sequences. In Proceedings of the IEEE BIBM 2012 Workshop on Data-Mining of Next-Generation Sequencing. IEEE Computer Society Press, October 2012. [ bib | DOI | .pdf ]
This paper presents an alignment-free technique to efficiently discover similar regions in large sets of biological sequences using position sensitive p-mer frequency clustering. A set of sequences is broken down into segment and then a frequency distribution over all oligomers of size p (referred to as p-mers) is obtained to summarize each segment. These summaries are clustered while the order of segments in the set of sequences is preserved in a Markov-type model. Sequence segments within each cluster have very similar DNA/RNA patterns and form a so called quasi-alignment. This fact can be used for a variety of tasks such as species characterization and identification, phylogenetic analysis, functional analysis of sequences and, as in this paper, for discovering conserved regions. Our method is computationally more efficient than multiple sequences alignment since it can apply modern data stream clustering algorithms which run in time linear in the number of segments and thus can help discover highly similar regions across a large number of sequences efficiently. In this paper, we apply the approach to efficiently discover and visualize conserved regions in 16S rRNA.
[8] Maya El Dayeh and Michael Hahsler. Biological pathway completion using network motifs and random walks on graphs. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2012), pages 229--236. IEEE, May 2012. [ bib | .pdf ]
Enhancing our understanding of cellular regulatory processes will ultimately lead to the development of better therapeutic strategies. Completing incomplete biological pathways through utilizing probabilistic protein-protein interaction (PPI) networks is one approach towards establishing knowledge of these regulatory processes. Previous complex/pathway membership methods focused on uncovering candidate protein members from a probabilistic protein-protein interaction (PPI) networks. In our previous work, we defined the pathway completion problem and developed a method that uses network motifs to complete incomplete biological pathways. Network motifs allow us to take into consideration the intrinsic local structures of the pathways to identify the possible points of insertion of candidate proteins. However, our previous approach requires a complete and correct PPI network. In this paper, we extend our previous work and use random walks on a graph to address the pathway completion problem with incomplete PPI networks. We evaluate our proposed method using three probabilistic PPI networks and two KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Moreover, we compare the accuracy of our network motif approach for pathway completion to the exiting approach for pathway membership. Our experiments show that our new approach achieves similar or better accuracy. In addition, our method identifies the possible locations and connections of the candidate proteins in the incomplete pathway, thus, allowing for targeted experimental verification.
[9] Maya El Dayeh and Michael Hahsler. Analyzing incomplete biological pathways using network motifs. In 27th Symposium On Applied Computing (SAC 2012), volume 2, pages 1355--1360. ACM, 2012. [ bib | .pdf ]
It is widely accepted that existing knowledge about the structure of many biological pathways is incomplete and uncovering missing proteins in a biological pathway can help guide targeted therapy and drug design and discovery. Current approaches address the complex/pathway membership problem by identifying potentially missing proteins using probabilistic protein-protein interaction (PPI) networks. In this paper we extend the idea of the pathway membership problem and define the pathway completion problem. In addition to finding possible protein candidates, this problem requires predicting the locations and connections of these proteins within a given incomplete pathway. We propose the use of network motifs to tackle the pathway completion problem. We present an algorithm which breaks down an incomplete pathway into a set of constituent motifs and then uses the proteins retrieved from a probabilistic PPI network to improve the motifs. This new approach also has the potential to improve solutions to the membership problem by better exploiting the local structures represented by network motifs. These new ideas are illustrated with a set of preliminary experiments.
[10] Rao M. Kotamarti, Michael Hahsler, Douglas Raiford, Monnie McGee, and Margaret H. Dunham. Analyzing taxonomic classification using extensible Markov models. Bioinformatics, 26(18):2235--2241, 2010. [ bib | DOI | at the publisher ]
Motivation: As next generation sequencing is rapidly adding new genomes, their correct placement in the taxonomy needs verification. However, the current methods for confirming classification of a taxon or suggesting revision for a potential misplacement relies on computationally intense multi-sequence alignment followed by an iterative adjustment of the distance matrix. Due to intra-heterogeneity issues with the 16S rRNA marker, no classifier is available for sub-genus level that could readily suggest a classification for a novel 16S rRNA sequence. Metagenomics further complicates the issue by generating fragmented 16S rRNA sequences. This paper proposes a novel alignment-free method for representing the microbial profiles using Extensible Markov Models (EMM) with an extended Karlin-Altschul statistical framework similar to the classic alignment paradigm. We propose a Log Odds (LOD) score classifier based on Gumbel difference distribution that confirms correct classifications with statistical significance qualifications and suggests revisions where necessary. Results: We tested our method by generating a sub-genus level classifier with which we re-evaluated classifications of 676 microbial organisms using the NCBI FTP database for the 16S rRNA. The results confirm current classification for all genera while ascertaining significance at 95%. Furthermore, this novel classifier isolates heterogeneity issues to a mere 12 strains while confirming classifications with significance qualification for the remaining 98%. The models require less memory than that needed by multi-sequence alignments and have better time complexity than the current methods. The classifier operates at sub-genus level and thus outperforms the naive Bayes classifier of the RNA Database Project where much of the taxonomic analysis is available online. Finally, using information redundancy in model building, we show that the method applies to metagenomic fragment classification of 19 E.coli strains.
[11] Rao M. Kotamarti, Michael Hahsler, Douglas W. Raiford, and Margaret H. Dunham. Sequence transformation to a complex signature form for consistent phylogenetic tree using extensible Markov model. In Proceedings of the 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2010). IEEE, 2010. [ bib | DOI | .pdf ]
Phylogenetic tree analysis using molecular sequences continues to expand beyond the 16S rRNA marker. By addressing the multi-copy issue known as the intra-heterogeneity, this paper restores the focus in using the 16S rRNA marker. Through use of a novel learning and model building algorithm, the multiple gene copies are integrated into a compact complex signature using the Extensible Markov Model (EMM). The method clusters related sequence segments while preserving their inherent order to create an EMM signature for a microbial organism. A library of EMM signatures is generated from which samples are drawn for phylogenetic analysis. By matching the components of two signatures, referred to as quasi-alignment, the differences are highlighted and scored. Scoring quasi-alignments is done using adapted Karlin-Altschul statistics to compute a novel distance metric. The metric satisfies conditions of identity, symmetry, triangular inequality and the four point rule required for a valid evolution distance metric. The resulting distance matrix is input to PHYologeny Inference Package (PHYLIP) to generate phylogenies using neighbor joining algorithms. Through control of clustering in signature creation, the diversity of similar organisms and their placement in the phylogeny is explained. The experiments include analysis of genus Burkholderia, a random microbial sample spanning several phyla and a diverse sample that includes RNA of Eukaryotic origin. The NCBI sequence data for 16S rRNA is used for validation.

Earth Science Data Research

[1] Shaiba Hadil and Michael Hahsler. A comparison of machine learning methods for predicting tropical cyclone rapid intensification events. Research Journal of Applied Sciences, Engineering and Technology, 13(8):638--651, 2016. [ bib | DOI | at the publisher ]
The aim of this study is to improve the intensity prediction of hurricanes by accounting for rapid intensification (RI) events. Modern machine learning methods offer much promise for predicting meteorological events. One application is providing timely and accurate predictions of tropical cyclone (TC) behavior, which is crucial for saving lives and reducing damage to property. Current TC track prediction models perform much better than intensity (wind speed) models. This is partially due to the existence of RI events. An RI event is defined as a sudden change in the maximum sustained wind speed of 30 knots or greater within 24 hours. Forecasting RI events is so important that it has been put on the National Hurricane Center top forecast priority list. The research on the use of machine learning methods for RI prediction is currently very limited. In this paper, we investigate the potential of popular machine learning methods to predict RI events. The evaluated models include support vector machines, logistic regression, naïve-Bayes classifiers, classification and regression trees and a wide range of ensemble methods including boosting and stacking. We also investigate dimensionality reduction and feature selection, and we address class imbalance using the Synthetic Minority Over-sampling Technique (SMOTE). The evaluation shows that some of the investigated models improve over the current operational Rapid Intensification Index model. Finally, we use RI predictions to make improved storm intensity predictions.
[2] Hadil Shaiba and Michael Hahsler. An experimental comparison of different classifiers for predicting tropical cyclone rapid intensification events. In Proceedings of the International Conference on Machine Learning, Electrical and Mechanical Engineering (ICMLEME'2014), Dubai, UAE, January 2014. [ bib | .pdf ]
Accurately predicting the intensity and track of a Tropical Cyclone (TC) can save the lives of people and help to significantly reduce damage to property and infrastructure. Current track prediction models outperform intensity models which is partially due to the existence of rapid intensification (RI) events. RI appears in the lifecycle of most major hurricanes and can be defined as a change in intensity within 24 hours which exceeds 30 knots. Improving the predicting of RI events has been identified as one of the top priority problems by the National Hurricane Center (NHC). In this paper we compare the RI event prediction performance of several popular classification methods: Logistic regression, naive Bayes classifier, classification and regression tree (CART), and support vector machine. The dataset used is derived from the data used by the Statistical Hurricane Intensity Prediction Scheme (SHIPS) model for intensity prediction which contains large-scale weather, ocean, and earth condition predictors from 1982 to 2011. 10-fold cross validation is applied to compare the models. The probability of detection (POD) and false alarm ratio (FAR) are used to measure performance. Predicting RI events is a difficult problem but initial experiments show potential for improving forecast using data mining and machine learning techniques.
[3] Hadil Shaiba and Michael Hahsler. Intensity prediction model for tropical cyclone rapid intensification events. In Proceedings of the IADIS Applied Computing 2013 (AC 2013) Conference, Fort Worth, TX, October 2013. [ bib ]
Tropical Cyclones (TC) create strong wind and rain and can cause significant human and financial losses. Many major hurricanes in the Atlantic Ocean undergo rapid intensification (RI). RI events happen when the strength of the storm increases rapidly within 24 hours. Improving the hurricane’s intensity prediction model by accurately detecting the occurrence and predicting the intensity of an RI event can help avoid human and financial losses. In this paper we analyzed RI events in the Atlantic Basin and investigated the use of a combination of three different models to predict RI events. The first and second models are simple location and time-based models which use the conditional probability of intensification given the day of the year and the location of the storm. The third model uses a data mining technique which is based on the Extensible Markov Chain Model (EMM) which clusters the hurricane’s lifecycle into states and then uses the transition probabilities between these states for prediction. One of the main characteristics of a Markov Chain is that the next state depends only on the current state and by knowing the current state we can predict future states which provide us with estimates for future intensities. In future research we plan to test each model independently and combinations of the models by comparing them to the current best prediction models.
[4] Vladimir Jovanovic, Margaret H. Dunham, Michael Hahsler, and Yu Su. Evaluating hurricane intensity prediction techniques in real time. In Third IEEE ICDM Workshop on Knowledge Discovery from Climate Data, Proceedings of the of the 2011 IEEE International Conference on Data Mining Workshops (ICDMW 2011), pages 23--29. IEEE, December 2011. [ bib | DOI | .pdf ]
While the accuracy of hurricane track prediction has been improving, predicting intensity, the maximum sustained wind speed, is still a very difficult challenge. This is problematic because the destructive power of a hurricane is directly related to its intensity. In this paper, we present Prediction Intensity Interval model for Hurricanes (PIIH) which combines sophisticated data mining techniques to create an online real time model for accurate intensity predictions and we present a web-based framework to dynamically compare PIIH to operational models used by the National Hurricane Center (NHC). The created dynamic website tracks, compares, and provides visualization to facilitate immediate comparisons of prediction techniques. This paper is a work in progress paper reporting on both, new features of the PIIH model and online visualization of the accuracy of that model as compared to other techniques.
[5] Yu Su, Sudheer Chelluboina, Michael Hahsler, and Margaret H. Dunham. A new data mining model for hurricane intensity prediction. In Second IEEE ICDM Workshop on Knowledge Discovery from Climate Data: Prediction, Extremes and Impacts, Proceedings of the of the 2010 IEEE International Conference on Data Mining Workshops (ICDMW 2010), pages 98--105. IEEE, December 2010. [ bib | DOI | .pdf ]
This paper proposes a new hurricane intensity prediction model, WFL-EMM, which is based on the data mining techniques of feature weight learning (WFL) and Extensible Markov Model (EMM). The data features used are those employed by one of the most popular intensity prediction models, SHIPS. In our algorithm, the weights of the features are learned by a genetic algorithm (GA) using historical hurricane data. As the GA's fitness function we use the error of the intensity prediction by an EMM learned using given feature weights. For fitness calculation we use a technique similar to k-fold cross validation on the training data. The best weights obtained by the genetic algorithm are used to build an EMM with all training data. This EMM is then applied to predict the hurricane intensities and compute prediction errors for the test data. Using historical data for the named Atlantic tropical cyclones from 1982 to 2003, experiments demonstrate that WFL-EMM provides significantly more accurate intensity predictions than SHIPS within 72 hours. Since we report here first results, we indicate how to improve WFL-EMM in the future.

