Elisabeth Georgii

Alumni

Empirical Inference

Publications

8 results (View BibTeX file of all listed publications)

2011

Multi-way set enumeration in weight tensors

Georgii, E., Tsuda, K., Schölkopf, B.

Machine Learning, 82(2):123-155, February 2011 (article)

Abstract

The analysis of n-ary relations receives attention in many different fields, for instance biology, web mining, and social studies. In the basic setting, there are n sets of instances, and each observation associates n instances, one from each set. A common approach to explore these n-way data is the search for n-set patterns, the n-way equivalent of itemsets. More precisely, an n-set pattern consists of specific subsets of the n instance sets such that all possible associations between the corresponding instances are observed in the data. In contrast, traditional itemset mining approaches consider only two-way data, namely items versus transactions. The n-set patterns provide a higher-level view of the data, revealing associative relationships between groups of instances. Here, we generalize this approach in two respects. First, we tolerate missing observations to a certain degree, that means we are also interested in n-sets where most (although not all) of the possible associations have been recorded in the data. Second, we take association weights into account. In fact, we propose a method to enumerate all n-sets that satisfy a minimum threshold with respect to the average association weight. Technically, we solve the enumeration task using a reverse search strategy, which allows for effective pruning of the search space. In addition, our algorithm provides a ranking of the solutions and can consider further constraints. We show experimental results on artificial and real-world datasets from different domains.

PDF DOI [BibTex]

2011

Georgii, E., Tsuda, K., Schölkopf, B. Multi-way set enumeration in weight tensors Machine Learning, 82(2):123-155, February 2011 (article)

PDF DOI [BibTex]

2010

Structural and Relational Data Mining for Systems Biology Applications

Georgii, E.

Eberhard Karls Universität Tübingen, Germany , 2010 (phdthesis)

Web [BibTex]

2010

Georgii, E. Structural and Relational Data Mining for Systems Biology Applications Eberhard Karls Universität Tübingen, Germany , 2010 (phdthesis)

Web [BibTex]

2009

Multi-way set enumeration in real-valued tensors

Georgii, E., Tsuda, K., Schölkopf, B.

In Proceedings of the 2nd Workshop on Data Mining using Matrices and Tensors (DMMT 2009), pages: 32-41, (Editors: C Ding and T Li), ACM Press, New York, NY, USA, 2nd Workshop on Data Mining using Matrices and Tensors (DMMT/KDD), June 2009 (inproceedings)

Abstract

The analysis of n-ary relations receives attention in many different fields, for instance biology, web mining, and social studies. In the basic setting, there are n sets of instances, and each observation associates n instances, one from each set. A common approach to explore these n-way data is the search for n-set patterns. An n-set pattern consists of specific subsets of the n instance sets such that all possible n- ary associations between the corresponding instances are observed. This provides a higher-level view of the data, revealing associative relationships between groups of instances. Here, we generalize this approach in two respects. First, we tolerate missing observations to a certain degree, that means we are also interested in n-sets where most (although not all) of the possible combinations have been recorded in the data. Second, we take association weights into account. More precisely, we propose a method to enumerate all n- sets that satisfy a minimum threshold with respect to the average association weight. Non-observed associations obtain by default a weight of zero. Technically, we solve the enumeration task using a reverse search strategy, which allows for effective pruning of the search space. In addition, our algorithm provides a ranking of the solutions and can consider further constraints. We show experimental results on artificial and real-world data sets from different domains.

PDF DOI [BibTex]

2009

Georgii, E., Tsuda, K., Schölkopf, B. Multi-way set enumeration in real-valued tensors In Proceedings of the 2nd Workshop on Data Mining using Matrices and Tensors (DMMT 2009), pages: 32-41, (Editors: C Ding and T Li), ACM Press, New York, NY, USA, 2nd Workshop on Data Mining using Matrices and Tensors (DMMT/KDD), June 2009 (inproceedings)

PDF DOI [BibTex]

Enumeration of condition-dependent dense modules in protein interaction networks

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K.

Bioinformatics, 25(7):933-940, February 2009 (article)

Abstract

Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles. Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants.

