Matrix decomposition methods represent a data matrix as a product of two factor matrices: one containing basis vectors that represent meaningful concepts in the data, and another describing how the observed data can be expressed as combinations of the basis vectors. Decomposition methods have been studied extensively, but many methods return real-valued matrices. Interpreting real-valued factor matrices is hard if the original data is Boolean. In this paper, we describe a matrix decomposition formulation for Boolean data, the Discrete Basis Problem. The problem seeks for a Boolean decomposition of a binary matrix, thus allowing the user to easily interpret the basis vectors. We also describe a variation of the problem, the Discrete Basis Partitioning Problem. We show that both problems are NP-hard. For the Discrete Basis Problem, we give a simple greedy algorithm for solving it; for the Discrete Basis Partitioning Problem we show how it can be solved using existing methods. We present experimental results for the greedy algorithm and compare it against other, well known methods. Our algorithm gives intuitive basis vectors, but its reconstruction error is usually larger than with the real-valued methods. We discuss about the reasons for this behavior.

The discovery of subsets with special properties from binary data hasbeen one of the key themes in pattern discovery. Pattern classes suchas frequent itemsets stress the co-occurrence of the value 1 in the data. While this choice makes sense in the context of sparse binary data, it disregards potentially interesting subsets of attributes that have some other type of dependency structure.

BACKGROUND: Haplotype Reconstruction is the problem of resolving the hidden phase information in genotype data obtained from laboratory measurements. Solving this problem is an important intermediate step in gene association studies, which seek to uncover the genetic basis of complex diseases. We propose a novel approach for haplotype reconstruction based on constrained hidden Markov models. Models are constructed by incrementally refining and regularizing the structure of a simple generative model for genotype data under Hardy-Weinberg equilibrium. RESULTS: The proposed method is evaluated on real-world and simulated population data. Results show that it is competitive with other recently proposed methods in terms of reconstruction accuracy, while offering a particularly good trade-off between computational costs and quality of results for large datasets. CONCLUSION: Relatively simple probabilistic approaches for haplotype reconstruction based on structured hidden Markov models are competitive with more complex, well-established techniques in this field.

The problem of assessing the significance of data mining results on high-dimensional 0--1 datasets has been studied extensively in the literature. For problems such as mining frequent sets and finding correlations, significance testing can be done by standard statistical tests such as chi-square, or other methods. However, the results of such tests depend only on the specific attributes and not on the dataset as a whole. Moreover, the tests are difficult to apply to sets of patterns or other complex results of data mining algorithms. In this article, we consider a simple randomization technique that deals with this shortcoming. The approach consists of producing random datasets that have the same row and column margins as the given dataset, computing the results of interest on the randomized instances and comparing them to the results on the actual data. This randomization technique can be used to assess the results of many different types of data mining algorithms, such as frequent sets, clustering, and spectral analysis. To generate random datasets with given margins, we use variations of a Markov chain approach which is based on a simple swap operation. We give theoretical results on the efficiency of different randomization methods, and apply the swap randomization method to several well-known datasets. Our results indicate that for some datasets the structure discovered by the data mining algorithms is expected, given the row and column margins of the datasets, while for other datasets the discovered structure conveys information that is not captured by the margin counts.

Many 0/1 datasets have a very large number of variables; however, they are sparse and the dependency structure of the variables is simpler than the number of variables would suggest. Defining the effective dimensionality of such a dataset is a nontrivial problem. We consider the problem of defining a robust measure of dimension for 0/1 datasets, and show that the basic idea of fractal dimension can be adapted for binary data. However, as such the fractal dimension is difficult to interpret. Hence we introduce the concept of normalized fractal dimension. For a dataset D, its normalized fractal dimension counts the number of independent columns needed to achieve the unnormalized fractal dimension of D. The normalized fractal dimension measures the degree of dependency structure of the data. We study the properties of the normalized fractal dimension and discuss its computation. We give empirical results on the normalized fractal dimension, comparing it against PCA.