Data Stream Mining

[1] Michael Hahsler, Matthew Bolaños, and John Forrest. stream: An extensible framework for data stream clustering research with R. Journal of Statistical Software, 76(14):1--52, February 2017. [ bib | DOI | .pdf ]
In recent years, data streams have become an increasingly important area of research for the computer science, database and statistics communities. Data streams are ordered and potentially unbounded sequences of data points created by a typically non-stationary data generating process. Common data mining tasks associated with data streams include clustering, classification and frequent pattern mining. New algorithms for these types of data are proposed regularly and it is important to evaluate them thoroughly under standardized conditions. In this paper we introduce stream, a research tool that includes modeling and simulating data streams as well as an extensible framework for implementing, interfacing and experimenting with algorithms for various data stream mining tasks. The main advantage of stream is that it seamlessly integrates with the large existing infrastructure provided by R. In addition to data handling, plotting and easy scripting capabilities, R also provides many existing algorithms and enables users to interface code written in many programming languages popular among data mining researchers (e.g., C/C++, Java and Python). In this paper we describe the architecture of stream and focus on its use for data stream clustering research. stream was implemented with extensibility in mind and will be extended in the future to cover additional data stream mining tasks like classification and frequent pattern mining.
[2] Michael Hahsler and Matthew Bolaños. Clustering data streams based on shared density between micro-clusters. IEEE Transactions on Knowledge and Data Engineering, 28(6):1449--1461, June 2016. [ bib | DOI | .pdf ]
As more and more applications produce streaming data, clustering data streams has become an important technique for data and knowledge engineering. A typical approach is to summarize the data stream in real-time with an online process into a large number of so called micro-clusters. Micro-clusters represent local density estimates by aggregating the information of many data points in a defined area. On demand, a (modified) conventional clustering algorithm is used in a second offline step to recluster the micro-clusters into larger final clusters. For reclustering, the centers of the micro-clusters are used as pseudo points with the density estimates used as their weights. However, information about density in the area between micro-clusters is not preserved in the online process and reclustering is based on possibly inaccurate assumptions about the distribution of data within and between micro-clusters (e.g., uniform or Gaussian). This paper describes DBSTREAM, the first micro-cluster-based online clustering component that explicitly captures the density between micro-clusters via a shared density graph. The density information in this graph is then exploited for reclustering based on actual density between adjacent micro-clusters. We discuss the space and time complexity of maintaining the shared density graph. Experiments on a wide range of synthetic and real data sets highlight that using shared density improves clustering quality over other popular data stream clustering methods which require the creation of a larger number of smaller micro-clusters to achieve comparable results.
[3] Matthew Bolaños, John Forrest, and Michael Hahsler. Clustering large datasets using data stream clustering techniques. In Myra Spiliopoulou, Lars Schmidt-Thieme, and Ruth Janning, editors, Data Analysis, Machine Learning and Knowledge Discovery, Studies in Classification, Data Analysis, and Knowledge Organization, pages 135--143. Springer-Verlag, 2014. [ bib | DOI | .pdf ]
Unsupervised identification of groups in large data sets is important for many machine learning and knowledge discovery applications. Conventional clustering approaches (k-means, hierarchical clustering, etc.) typically do not scale well for very large data sets. In recent years, data stream clustering algorithms have been proposed which can deal efficiently with potentially unbounded streams of data. This paper is the first to investigate the use of data stream clustering algorithms as light-weight alternatives to conventional algorithms on large non-streaming data. We will discuss important issue including order dependence and report the results of an initial study using several synthetic and real-world data sets.
[4] Anurag Nagar and Michael Hahsler. Using text and data mining techniques to extract stock market sentiment from live news streams. In 2012 International Conference on Computer Technology and Science (ICCTS 2012), August 2012. [ bib | .pdf ]
Analyzing stock market trends and sentiment is an interdisciplinary area of research being undertaken by many disciplines such as Finance, Computer Science, Statistics, and Economics. It has been well established that real time news plays a strong role in the movement of stock prices. With the advent of electronic and online news sources, analysts have to deal with enormous amounts of real-time, unstructured streaming data. In this paper, we present an automated text mining based approach to aggregate news stories from diverse sources and create a News Corpus. The Corpus is filtered down to relevant sentences and analyzed using Natural Language Processing (NLP) techniques. A sentiment metric, called NewsSentiment, utilizing the count of positive and negative polarity words is proposed as a measure of the sentiment of the overall news corpus. We have used various open source packages and tools to develop the news collection and aggregation engine as well as the sentiment evaluation engine. Extensive experimentation has been done using news stories about various stocks. The time variation of NewsSentiment shows a very strong correlation with the actual stock price movement. Our proposed metric has many applications in analyzing current news stories and predicting stock trends for specific companies and sectors of the economy.
[5] Charlie Isaksson, Margaret H. Dunham, and Michael Hahsler. SOStream: Self organizing density-based clustering over data stream. In Petra Perner, editor, International Conference on Machine Learning and Data Mining (MLDM'2012), Lecture Notes in Computer Science LNAI 7376, pages 264--278. Springer, July 2012. [ bib | at the publisher | .pdf ]
In this paper we propose a data stream clustering algorithm, called Self Organizing density based clustering over data Stream (SOStream). This algorithm has several novel features. Instead of using a fixed, user defined similarity threshold or a static grid, SOStream detects structure within fast evolving data streams by automatically adapting the threshold for density-based clustering. It also employs a novel cluster updating strategy which is inspired by competitive learning techniques developed for Self Organizing Maps (SOMs). In addition, SOStream has built-in online functionality to support advanced stream clustering operations including merging and fading. This makes SOStream completely online with no separate offline components. Experiments performed on KDD Cup'99 and artificial datasets indicate that SOStream is an effective and superior algorithm in creating clusters of higher purity while having lower space and time requirements compared to previous stream clustering algorithms.
[6] Vladimir Jovanovic, Margaret H. Dunham, Michael Hahsler, and Yu Su. Evaluating hurricane intensity prediction techniques in real time. In Third IEEE ICDM Workshop on Knowledge Discovery from Climate Data, Proceedings of the of the 2011 IEEE International Conference on Data Mining Workshops (ICDMW 2011), pages 23--29. IEEE, December 2011. [ bib | DOI | .pdf ]
While the accuracy of hurricane track prediction has been improving, predicting intensity, the maximum sustained wind speed, is still a very difficult challenge. This is problematic because the destructive power of a hurricane is directly related to its intensity. In this paper, we present Prediction Intensity Interval model for Hurricanes (PIIH) which combines sophisticated data mining techniques to create an online real time model for accurate intensity predictions and we present a web-based framework to dynamically compare PIIH to operational models used by the National Hurricane Center (NHC). The created dynamic website tracks, compares, and provides visualization to facilitate immediate comparisons of prediction techniques. This paper is a work in progress paper reporting on both, new features of the PIIH model and online visualization of the accuracy of that model as compared to other techniques.
[7] Michael Hahsler and Margaret H. Dunham. Temporal structure learning for clustering massive data streams in real-time. In SIAM Conference on Data Mining (SDM11), pages 664--675. SIAM, April 2011. [ bib | at the publisher | .pdf ]
This paper describes one of the first attempts to model the temporal structure of massive data streams in real-time using data stream clustering. Recently, many data stream clustering algorithms have been developed which efficiently find a partition of the data points in a data stream. However, these algorithms disregard the information represented by the temporal order of the data points in the stream which for many applications is an important part of the data stream. In this paper we propose a new framework called Temporal Relationships Among Clusters for Data Streams (TRACDS) which allows to learn the temporal structure while clustering a data stream. We identify, organize and describe the clustering operations which are used by state-of-the-art data stream clustering algorithms. Then we show that by defining a set of new operations to transform Markov Chains with states representing clusters dynamically, we can efficiently capture temporal ordering information. This framework allows us to preserve temporal relationships among clusters for any state-of-the-art data stream clustering algorithm with only minimal overhead.