Web DOI [BibTex]

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K. Enumeration of condition-dependent dense modules in protein interaction networks Bioinformatics, 25(7):933-940, February 2009 (article)

Web DOI [BibTex]

The DICS repository: module-assisted analysis of disease-related gene lists

Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, H.

Bioinformatics, 25(6):830-831, January 2009 (article)

Abstract

The DICS database is a dynamic web repository of computationally predicted functional modules from the human proteinprotein interaction network. It provides references to the CORUM, DrugBank, KEGG and Reactome pathway databases. DICS can be accessed for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby providing valuable information about the functional context.

Web DOI [BibTex]

Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, H. The DICS repository: module-assisted analysis of disease-related gene lists Bioinformatics, 25(6):830-831, January 2009 (article)

Web DOI [BibTex]

2007

Mining expression-dependent modules in the human interaction network

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K.

BMC Bioinformatics, 8(Suppl. 8):S4, November 2007 (poster)

PDF DOI [BibTex]

2007

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K. Mining expression-dependent modules in the human interaction network BMC Bioinformatics, 8(Suppl. 8):S4, November 2007 (poster)

PDF DOI [BibTex]

2006

Global Biclustering of Microarray Data

Wolf, T., Brors, B., Hofmann, T., Georgii, E.

In ICDMW 2006, pages: 125-129, (Editors: Tsumoto, S. , C. W. Clifton, N. Zhong, X. Wu, J. Liu, B. W. Wah, Y.-M. Cheung), IEEE Computer Society, Los Alamitos, CA, USA, Sixth IEEE International Conference on Data Mining, December 2006 (inproceedings)

Abstract

We consider the problem of simultaneously clustering genes and conditions of a gene expression data matrix. A bicluster is defined as a subset of genes that show similar behavior within a subset of conditions. Finding biclusters can be useful for revealing groups of genes involved in the same molecular process as well as groups of conditions where this process takes place. Previous work either deals with local, bicluster-based criteria or assumes a very specific structure of the data matrix (e.g. checkerboard or block-diagonal) [11]. In contrast, our goal is to find a set of flexibly arranged biclusters which is optimal in regard to a global objective function. As this is a NP-hard combinatorial problem, we describe several techniques to obtain approximate solutions. We benchmarked our approach successfully on the Alizadeh B-cell lymphoma data set [1].

Web DOI [BibTex]

2006

Wolf, T., Brors, B., Hofmann, T., Georgii, E. Global Biclustering of Microarray Data In ICDMW 2006, pages: 125-129, (Editors: Tsumoto, S. , C. W. Clifton, N. Zhong, X. Wu, J. Liu, B. W. Wah, Y.-M. Cheung), IEEE Computer Society, Los Alamitos, CA, USA, Sixth IEEE International Conference on Data Mining, December 2006 (inproceedings)

Web DOI [BibTex]

2005

Analyzing microarray data using quantitative association rules

Georgii, E., Richter, L., Rückert, U., Kramer, S.

Bioinformatics, 21(Suppl. 2):123-129, September 2005 (article)

Abstract

Motivation: We tackle the problem of finding regularities in microarray data. Various data mining tools, such as clustering, classification, Bayesian networks and association rules, have been applied so far to gain insight into gene-expression data. Association rule mining techniques used so far work on discretizations of the data and cannot account for cumulative effects. In this paper, we investigate the use of quantitative association rules that can operate directly on numeric data and represent cumulative effects of variables. Technically speaking, this type of quantitative association rules based on half-spaces can find non-axis-parallel regularities. Results: We performed a variety of experiments testing the utility of quantitative association rules for microarray data. First of all, the results should be statistically significant and robust against fluctuations in the data. Next, the approach should be scalable in the number of variables, which is important for such high-dimensional data. Finally, the rules should make sense biologically and be sufficiently different from rules found in regular association rule mining working with discretizations. In all of these dimensions, the proposed approach performed satisfactorily. Therefore, quantitative association rules based on half-spaces should be considered as a tool for the analysis of microarray gene-expression data.

Web DOI [BibTex]

2005

Georgii, E., Richter, L., Rückert, U., Kramer, S. Analyzing microarray data using quantitative association rules Bioinformatics, 21(Suppl. 2):123-129, September 2005 (article)

Web DOI [BibTex]