The problem of assessing the significance of data mining results on high-dimensional 0-1 data sets has been studied extensively in the literature. For problems such as mining frequent sets and finding correlations, significance testing can be done by, e.g., chi-square tests, or many other methods. However, the results of such tests depend only on the specific attributes and not on the dataset as a whole. Moreover, the tests are more difficult to apply to sets of patterns or other complex results of data mining. In this paper, we consider a simple randomization technique that deals with this shortcoming. The approach consists of producing random datasets that have the same row and column margins with the given dataset, computing the results of interest on the randomized instances, and comparing them against the results on the actual data. This randomization technique can be used to assess the results of many different types of data mining algorithms, such as frequent sets, clustering, and rankings. To generate random datasets with given margins, we use variations of a Markov chain approach, which is based on a simple swap operation. We give theoretical results on the efficiency of different randomization methods, and apply the swap randomization method to several well-known datasets. Our results indicate that for some datasets the structure discovered by the data mining algorithms is a random artifact, while for other datasets the discovered structure conveys meaningful information.

We propose private protocols implementing the Kernel Adatron and Kernel Perceptron learning algorithms, give private classification protocols and private polynomial kernel computation protocols. The new protocols return their outputs - either the kernel value, the classifier or the classifications - in encrypted form so that they can be decrypted only by a common agreement by the protocol participants. We show how to use the encrypted classifications to privately estimate many properties of the data and the classifier. The new SVM classifiers are the first to be proven private according to the standard cryptographic definitions.

Partitions of sequential data exist either per se or as a result of sequence segmentation algorithms. It is often the case that the same timeline is partitioned in many different ways. For example, different segmentation algorithms produce different partitions of the same underlying data points. In such cases, we are interested in producing an aggregate partition, i.e., a segmentation that agrees as much as possible with the input segmentations. Each partition is defined as a set of continuous non-overlapping segments of the timeline. We show that this problem can be solved optimally in polynomial time using dynamic programming. We also propose faster greedy heuristics that work well in practice. We experiment with our algorithms and we demonstrate their utility in clustering the behavior of mobile-phone users and combining the results of different segmentation algorithms on genomic sequences.

MOTIVATION: Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the development of isotopomer measurement techniques for intermediate metabolites is a demanding task. Careful planning of isotopomer measurements is thus needed to maximize the available flux information while minimizing the experimental effort. RESULTS: In this paper we study the question of finding the smallest subset of metabolites to measure that ensure the same level of isotopomer information as the measurement of every metabolite in the metabolic network. We study the computational complexity of this optimization problem in the case of the so-called positional enrichment data, give methods for obtaining exact and fast approximate solutions, and evaluate empirically the efficacy of the proposed methods by analyzing a metabolic network that models the central carbon metabolism of Saccharomyces cerevisiae.

Traditional data mining applications consider the problem of mining a single relation between two attributes. For example, in a scientific bibliography database, authors are related to papers, and we may be interested in discovering association rules between authors. However, in real life, we often have multiple attributes related though chains of relations. For example, authors write papers, and papers concern one or more topics. Mining such relational chains poses additional challenges. In this paper we consider the following problem: given a chain of two relations R/sub 1/ (A, P) and R/sub 2/(P, T) we want to find selectors for the objects in T such that the projected relation between A and P satisfies a specific property. The motivation for our approach is that a given property might not hold on the whole dataset, but it might hold when projecting the data on a selector set. We discuss various algorithms and we examine the conditions under which the a priori technique can be used. We experimentally demonstrate the effectiveness of our methods.

A very important problem in data mining is finding patterns from sequential data. There is a vast number of sources for sequential data such as biological sequences, text documents, telecommunication alarm sequences, click streams, market basket data, Web logs, and other time series. One of the most popular patterns mined from sequential data are the episodes, i.e., directed acyclic graphs with labeled nodes (Mannila et al., 1997), An important subclass of episodes are the serial episodes, which are essentially sequences. Serial episodes are useful in many applications, including network monitoring and molecular biology. Currently, there are many situations were so much sequential data is produced that it cannot even be stored without great difficulties. That kind of sequential sources are called data streams. In this paper we focus on finding serial episodes from data streams. To the best of our knowledge the problem of mining serial episodes from data streams has been studied in depth only for length-1 episodes (Karp et al., 2003).

We introduce a generalization of association rules: change profiles. We analyze their properties, describe their relationship to other structures in pattern discovery and sketch their possible applications. We study how the frequent patterns can be clustered based on their change profiles and propose methods for approximating the frequencies of the patterns from the approximate change profiles and bounding the intervals where the frequencies of the patterns are guaranteed to be. We evaluate empirically the methods for estimating the frequencies and the stability of their frequency estimates under different kinds of noise.