To investigate the usefulness of TRACDS, we evaluate the improvement of TRACDS over pure data stream clustering for anomaly detection using several synthetic and real-world data sets. The experiments show that TRACDS is able to considerably improve the results even if we introduce a high rate of incorrect time stamps which is typical for real-world data streams.

[8] Yu Su, Sudheer Chelluboina, Michael Hahsler, and Margaret H. Dunham. A new data mining model for hurricane intensity prediction. In Second IEEE ICDM Workshop on Knowledge Discovery from Climate Data: Prediction, Extremes and Impacts, Proceedings of the of the 2010 IEEE International Conference on Data Mining Workshops (ICDMW 2010), pages 98--105. IEEE, December 2010. [ bib | DOI | .pdf ]
This paper proposes a new hurricane intensity prediction model, WFL-EMM, which is based on the data mining techniques of feature weight learning (WFL) and Extensible Markov Model (EMM). The data features used are those employed by one of the most popular intensity prediction models, SHIPS. In our algorithm, the weights of the features are learned by a genetic algorithm (GA) using historical hurricane data. As the GA's fitness function we use the error of the intensity prediction by an EMM learned using given feature weights. For fitness calculation we use a technique similar to k-fold cross validation on the training data. The best weights obtained by the genetic algorithm are used to build an EMM with all training data. This EMM is then applied to predict the hurricane intensities and compute prediction errors for the test data. Using historical data for the named Atlantic tropical cyclones from 1982 to 2003, experiments demonstrate that WFL-EMM provides significantly more accurate intensity predictions than SHIPS within 72 hours. Since we report here first results, we indicate how to improve WFL-EMM in the future.
[9] Margaret H. Dunham, Michael Hahsler, and Myra Spiliopoulou. Novel data stream pattern mining, Report on the StreamKDD'10 Workshop. SIGKDD Explorations, 12(2):54--55, 2010. [ bib | at the publisher ]
This report summarizes the First International Workshop on Novel Data Stream Pattern Mining held at the 16th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, on July 25 2010 in Washington, DC.
[10] Margaret H. Dunham, Michael Hahsler, and Myra Spiliopoulou, editors. Proceedings of the First International Workshop on Novel Data Stream Pattern Mining Techniques (StreamKDD'10). ACM Press, New York, NY, USA, 2010. [ bib | at the publisher ]
Data stream mining gained in importance over the last years because it is indispensable for many real applications such as prediction and evolution of weather phenomena; security and anomaly detection in networks; evaluating satellite data; and mining health monitoring streams. Stream mining algorithms must take account of the unique properties of stream data: infinite data, temporal ordering, concept drifts and shifts, demand for scalability etc. This workshop brings together scholars working in different areas of learning on streams, including sensor data and other forms of accumulating data. Most of the papers in the next pages are on unsupervised learning with clustering methods. Issues addressed include the detection of outliers and anomalies, evolutionary clustering and incremental clustering, learning in subspaces of the complete feature space and learning with exploitation of context, deriving models from text streams and visualizing them.
[11] Michael Hahsler and Margaret H. Dunham. rEMM: Extensible Markov model for data stream clustering in R. Journal of Statistical Software, 35(5):1--31, 2010. [ bib | DOI | .pdf ]
Clustering streams of continuously arriving data has become an important application of data mining in recent years and efficient algorithms have been proposed by several researchers. However, clustering alone neglects the fact that data in a data stream is not only characterized by the proximity of data points which is used by clustering, but also by a temporal component. The Extensible Markov Model (EMM) adds the temporal component to data stream clustering by superimposing a dynamically adapting Markov Chain. In this paper we introduce the implementation of the R extension package rEMM which implements EMM and we discuss some examples and applications.

Digital Libraries

[1] Georg Fessler, Michael Hahsler, and Michaela Putz. ePubWU -- Erfahrungen mit einer Volltext an der Wirtschaftsuniversität Wien. In Christian Enichlmayr, editor, Bibliotheken -- Fundament der Bildung, 28. Österreichischer Bibliothekartag 2004, Schriftenreihe der Oö. Landesbibliothek, pages 190--193, 2005. [ bib ]
ePubWU ist eine elektronische Plattform für wissenschaftliche Publikationen der Wirtschaftsuniversität Wien, wo forschungsbezogene Veröffentlichungen der WU im Volltext über das WWW zugänglich gemacht werden. ePubWU wird als Gemeinschaftsprojekt der Universitätsbibliothek der Wirtschaftsuniversität Wien und der Abteilung für Informationswirtschaft betrieben. Derzeit werden in ePubWU zwei Publikationsarten gesammelt - Working Papers und Dissertationen. In dem Beitrag werden Erfahrungen der über zweijährigen Laufzeit des Projektes dargestellt, u.a. in den Bereichen Akquisition, Workflows, Erschließung, Vermittlung.
[2] Georg Fessler, Michael Hahsler, Michaela Putz, Judith Schwarz, and Brigitta Wiebogen. Projektbericht ePubWU 2001--2003. Augasse 2--6, 1090 Wien, Wirtschaftsuniversität Wien, January 2004. [ bib | .pdf ]
ePubWU ist eine elektronische Plattform für wissenschaftliche Publikationen der Wirtschaftsuniversität Wien, wo forschungsbezogene Veröffentlichungen der WU im Volltext über das WWW zugänglich gemacht werden. ePubWU ist seit Jänner 2002 im Echtbetrieb und wird als Gemeinschaftsprojekt der Universitätsbibliothek der Wirtschaftsuniversität Wien und der Abteilung für Informationswirtschaft betrieben. Dieser Bericht beinhaltet die Erfahrungen aus der 2-jährigen Pilotphase des Projekts.
[3] Michael Hahsler. Integrating digital document acquisition into a university library: A case study of social and organizational challenges. Journal of Digital Information Management, 1(4):162--171, December 2003. [ bib | at the publisher | .pdf ]
In this article we report on the effort of the university library of the Vienna University of Economics and Business Administration to integrate a digital library component for research documents authored at the university into the existing library infrastructure. Setting up a digital library has become a relatively easy task using the current data base technology and the components and tools freely available. However, to integrate such a digital library into existing library systems and to adapt existing document acquisition work-flows in the organization are non-trivial tasks. We use a research frame work to identify the key players in this change process and to analyze their incentive structures. Then we describe the light-weight integration approach employed by our university and show how it provides incentives to the key players and at the same time requires only minimal adaptation of the organization in terms of changing existing work-flows. Our experience suggests that this light-weight integration offers a cost efficient and low risk intermediate step towards switching to exclusive digital document acquisition.

Marketing Research

[1] Michael Hahsler and Radoslaw Karpienko. Visualizing association rules in hierarchical groups. Journal of Business Economics, pages 1--19, May 2016. [ bib | DOI | .pdf ]
Association rule mining is one of the most popular data mining methods. However, mining association rules often results in a very large number of found rules, leaving the analyst with the task to go through all the rules and discover interesting ones. Sifting manually through large sets of rules is time consuming and strenuous. Visualization has a long history of making large amounts of data better accessible using techniques like selecting and zooming. However, most association rule visualization techniques are still falling short when it comes to a large number of rules. In this paper we present an integrated framework for post-processing and visualization of association rules, which allows to intuitively explore and interpret highly complex scenarios. We demonstrate how this framework can be used to analyze large sets of association rules using the R software for statistical computing, and provide examples from the implementation in the R-package arulesViz.
[2] Christoph Breidert and Michael Hahsler. Adaptive conjoint analysis for pricing music downloads. In R. Decker and H.-J. Lenz, editors, Advances in Data Analysis, Studies in Classification, Data Analysis, and Knowledge Organization, pages 409--416. Springer-Verlag, 2007. [ bib | at the publisher | .pdf ]
Finding the right pricing for music downloads is of ample importance to the recording industry and music download service providers. For the recently introduced music downloads, reference prices are still developing and to find a revenue maximizing pricing scheme is a challenging task. The most commonly used approach is to employ linear pricing (e.g., iTunes, musicload). Lately, subscription models have emerged, offering their customers unlimited access to streaming music for a monthly fee (e.g., Napster, RealNetworks). However, other pricing strategies could also be used, such as quantity rebates starting at certain download volumes. Research has been done in this field and Buxmann et al. (2005) have shown that price cuts can improve revenue. In this paper we apply different approaches to estimate consumer's willingness to pay (WTP) for music downloads and compare our findings with the pricing strategies currently used in the market. To make informed decisions about pricing, knowledge about the consumer's WTP is essential. Three approaches based on adaptive conjoint analysis to estimate the WTP for bundles of music downloads are compared. Two of the approaches are based on a status-quo product (at market price and alternatively at an individually self-stated price), the third approach uses a linear model assuming a fixed utility per title. All three methods seem to be robust and deliver reasonable estimations of the respondent's WTPs. However, all but the linear model need an externally set price for the status-quo product which can introduce a bias.
[3] Thomas Reutterer, Michael Hahsler, and Kurt Hornik. Data Mining und Marketing am Beispiel der explorativen Warenkorbanalyse. Marketing ZFP, 29(3):165--181, 2007. [ bib | at the publisher ]
Techniken des Data Mining stellen für die Marketingforschung und -praxis eine zunehmend bedeutsamere Bereicherung des herkömmlichen Methodenarsenals dar. Mit dem Einsatz solcher primär datengetriebener Analysewerkzeuge wird das Ziel verfolgt, marketingrelevante Informationen ”intelligent” aus großen Datenbanken (sog. Data Warehouses) zu extrahieren und für die weitere Entscheidungsvorbereitung in geeigneter Form aufzubereiten. Im vorliegenden Beitrag werden Berührungspunkte zwischen Data Mining und Marketing diskutiert und der konkrete Einsatz ausgewählter Data-Mining-Methoden am Beispiel der explorativen Warenkorb- bzw. Sortimentsverbundanalyse für einen Transaktionsdatensatz aus dem Lebensmitteleinzelhandel demonstriert. Zur Anwendung gelangen dabei Techniken aus dem Bereich der klassischen Affinitätsanalyse, ein K-Medoid-Verfahren der Clusteranalyse sowie Werkzeuge zur Generierung und anschließenden Beurteilung von Assoziationsregeln zwischen im Sortiment enthaltenen Warengruppen. Die Vorgehensweise wird dabei anhand des mit der Statistik-Software R frei verfügbaren Erweiterungspakets arules illustriert.
[4] Christoph Breidert, Michael Hahsler, and Thomas Reutterer. A review of methods for measuring willingness-to-pay. Innovative Marketing, 2(4):8--32, 2006. [ bib | .pdf ]
Knowledge about a product's willingness-to-pay on behalf of its (potential) customers plays a crucial role in many areas of marketing management like pricing decisions or new product development. Numerous approaches to measure willingness-to-pay with differential conceptual foundations and methodological implications have been presented in the relevant literature so far. This article provides the reader with a systematic overview of the relevant literature on these competing approaches and associated schools of thought, recognizes their respective merits and discusses obstacles and issues regarding their adoption to measuring willingness-to-pay. Because of its practical relevance, special focus will be put on indirect surveying techniques and, in particular, conjoint-based applications will be discussed in more detail. The strengths and limitations of the individual approaches are discussed and evaluated from a managerial point of view.
[5] Michael Hahsler, Kurt Hornik, and Thomas Reutterer. Warenkorbanalyse mit Hilfe der Statistik-Software R. In Peter Schnedlitz, Renate Buber, Thomas Reutterer, Arnold Schuh, and Christoph Teller, editors, Innovationen in Marketing, pages 144--163. Linde-Verlag, 2006. [ bib | at the publisher | .pdf ]
Die Warenkorb- oder Sortimentsverbundanalyse bezeichnet eine Reihe von Methoden zur Untersuchung der bei einem Einkauf gemeinsam nachgefragten Produkte oder Kategorien aus einem Handelssortiment. In diesem Beitrag wird die explorative Warenkorbanalyse näher beleuchtet, welche eine Verdichtung und kompakte Darstellung der in (zumeist sehr umfangreichen) Transaktionsdaten des Einzelhandels auffindbaren Verbundbeziehungen beabsichtigt. Mit einer enormen Anzahl an verfügbaren Erweiterungspaketen bietet sich die frei verfügbare Statistik-Software R als ideale Basis für die Durchführung solcher Warenkorbanalysen an. Die im Erweiterungspaket arules vorhandene Infrastruktur für Transaktionsdaten stellt eine flexible Basis für die Warenkorbanalyse bereit. Unterstützt wird die effiziente Darstellung, Bearbeitung und Analyse von Warenkorbdaten mitsamt beliebigen Zusatzinformationen zu Produkten (zum Beispiel Sortimentshierarchie) und zu Transaktionen (zum Beispiel Umsatz oder Deckungsbeitrag). Das Paket ist nahtlos in R integriert und ermöglicht dadurch die direkte Anwendung von bereits vorhandenen modernsten Verfahren für Sampling, Clusterbildung und Visualisierung von Warenkorbdaten. Zusätzlich sind in arules gängige Algorithmen zum Auffinden von Assoziationsregeln und die notwendigen Datenstrukturen zur Analyse von Mustern vorhanden. Eine Auswahl der wichtigsten Funktionen wird anhand eines realen Transaktionsdatensatzes aus dem Lebensmitteleinzelhandel demonstriert.
[6] Christoph Breidert, Michael Hahsler, and Lars Schmidt-Thieme. Reservation price estimation by adaptive conjoint analysis. In Claus Weihs and Wolfgang Gaul, editors, Classification - the Ubiquitous Challenge, Studies in Classification, Data Analysis, and Knowledge Organization, pages 577--584. Springer-Verlag, 2005. [ bib | at the publisher | .pdf ]
Though reservation prices are needed for many business decision processes, e.g., pricing new products, it often turns out to be difficult to measure them. Many researchers reuse conjoint analysis data with price as an attribute for this task (e.g., Kohli and Mahajan (1991)). In this setting the information if a consumer buys a product at all is not elicited which makes reservation price estimation impossible. We propose an additional interview scene at the end of the adaptive conjoint analysis (Johnson (1987)) to estimate reservation prices for all product configurations. This will be achieved by the usage of product stimuli as well as price scales that are adapted for each proband to reflect individual choice behavior. We present preliminary results from an ongoing large-sample conjoint interview of customers of a major mobile phone retailer in Germany.
[7] Michael Hahsler. Optimizing web sites for customer retention. In Bing Liu, Myra Spiliopoulou, Jaideep Srivastava, and Alex Tuzhilin, editors, Proceedings of the 2005 International Workshop on Customer Relationship Management: Data Mining Meets Marketing, November 18--19, 2005, New York City, USA, 2005. [ bib | .pdf ]
With customer relationship management (CRM) companies move away from a mainly product-centered view to a customer-centered view. Resulting from this change, the effective management of how to keep contact with customers throughout different channels is one of the key success factors in today's business world. Company Web sites have evolved in many industries into an extremely important channel through which customers can be attracted and retained. To analyze and optimize this channel, accurate models of how customers browse through the Web site and what information within the site they repeatedly view are crucial. Typically, data mining techniques are used for this purpose. However, there already exist numerous models developed in marketing research for traditional channels which could also prove valuable to understanding this new channel. In this paper we propose the application of an extension of the Logarithmic Series Distribution (LSD) model repeat-usage of Web-based information and thus to analyze and optimize a Web Site's capability to support one goal of CRM, to retain customers. As an example, we use the university's blended learning web portal with over a thousand learning resources to demonstrate how the model can be used to evaluate and improve the Web site's effectiveness.
[8] Edward Bernroider, Michael Hahsler, Stefan Koch, and Volker Stix. Data Envelopment Analysis zur Unterstützung der Auswahl und Einführung von ERP-Systemen. In Andreas Geyer-Schulz and Alfred Taudes, editors, Informationswirtschaft: Ein Sektor mit Zukunft, Symposium 4.--5. September 2003, Wien, Österreich, Lecture Notes in Informatics (LNI) P-33, pages 11--26. Gesellschaft für Informatik, 2003. [ bib | at the publisher ]
Immer mehr Unternehmen setzen betriebswirtschaftliche Standardsoftwarepakete wie beispielsweise SAP R/3 oder BaaN ein. Die Auswahl und die Einführung solcher Systeme stellt für die meisten Unternehmen ein strategisch wichtiges IT-Projekt dar, das mit massiven Risiken verbunden ist. Bei der Auswahl des am besten geeigneten Systems gilt es einen Gruppenentscheidungsprozess zu unterstützen. Das darauf folgende Einführungsprojekt muss effizient, den ”best practices” entsprechend, durchgeführt werden. In dieser Arbeit wird anhand von Beispielen aufgezeigt, wie beide Prozesse - die Auswahl und die Einführung - durch die Data Envelopment Analysis unterstützt werden können.
[9] Wolfgang Gaul, Andreas Geyer-Schulz, Michael Hahsler, and Lars Schmidt-Thieme. eMarketing mittels Recommendersystemen. Marketing ZFP, 24:47--55, 2002. [ bib | at the publisher ]
Recommendersysteme liefern einen wichtigen Beitrag für die Ausgestaltung von eMarketing Aktivitäten. Ausgehend von einer Diskussion von Input/Output Charakteristika zur Beschreibung solcher Systeme, die bereits eine geeignete Unterscheidung praxisrelevanter Erscheinungsformen erlauben, wird motiviert, warum eine solche Charakterisierung durch die Einbeziehung methodischer Aspekte aus der Marketing Forschung angereichert werden muss. Ein auf der Theorie des Wiederkaufverhaltens basierendes Recommendersystem sowie ein System, das Empfehlungen mittels Analyse des Navigationsverhaltens von Site Besuchern erzeugt, werden vorgestellt. Am Beispiel der Amazon Site werden die Marketing Möglichkeiten von Recommendersystemen verdeutlicht. Abschließend wird zur Abrundung auf weitere Literatur mit Recommendersystem Bezug eingegangen. In einem Ausblick werden Hinweise gegeben, in welche Richtungen Weiterentwicklungen geplant sind.
[10] Michael Hahsler and Bernd Simon. User-centered navigation re-design for web-based information systems. In H. Michael Chung, editor, Proceedings of the Sixth Americas Conference on Information Systems (AMCIS 2000), pages 192--198, Long Beach, CA, 2000. Association for Information Systems. [ bib | at the publisher | .pdf ]
Navigation design for web-based information systems (e.g. e-commerce sites, intranet solutions) that ignores user-participation reduces the system's value and can even lead to system failure. In this paper we introduce a user-centered, explorative approach to re-designing navigation structures of web-based information systems, and describe how it can be implemented in order to provide flexibility and reduce maintenance costs. We conclude with lessons learned from the navigation re-design project at the Vienna University of Economics and Business Administration.

Discrete Optimization

[1] Michael Hahsler. An experimental comparison of seriation methods for one-mode two-way data. European Journal of Operational Research, 257:133--143, February 2017. [ bib | DOI | .pdf ]
Seriation aims at finding a linear order for a set of objects to reveal structural information which can be used for deriving data-driven decisions. It presents a difficult combinatorial optimization problem with its roots and applications in many fields including operations research. This paper focuses on a popular seriation problem which tries to find an order for a single set of objects that optimizes a given seriation criterion defined on one-mode two-way data, i.e., an object-by-object dissimilarity matrix. Over the years, members of different research communities have introduced many criteria and seriation methods for this problem. It is often not clear how different seriation criteria and methods relate to each other and which criterion or seriation method to use for a given application. These methods are represent tools for analytics and therefore are of theoretical and practical interest to the operations research community. The purpose of this paper is to provide a consistent overview of the most popular criteria and seriation methods and to present a comprehensive experimental study to compare their performance using artificial and a representative set of real-world datasets.
[2] Michael Hahsler and Kurt Hornik. Dissimilarity plots: A visual exploration tool for partitional clustering. Journal of Computational and Graphical Statistics, 10(2):335--354, June 2011. [ bib | DOI | .pdf ]
For hierarchical clustering, dendrograms are a convenient and powerful visualization technique. Although many visualization methods have been suggested for partitional clustering, their usefulness deteriorates quickly with increasing dimensionality of the data and/or they fail to represent structure between and within clusters simultaneously. In this paper we extend (dissimilarity) matrix shading with several reordering steps based on seriation techniques. Both ideas, matrix shading and reordering, have been well-known for a long time. However, only recent algorithmic improvements allow us to solve or approximately solve the seriation problem efficiently for larger problems. Furthermore, seriation techniques are used in a novel stepwise process (within each cluster and between clusters) which leads to a visualization technique that is able to present the structure between clusters and the micro-structure within clusters in one concise plot. This not only allows us to judge cluster quality but also makes mis-specification of the number of clusters apparent. We give a detailed discussion of the construction of dissimilarity plots and demonstrate their usefulness with several examples. Experiments show that dissimilarity plots scale very well with increasing data dimensionality.
[3] Michael Hahsler, Kurt Hornik, and Christian Buchta. Getting things in order: An introduction to the R package seriation. Journal of Statistical Software, 25(3):1--34, March 2008. [ bib | DOI | .pdf ]
Seriation, i.e., finding a linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem's combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides the infrastructure for seriation with R. The infrastructure comprises data structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.
[4] Michael Hahsler and Kurt Hornik. TSP -- Infrastructure for the traveling salesperson problem. Journal of Statistical Software, 23(2):1--21, December 2007. [ bib | DOI | .pdf ]
The traveling salesperson (or, salesman) problem (TSP) is a well known and important combinatorial optimization problem. The goal is to find the shortest tour that visits each city in a given list exactly once and then returns to the starting city. Despite this simple problem statement, solving the TSP is difficult since it belongs to the class of NP-complete problems. The importance of the TSP arises besides from its theoretical appeal from the variety of its applications. Typical applications in operations research include vehicle routing, computer wiring, cutting wallpaper and job sequencing. The main application in statistics is combinatorial data analysis, e.g., reordering rows and columns of data matrices or identifying clusters. In this paper we introduce the R package TSP which provides a basic infrastructure for handling and solving the traveling salesperson problem. The package features S3 classes for specifying a TSP and its (possibly optimal) solution as well as several heuristics to find good solutions. In addition, it provides an interface to Concorde, one of the best exact TSP solvers currently available.
[5] Christoph Breidert and Michael Hahsler. Adaptive conjoint analysis for pricing music downloads. In R. Decker and H.-J. Lenz, editors, Advances in Data Analysis, Studies in Classification, Data Analysis, and Knowledge Organization, pages 409--416. Springer-Verlag, 2007. [ bib | at the publisher | .pdf ]
Finding the right pricing for music downloads is of ample importance to the recording industry and music download service providers. For the recently introduced music downloads, reference prices are still developing and to find a revenue maximizing pricing scheme is a challenging task. The most commonly used approach is to employ linear pricing (e.g., iTunes, musicload). Lately, subscription models have emerged, offering their customers unlimited access to streaming music for a monthly fee (e.g., Napster, RealNetworks). However, other pricing strategies could also be used, such as quantity rebates starting at certain download volumes. Research has been done in this field and Buxmann et al. (2005) have shown that price cuts can improve revenue. In this paper we apply different approaches to estimate consumer's willingness to pay (WTP) for music downloads and compare our findings with the pricing strategies currently used in the market. To make informed decisions about pricing, knowledge about the consumer's WTP is essential. Three approaches based on adaptive conjoint analysis to estimate the WTP for bundles of music downloads are compared. Two of the approaches are based on a status-quo product (at market price and alternatively at an individually self-stated price), the third approach uses a linear model assuming a fixed utility per title. All three methods seem to be robust and deliver reasonable estimations of the respondent's WTPs. However, all but the linear model need an externally set price for the status-quo product which can introduce a bias.
[6] Christoph Breidert, Michael Hahsler, and Lars Schmidt-Thieme. Reservation price estimation by adaptive conjoint analysis. In Claus Weihs and Wolfgang Gaul, editors, Classification - the Ubiquitous Challenge, Studies in Classification, Data Analysis, and Knowledge Organization, pages 577--584. Springer-Verlag, 2005. [ bib | at the publisher | .pdf ]
Though reservation prices are needed for many business decision processes, e.g., pricing new products, it often turns out to be difficult to measure them. Many researchers reuse conjoint analysis data with price as an attribute for this task (e.g., Kohli and Mahajan (1991)). In this setting the information if a consumer buys a product at all is not elicited which makes reservation price estimation impossible. We propose an additional interview scene at the end of the adaptive conjoint analysis (Johnson (1987)) to estimate reservation prices for all product configurations. This will be achieved by the usage of product stimuli as well as price scales that are adapted for each proband to reflect individual choice behavior. We present preliminary results from an ongoing large-sample conjoint interview of customers of a major mobile phone retailer in Germany.

Recommender Systems (Collaborative Filtering)

[1] Michael Hahsler. Optimizing web sites for customer retention. In Bing Liu, Myra Spiliopoulou, Jaideep Srivastava, and Alex Tuzhilin, editors, Proceedings of the 2005 International Workshop on Customer Relationship Management: Data Mining Meets Marketing, November 18--19, 2005, New York City, USA, 2005. [ bib | .pdf ]
With customer relationship management (CRM) companies move away from a mainly product-centered view to a customer-centered view. Resulting from this change, the effective management of how to keep contact with customers throughout different channels is one of the key success factors in today's business world. Company Web sites have evolved in many industries into an extremely important channel through which customers can be attracted and retained. To analyze and optimize this channel, accurate models of how customers browse through the Web site and what information within the site they repeatedly view are crucial. Typically, data mining techniques are used for this purpose. However, there already exist numerous models developed in marketing research for traditional channels which could also prove valuable to understanding this new channel. In this paper we propose the application of an extension of the Logarithmic Series Distribution (LSD) model repeat-usage of Web-based information and thus to analyze and optimize a Web Site's capability to support one goal of CRM, to retain customers. As an example, we use the university's blended learning web portal with over a thousand learning resources to demonstrate how the model can be used to evaluate and improve the Web site's effectiveness.
[2] Andreas Geyer-Schulz, Michael Hahsler, Andreas Neumann, and Anke Thede. Behavior-based recommender systems as value-added services for scientific libraries. In Hamparsum Bozdogan, editor, Statistical Data Mining & Knowledge Discovery, pages 433--454. Chapman & Hall / CRC, July 2003. [ bib | .pdf ]
Amazon.com paved the way for several large-scale, behavior-based recommendation services as an important value-added expert advice service for online book shops. In this contribution we discuss the effects (and possible reductions of transaction costs) for such services and investigate how such value-added services can be implemented in context of scientific libraries. For this purpose we present a new, recently developed recommender system based on a stochastic purchase incidence model, present the underlying stochastic model from repeat-buying theory and analyze whether the underlying assumptions on consumer behavior holds for users of scientific libraries, too. We analyzed the logfiles with approximately 85 million HTTP-transactions of the web-based online public access catalog (OPAC) of the library of the Universität Karlsruhe (TH) since January 2001 and performed some diagnostic checks. The recommender service is fully operational within the library system of the Universität Karlsruhe (TH) since 2002/06/22.
[3] Andreas Geyer-Schulz, Michael Hahsler, Andreas Neumann, and Anke Thede. An integration strategy for distributed recommender services in legacy library systems. In M. Schader, W. Gaul, and M. Vichi, editors, Between Data Science and Applied Data Analysis, Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation e.V., University of Mannheim, July 22--24, 2002, Studies in Classification, Data Analysis, and Knowledge Organization, pages 412--420. Springer-Verlag, July 2003. [ bib | at the publisher ]
Scientific library systems are a very promising application area for recommender services. Scientific libraries could easily develop customer-oriented service portals in the style of amazon.com. Students, university teachers and researchers can reduce their transaction cost (i.e. search and evaluation cost of information products). For librarians, the advantage is an improvement of the customer support by recommendations and the additional support in marketing research, product evaluation, and book selection. In this contribution we present a strategy for integrating a behavior-based distributed recommender service in legacy library systems with minimal changes in the legacy system.
[4] Andreas Geyer-Schulz, Michael Hahsler, and Anke Thede. Comparing association-rules and repeat-buying based recommender systems in a B2B environment. In M. Schader, W. Gaul, and M. Vichi, editors, Between Data Science and Applied Data Analysis, Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation e.V., University of Mannheim, July 22--24, 2002, Studies in Classification, Data Analysis, and Knowledge Organization, pages 421--429. Springer-Verlag, July 2003. [ bib | at the publisher ]
In this contribution we present a systematic evaluation and comparison of recommender systems based on simple association rules and on repeat-buying theory. Both recommender services are based on the customer purchase histories of a medium-sized B2B-merchant for computer accessories. With the help of product managers an evaluation set for recommendations was generated. With regard to this evaluation set, recommendations produced by both methods are evaluated and several error measures are computed. This provides an empirical test whether frequent item sets or outliers of a stochastic purchase incidence model are suitable concepts for automatically generation recommendations. Furthermore, the loss function (performance measures) of the two models are compared and the sensitivity with regard to a misspecification of the model parameters is discussed.
[5] Andreas Geyer-Schulz and Michael Hahsler. Comparing two recommender algorithms with the help of recommendations by peers. In O.R. Zaiane, J. Srivastava, M. Spiliopoulou, and B. Masand, editors, WEBKDD 2002 - Mining Web Data for Discovering Usage Patterns and Profiles 4th International Workshop, Edmonton, Canada, July 2002, Revised Papers, Lecture Notes in Computer Science LNAI 2703, pages 137--158. Springer-Verlag, 2003. (Revised version of the WEBKDD 2002 paper “Evaluation of Recommender Algorithms for an Internet Information Broker based on Simple Association Rules and on the Repeat-Buying Theory”). [ bib | at the publisher | .pdf ]
Since more and more Web sites, especially sites of retailers, offer automatic recommendation services using Web usage mining, evaluation of recommender algorithms has become increasingly important. In this paper we present a framework for the evaluation of different aspects of recommender systems based on the process of discovering knowledge in databases introduced by Fayyad et al. and we summarize research already done in this area. One aspect identified in the presented evaluation framework is widely neglected when dealing with recommender algorithms. This aspect is to evaluate how useful patterns extracted by recommender algorithms are to support the social process of recommending products to others, a process normally driven by recommendations by peers or experts. To fill this gap for recommender algorithms based on frequent itemsets extracted from usage data we evaluate the usefulness of two algorithms. The first recommender algorithm uses association rules, and the other algorithm is based on the repeat-buying theory known from marketing research. We use 6 months of usage data from an educational Internet information broker and compare useful recommendations identified by users from the target group of the broker (peers) with the recommendations produced by the algorithms. The results of the evaluation presented in this paper suggest that frequent itemsets from usage histories match the concept of useful recommendations expressed by peers with satisfactory accuracy (higher than 70%) and precision (between 60% and 90%). Also the evaluation suggests that both algorithms studied in the paper perform similar on real-world data if they are tuned properly.
[6] Andreas Geyer-Schulz, Michael Hahsler, Andreas Neumann, and Anke Thede. Recommenderdienste für wissenschaftliche Bibliotheken und Bibliotheksverbünde. In Andreas Geyer-Schulz and Alfred Taudes, editors, Informationswirtschaft: Ein Sektor mit Zukunft, Symposium 4.--5. September 2003, Wien, Österreich, Lecture Notes in Informatics (LNI) P-33, pages 43--58. Gesellschaft für Informatik, 2003. [ bib | at the publisher ]
Wissenschaftliche Bibliotheken stellen ein vielversprechendes Anwendungsfeld für Recommenderdienste dar. Wissenschaftliche Bibliotheken können leicht kundenzentrierte Serviceportale im Stil von amazon.com entwickeln. Studenten, Universitätslehrer und -forscher können ihren Anteil an den Transaktionskosten (z.B. Such- und Bewertungskosten für Informationsprodukte) reduzieren. Für Bibliothekare liegt der Vorteil in einer Verbesserung der Kundenberatung durch Empfehlungen und einer zusätzlichen Unterstützung bei der Marktforschung, Produktbewertung und dem Bestandsmanagement. In diesem Beitrag präsentieren wir eine Strategie, mit der verhaltensbasierte, verteilte Recommenderdienste in bestehende Bibliothekssysteme mit minimalem Aufwand integriert werden können und berichten über unsere Erfahrungen bei der Einführung eines solchen Dienstes an der Universitätsbibliothek der Universität Karlsruhe (TH).
[7] Andreas Geyer-Schulz and Michael Hahsler. Evaluation of recommender algorithms for an internet information broker based on simple association rules and on the repeat-buying theory. In Brij Masand, Myra Spiliopoulou, Jaideep Srivastava, and Osmar R. Zaiane, editors, Fourth WEBKDD Workshop: Web Mining for Usage Patterns & User Profiles, pages 100--114, Edmonton, Canada, July 2002. [ bib | .pdf ]
Association rules are a widely used technique to generate recommendations in commercial and research recommender systems. Since more and more Web sites, especially of retailers, offer automatic recommender services using Web usage mining, evaluation of recommender algorithms becomes increasingly important. In this paper we first present a framework for the evaluation of different aspects of recommender systems based on the process of discovering knowledge in databases of Fayyad et al. and then we focus on the comparison of the performance of two recommender algorithms based on frequent itemsets. The first recommender algorithm uses association rules, and the other recommender algorithm is based on the repeat-buying theory known from marketing research. For the evaluation we concentrated on how well the patterns extracted from usage data match the concept of useful recommendations of users. We use 6 month of usage data from an educational Internet information broker and compare useful recommendations identified by users from the target group of the broker with the results of the recommender algorithms. The results of the evaluation presented in this paper suggest that frequent itemsets from purchase histories match the concept of useful recommendations expressed by users with satisfactory accuracy (higher than 70%) and precision (between 60% and 90%). Also the evaluation suggests that both algorithms studied in the paper perform similar on real-world data if they are tuned properly.
[8] Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. A customer purchase incidence model applied to recommender systems. In R. Kohavi, B.M. Masand, M. Spiliopoulou, and J. Srivastava, editors, WEBKDD 2001 - Mining Log Data Across All Customer Touch Points, Third International Workshop, San Francisco, CA, USA, August 26, 2001, Revised Papers, Lecture Notes in Computer Science LNAI 2356, pages 25--47. Springer-Verlag, July 2002. (Revised version of the WEBKDD 2001 paper “A Customer Purchase Incidence Model Applied to Recommender Systems”). [ bib | at the publisher | .pdf ]
In this contribution we transfer a customer purchase incidence model for consumer products which is based on Ehrenberg s repeat-buying theory to Web-based information products. Ehrenberg s repeat-buying theory successfully describes regularities on a large number of consumer product markets. We show that these regularities exist in electronic markets for information goods, too, and that purchase incidence models provide a well founded theoretical base for re-commender and alert services. The article consists of two parts. In the first part Ehrenberg s repeat-buying theory and its assumptions are reviewed and adapted for web-based information markets. Second, we present the empirical validation of the model based on data collected from the information market of the Virtual University of the Vienna University of Economics and Business Administration from September 1999 to May 2001.
[9] Walter Böhm, Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. Repeat buying theory and its application for recommender services. In O. Opitz and M. Schwaiger, editors, Exploratory Data Analysis in Empirical Research, Proceedings of the 25th Annual Conference of the Gesellschaft für Klassifikation e.V., University of Munich, March 14--16, 2001, pages 229--239. Springer-Verlag, 2002. [ bib | at the publisher | .pdf ]
In the context of a virtual university's information broker we study the consumption patterns for information goods and we investigate if Ehrenberg's repeat-buying theory which successfully models regularities in a large number of consumer product markets can be applied in electronic markets for information goods too. First results indicate that Ehrenberg's repeat-buying theory succeeds in describing the consumption patterns of bundles of complementary information goods reasonably well and that this can be exploited for automatically generating anonymous recommendation services based on such information bundles. An experimental anonymous recommender service has been implemented and is currently evaluated in the Virtual University of the Vienna University of Economics and Business Administration at http://vu.wu-wien.ac.at.
[10] Wolfgang Gaul, Andreas Geyer-Schulz, Michael Hahsler, and Lars Schmidt-Thieme. eMarketing mittels Recommendersystemen. Marketing ZFP, 24:47--55, 2002. [ bib | at the publisher ]
Recommendersysteme liefern einen wichtigen Beitrag für die Ausgestaltung von eMarketing Aktivitäten. Ausgehend von einer Diskussion von Input/Output Charakteristika zur Beschreibung solcher Systeme, die bereits eine geeignete Unterscheidung praxisrelevanter Erscheinungsformen erlauben, wird motiviert, warum eine solche Charakterisierung durch die Einbeziehung methodischer Aspekte aus der Marketing Forschung angereichert werden muss. Ein auf der Theorie des Wiederkaufverhaltens basierendes Recommendersystem sowie ein System, das Empfehlungen mittels Analyse des Navigationsverhaltens von Site Besuchern erzeugt, werden vorgestellt. Am Beispiel der Amazon Site werden die Marketing Möglichkeiten von Recommendersystemen verdeutlicht. Abschließend wird zur Abrundung auf weitere Literatur mit Recommendersystem Bezug eingegangen. In einem Ausblick werden Hinweise gegeben, in welche Richtungen Weiterentwicklungen geplant sind.
[11] Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. Recommendations for virtual universities from observed user behavior. In W. Gaul and G. Ritter, editors, Classification, Automation, and New Media, Proceedings of the 24th Annual Conference of the Gesellschaft für Klassifikation e.V., University of Passau, March 15--17, 2000, pages 273--280. Springer-Verlag, 2002. [ bib | at the publisher | .pdf ]
Recently recommender systems started to gain ground in commercial Web-applications. For example, the online-bookseller amazon.com recommends his customers books similar to the ones they bought using the analysis of observed purchase behavior of consumers. In this article we describe a generic architecture for recommender services for information markets which has been implemented in the setting of the Virtual University of the Vienna University of Economics and Business Administration (http://vu.wu-wien.ac.at). The architecture of a recommender service is defined as an agency of interacting software agents. It consists of three layers, namely the meta-data management system, the broker management system and the business-to-customer interface.
[12] Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. Wissenschaftliche Recommendersysteme in Virtuellen Universitäten. In H.-J. Appelrath, R. Beyer, U. Marquardt, H.C. Mayr, and C. Steinberger, editors, Unternehmen Hochschule, Wien, Österreich, September 2001. Symposium UH2001, GI Lecture Notes in Informatics (LNI). [ bib | at the publisher | .pdf ]
In diesem Beitrag wird die Rolle von Recommendersystemen und ihr Potential in der Lehr-, Lern- und Forschungsumgebung einer Virtuellen Universität untersucht.Die Hauptidee dieses Beitrags besteht darin, die Informationsaggregationsfähigkeiten von Recommendersystemen in einer Virtuellen Universität auszunutzen, um Tutoren-und Beratungsdienste in einer Virtuellen Universität automatisch zu verbessern, um damit Betreuung und Beratung von Studierenden zu personalisieren und für eine größere Anzahl von Teilnehmern bei gleichzeitiger Entlastung der Lehrenden verfügbar zu machen. Im zweiten Teil dieses Beitrags werden die Recommenderdienste von myVU, der Sammlung der personalisierten Dienste der Virtuellen Universität (VU) der Wirtschaftsuniversität Wien und ihre nicht-personalisierten Variantenbeschrieben, die im Wesentlichen auf beobachtetem Benutzerverhalten und, in der personalisierten Variante, zusätzlich auf Selbstselektion durch Selbsteinschätzung der Erfahrung in einem Fachgebiet beruhen. Abschließend wird noch der innovative Einsatz solcher Systeme diskutiert und an einigen Szenarien beschrieben.
[13] Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. A customer purchase incidence model applied to recommender systems. In WEBKDD2001 Workshop: Mining Log Data Across All Customer TouchPoints, pages 35--45, San Francisco, CA, August 2001. [ bib | .pdf ]
In this contribution we transfer a customer purchase incidence model for consumer products which is based on Ehrenberg's repeat-buying theory to Web-based information products. Ehrenberg's repeat-buying theory successfully describes regularities in a large number of consumer product markets. We show that these regularities exist in electronic markets for information goods too, and that purchase incidence models provide a well founded theoretical foundation for recommender and alert systems. The article consists of three parts. First, we present the architecture of an information market and its instrumentation for collecting data on customer behavior. In the second part Ehrenberg's repeat-buying theory and its assumptions are reviewed and adapted for Web-based information markets. Finally, we present the empirical validation of the model based on data collected from the information market of the Virtual University of the Vienna University of Economics and Business Administration at http://vu.wu-wien.ac.at
[14] Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. Educational and scientific recommender systems: Designing the information channels of the virtual university. International Journal of Engineering Education, 17(2):153--163, 2001. [ bib | .pdf ]
In this article we investigate the role of recommender systems and their potential in the educational and scientific environment of a Virtual University. The key idea is to use the information aggregation capabilities of a recommender system to improve the tutoring and consulting services of a Virtual University in an automated way and thus scale tutoring and consulting in a personalized way to a mass audience. We describe the recommender services of myVU, the collection of the personalized services of the Virtual University (VU) of the Vienna University of Economics and Business Administration which are based on observed user behavior and self assignment of experience which are currently field-tested. We show, how the usual mechanism design problems inherent to recommender systems are addressed in this prototype.
[15] Andreas Geyer-Schulz and Michael Hahsler. Automatic labelling of references for information systems. In Reinhold Decker and Wolfgang Gaul, editors, Classification and Information Processing at the Turn of the Millennium, Proceedings of the 23rd Annual Conference of the Gesellschaft für Klassifikation e.V., University of Bielefeld, March 10--12, 1999, Studies in Classification, Data Analysis, and Knowledge Organization, pages 451--459. Springer-Verlag, 2000. [ bib | at the publisher | .pdf ]
Today users of Internet information services like e.g. Yahoo! or AltaVista often experience high search costs. One important reason for this is the necessity to browse long reference lists manually, because of the well-known problems of relevance ranking. A possible remedy is to complement the references with automatically generated labels which provide valuable information about the referenced information source. Presenting suitably labelled lists of references to users aims at improving the clarity and thus comprehensibility of the information offered and at reducing the search cost. In the following we survey several dimensions for labelling (time, frequency of usage, region, language, subject, industry, and preferences) and the corresponding classification problems. To solve these problems automatically we sketch for each problem a pragmatic mix of machine learning methods and report selected results.
[16] Andreas Geyer-Schulz, Michael Hahsler, and Maximillian Jahn. myvu: A next generation recommender system based on observed consumer behavior and interactive evolutionary algorithms. In Wolfgang Gaul, Otto Opitz, and Martin Schader, editors, Data Analysis: Scientific Modeling and Practical Applications, Studies in Classification, Data Analysis, and Knowledge Organization, pages 447--457. Springer Verlag, Heidelberg, Germany, 2000. [ bib | at the publisher | .pdf ]
myVU is a next generation recommender system based on observed consumer behavior and interactive evolutionary algorithms implementing customer relationship management and one-to-one marketing in the educational and scientific broker system of a virtual university. myVU provides a personalized, adaptive WWW-based user interface for all members of a virtual university and it delivers routine recommendations for frequently used scientific and educational Web-sites.

Software Engineering (with Patterns)

[1] Michael Hahsler. A quantitative study of the adoption of design patterns by open source software developers. In S. Koch, editor, Free/Open Source Software Development, pages 103--123. Idea Group Publishing, 2005. [ bib | at the publisher | .pdf ]
Several successful projects (Linux, Free-BSD, BIND, Apache, etc.) showed that the collaborative and self-organizing process of developing open source software produces reliable, high quality software. Without doubt, the open source software development process differs in many ways from the traditional development process in a commercial environment. An interesting research question is how these differences influence the adoption of traditional software engineering practices. In this chapter we investigate how design patterns, a widely accepted software engineering practice, are adopted by open source developers for documenting changes. We analyze the development process of almost 1,000 open source software projects using version control information and explore differences in pattern adoption using characteristics of projects and developers. By analyzing these differences we provide evidence that design patterns are an important practice in open source projects and that there exist significant differences between developers who use design patterns and who do not.
[2] Michael Hahsler and Stefan Koch. Discussion of a large-scale open source data collection methodology. In 38th Annual Hawaii International Conference on System Sciences (HICSS'05), January 3--6, 2005 Hilton Waikoloa Village, Big Island, Hawaii. IEEE Computer Society Press, 2005. [ bib | at the publisher | .pdf ]
In this paper we discusses in detail a possible methodology for collecting repository data on a large number of open source software projects from a single project hosting and community site. The process of data retrieval is described along with the possible metrics that can be computed and which can be used for further analyses. Example research areas to be addressed with the available data and first results are given. Then, both advantages and disadvantages of the proposed methodology are discussed together with implications for future approaches.
[3] Michael Hahsler and Stefan Koch. Cooperation and disruptive behaviour - learning from a multi-player internet gaming community. In Piet Kommers, Pedro Isaias, and Miguel Baptista Nunes, editors, IADIS International Conference Web Based Communities 2004, Lisbon, Portugal, 24--26 March 2004, pages 35--42. International Association for Development of the Information Society (IADIS), 2004. [ bib | .pdf ]
In this paper we report possibilities and experiences from employing Counter-Strike, a popular multi-player Internet computer game and its resulting online community in research on cooperative behaviour. Advantages from using this game include easy availability of rich data, the emphasis on team-playing, as well as numerous possibilities to change the experiment settings. We use descriptive game theory and statistical methods to explore cooperation within the game as well as the way the player community deals with disruptive behaviour. After a quick introduction to the basic rules of Counter-Strike, we describe the setup of the Internet game server used. We then present empirical results from the game server logs where cooperation within the game is analyzed from a game theoretic perspective. Finally we discuss the applications of our results to other online communities, including cooperation and self-regulation in open source teams.
[4] Andreas Geyer-Schulz and Michael Hahsler. Software reuse with analysis patterns. In Proceedings of the 8th AMCIS, pages 1156--1165, Dallas, TX, August 2002. Association for Information Systems. [ bib | .pdf ]
The purpose of this article is to promote reuse of domain knowledge by introducing patterns already in the analysis phase of the software life-cycle. We propose an outline template for analysis patterns that strongly supports the whole analysis process from the requirements analysis to the analysis model and further on to its transformation into a flexible and reusable design and implementation. As an example we develop a family of analysis patterns in this paper that deal with a series of pressing problems in cooperative work, collaborative information filtering and sharing, and knowledge management. We evaluate the reuse potential of these patterns by analyzing several components of an information system, that was developed for the Virtual University project of the Vienna University of Economics and Business Administration. The findings of this analysis suggest that using patterns in the analysis phase has the potential to reducing development time significantly by introducing reuse already at the analysis stage and by improving the interface between analysis and design phase.
[5] Michael Hahsler. Analyse Patterns im Softwareentwicklungsprozeß mit Beispielen für Informationsmanagement und deren Anwendungen für die Virtuellen Universität der Wirtschaftsuniversität Wien. Dissertation, Wirtschaftsuniversität Wien, Augasse 2--6, A 1090 Wien, Österreich, January 2001. [ bib | at the publisher | .pdf ]
Diese Arbeit beschäftigt sich mit Analyse Patterns, der Anwendung von Patterns in der Analysephase der Softwareentwicklung. In der Designphase werden Patterns seit einigen Jahren eingesetzt, um Expertenwissen und Wiederverwendbarkeit in den Designprozeß einfließen zu lassen. Es existiert bereits eine Fülle an solchen Design Patterns. Die Analysephase ist ein neuer Anwendungsbereich für Patterns, der bisher in der Literatur noch nicht ausreichend behandelt wurde. In dieser Arbeit wird die Anwendung des Pattern-Ansatzes in der Analysephase aufgearbeitet und konkretisiert. Analyse Patterns unterstützen den gesamten Softwareentwicklungsprozeß und helfen bekannte Probleme während der Analysephase zu lösen. Dadurch können Zeit und Kosten bei der Entwicklung neuer Softwaresysteme eingespart werden. Diese Eigenschaften von Analyse Patterns werden anhand konkreter Beispiele in einer Case Study nachgewiesen. Diese Case Study beschreibt den Einsatz von in dieser Arbeit entwickelten Analyse Pattern für Informationsmanagement anhand des Projekts Virtuelle Universität der Wirtschaftsuniversität Wien, in dem ein Internet-Informationsbroker zur Unterstützung von Lehre und Forschung realisiert wird. Die Erfahrungen aus diesem Projekt werden untersucht, und die Auswirkungen der Analyse Patterns auf Wiederverwendung bei der Softwareentwicklung und auf die Akzeptanz des resultierenden Systems werden präsentiert.
[6] Michael Hahsler. Software Patterns: Pinwände. Diplomarbeit, Wirtschaftsuniversität Wien, Augasse 2--6, A 1090 Wien, Österreich, November 1997. [ bib | .pdf ]
Diese Arbeit beschäftigt sich mit dem Pattern-Ansatz für die Architektur von Software. Nach einer kurzen Darstellung des Ansatzes werden das Pinwand-Pattern und seine Varianten beschrieben. Pinwände werden verwendet, um Informationen zu sammeln und Interessierten zur Verfügung zu stellen. Sie finden unter anderem in den folgenden Bereichen Anwendung: Groupware-Anwendungen, Conferencing Systeme, Diskussionsforen und Virtuelle Bibliotheken.

Visualization

[1] Michael Hahsler and Radoslaw Karpienko. Visualizing association rules in hierarchical groups. Journal of Business Economics, pages 1--19, May 2016. [ bib | DOI | .pdf ]
Association rule mining is one of the most popular data mining methods. However, mining association rules often results in a very large number of found rules, leaving the analyst with the task to go through all the rules and discover interesting ones. Sifting manually through large sets of rules is time consuming and strenuous. Visualization has a long history of making large amounts of data better accessible using techniques like selecting and zooming. However, most association rule visualization techniques are still falling short when it comes to a large number of rules. In this paper we present an integrated framework for post-processing and visualization of association rules, which allows to intuitively explore and interpret highly complex scenarios. We demonstrate how this framework can be used to analyze large sets of association rules using the R software for statistical computing, and provide examples from the implementation in the R-package arulesViz.
[2] Anurag Nagar and Michael Hahsler. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. BMC Bioinformatics, 14(Suppl. 11), 2013. [ bib | DOI | at the publisher ]
Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment, which has a polynomial run time in terms of the number of sequences. Often significant computational resources are required. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments can be used for a variety of tasks such as species characterization and identification, phylogenetic analysis, functional analysis of sequences and, as in this paper, for discovering conserved regions. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with know hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time linear in the number of sequences, whereas existing multiple sequence alignment methods (such as Clustal) need a superlinear polynomial run time. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.
[3] Anurag Nagar and Michael Hahsler. A novel quasi-alignment-based method for discovering conserved regions in genetic sequences. In Proceedings of the IEEE BIBM 2012 Workshop on Data-Mining of Next-Generation Sequencing. IEEE Computer Society Press, October 2012. [ bib | DOI | .pdf ]
This paper presents an alignment-free technique to efficiently discover similar regions in large sets of biological sequences using position sensitive p-mer frequency clustering. A set of sequences is broken down into segment and then a frequency distribution over all oligomers of size p (referred to as p-mers) is obtained to summarize each segment. These summaries are clustered while the order of segments in the set of sequences is preserved in a Markov-type model. Sequence segments within each cluster have very similar DNA/RNA patterns and form a so called quasi-alignment. This fact can be used for a variety of tasks such as species characterization and identification, phylogenetic analysis, functional analysis of sequences and, as in this paper, for discovering conserved regions. Our method is computationally more efficient than multiple sequences alignment since it can apply modern data stream clustering algorithms which run in time linear in the number of segments and thus can help discover highly similar regions across a large number of sequences efficiently. In this paper, we apply the approach to efficiently discover and visualize conserved regions in 16S rRNA.
[4] Michael Hahsler and Sudheer Chelluboina. Visualizing association rules in hierarchical groups. Unpublished. Presented at the 42nd Symposium on the Interface: Statistical, Machine Learning, and Visualization Algorithms (Interface 2011), June 2011. [ bib | .pdf ]
Association rule mining is one of the most popular data mining methods. However, mining association rules often results in a very large number of found rules, leaving the analyst with the task to go through all the rules and discover interesting ones. Sifting manually through large sets of rules is time consuming and strenuous. Visualization has a long history of making large amounts of data better accessible using techniques like selecting and zooming. However, most association rule visualization techniques are still falling short when it comes to a large number of rules. In this paper we present a new interactive visualization technique which lets the user navigate through a hierarchy of groups of association rules. We demonstrate how this new visualization techniques can be used to analyze a large sets of association rules with examples from our implementation in the R-package arulesViz.
[5] Michael Hahsler and Kurt Hornik. Dissimilarity plots: A visual exploration tool for partitional clustering. Journal of Computational and Graphical Statistics, 10(2):335--354, June 2011. [ bib | DOI | .pdf ]
For hierarchical clustering, dendrograms are a convenient and powerful visualization technique. Although many visualization methods have been suggested for partitional clustering, their usefulness deteriorates quickly with increasing dimensionality of the data and/or they fail to represent structure between and within clusters simultaneously. In this paper we extend (dissimilarity) matrix shading with several reordering steps based on seriation techniques. Both ideas, matrix shading and reordering, have been well-known for a long time. However, only recent algorithmic improvements allow us to solve or approximately solve the seriation problem efficiently for larger problems. Furthermore, seriation techniques are used in a novel stepwise process (within each cluster and between clusters) which leads to a visualization technique that is able to present the structure between clusters and the micro-structure within clusters in one concise plot. This not only allows us to judge cluster quality but also makes mis-specification of the number of clusters apparent. We give a detailed discussion of the construction of dissimilarity plots and demonstrate their usefulness with several examples. Experiments show that dissimilarity plots scale very well with increasing data dimensionality.
[6] Michael Hahsler, Sudheer Chelluboina, Kurt Hornik, and Christian Buchta. The arules R-package ecosystem: Analyzing interesting patterns from large transaction datasets. Journal of Machine Learning Research, 12:1977--1981, 2011. [ bib | at the publisher ]
This paper describes the ecosystem of R add-on packages developed around the infrastructure provided by the package arules. The packages provide comprehensive functionality for analyzing interesting patterns including frequent itemsets, association rules, frequent sequences and for building applications like associative classification. After discussing the ecosystem's design we illustrate the ease of mining and visualizing rules with a short example.
[7] Michael Hahsler, Kurt Hornik, and Christian Buchta. Getting things in order: An introduction to the R package seriation. Journal of Statistical Software, 25(3):1--34, March 2008. [ bib | DOI | .pdf ]
Seriation, i.e., finding a linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem's combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides the infrastructure for seriation with R. The infrastructure comprises data structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.
[8] Michael Hahsler and Kurt Hornik. TSP -- Infrastructure for the traveling salesperson problem. Journal of Statistical Software, 23(2):1--21, December 2007. [ bib | DOI | .pdf ]
The traveling salesperson (or, salesman) problem (TSP) is a well known and important combinatorial optimization problem. The goal is to find the shortest tour that visits each city in a given list exactly once and then returns to the starting city. Despite this simple problem statement, solving the TSP is difficult since it belongs to the class of NP-complete problems. The importance of the TSP arises besides from its theoretical appeal from the variety of its applications. Typical applications in operations research include vehicle routing, computer wiring, cutting wallpaper and job sequencing. The main application in statistics is combinatorial data analysis, e.g., reordering rows and columns of data matrices or identifying clusters. In this paper we introduce the R package TSP which provides a basic infrastructure for handling and solving the traveling salesperson problem. The package features S3 classes for specifying a TSP and its (possibly optimal) solution as well as several heuristics to find good solutions. In addition, it provides an interface to Concorde, one of the best exact TSP solvers currently available.

Other

[1] Jake Drew, Michael Hahsler, and Tyler Moore. Polymorphic malware detection using sequence classification methods. EURASIP Journal on Information Security, 2017(1):1--12, January 2017. [ bib | DOI | at the publisher ]
Identifying malicious software executables is made difficult by the constant adaptations introduced by miscreants in order to evade detection by antivirus software. Such changes are akin to mutations in biological sequences. Recently, high-throughput methods for gene sequence classification have been developed by the bioinformatics and computational biology communities. In this paper, we apply methods designed for gene sequencing to detect malware in a manner robust to attacker adaptations. Whereas most gene classification tools are optimized for and restricted to an alphabet of four letters (nucleic acids), we have selected the Strand gene sequence classifier for malware classification. Strand's design can easily accommodate unstructured data with any alphabet, including source code or compiled machine code. To demonstrate that gene sequence classification tools are suitable for classifying malware, we apply Strand to approximately 500GB of malware data provided by the Kaggle Microsoft Malware Classification Challenge (BIG 2015) used for predicting 9 classes of polymorphic malware. Experiments show that, with minimal adaptation, the method achieves accuracy levels well above 95% requiring only a fraction of the training times used by the winning team's method.
[2] Jake Drew, Michael Hahsler, and Tyler Moore. Polymorphic malware detection using sequence classification methods. In International Workshop on Bio-inspired Security, Trust, Assurance and Resilience (BioSTAR 2016), May 2016. [ bib | .pdf ]
Polymorphic malware detection is challenging due to the continual mutations miscreants introduce to successive instances of a particular virus. Such changes are akin to mutations in biological sequences. Recently, high-throughput methods for gene sequence classification have been developed by the bioinformatics and computational biology communities. In this paper, we argue that these methods can be usefully applied to malware detection. Unfortunately, gene classification tools are usually optimized for and restricted to an alphabet of four letters (nucleic acids). Consequently, we have selected the Strand gene sequence classifier, which offers a robust classification strategy that can easily accommodate unstructured data with any alphabet including source code or compiled machine code. To demonstrate Stand's suitability for classifying malware, we execute it on approximately 500GB of malware data provided by the Kaggle Microsoft Malware Classification Challenge (BIG 2015) used for predicting 9 classes of polymorphic malware. Experiments show that, with minimal adaptation, the method achieves accuracy levels well above 95% requiring only a fraction of the training times used by the winning team's method.
[3] Becca Mokhtarpour, Jerrell T. Stracener, and Michael Hahsler. A data-analysis approach for improved decision-making in selecting the preferred SoS capability solution. In 2016 Conference on Systems Engineering Research, March 2016. [ bib ]
A system of systems (SoS) approach for providing a new capability has been gaining increased attention, and consequently resulted in numerous research activities. However, decision-making methods and frameworks are still lacking in this area. In this paper, a general method is presented for selecting the preferred SoS solution within a large and complex solution space. The method presented in this paper combines statistical data analysis and ranking methods to screen a large number of feasible SoS solutions in a high-dimensional space and present the best SoS solution to the stakeholders. This method reduces the order of the solution space to a manageable level to enable communication among stakeholders. The advantage of the method is in increased participation of stakeholders by providing a smaller palette of solutions that can be effectively negotiated and compared in terms of various estimated decision factors. The effectiveness of this method is demonstrated through a hypothetical case of a search-and-rescue mission.
[4] Sudheer Chelluboina and Michael Hahsler. Trajectory segmentation using oblique envelopes. In 2015 IEEE International Conference on Information Reuse and Integration (IRI), pages 470--475. IEEE, August 2015. [ bib | DOI ]
Trajectory segmentation, i.e., breaking the trajectory into sub-trajectories, is a fundamental task needed for many applications dealing with moving objects. Several methods for trajectory segmentation, e.g., based on minimum description length (MDL), have been proposed. In this paper, we develop a novel technique for trajectory segmentation which created a series of oblique envelopes to partition the trajectory into sub-trajectories. Experiments with the new algorithm on hurricane trajectory data, taxi GPS data and simulated data of tracks show that oblique envelopes out-perform MDL-based trajectory segmentation.

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