Subspace clustering has gained increasing popularity in the analysis of gene expression data. Among subspace cluster models, the recently introduced order-preserving sub-matrix (OPSM) has demonstrated high promise. An OPSM, essentially a pattern-based subspace cluster, is a subset of rows and columns in a data matrix for which all the rows induce the same linear ordering of columns. Existing OPSM discovery methods do not scale well to increasingly large expression datasets. In particular, twig clusters having few genes and many experiments incur explosive computational costs and are completely pruned off by existing methods. However, it is of particular interest to determine small groups of genes that are tightly coregulated across many conditions. In this paper, we present KiWi, an OPSM subspace clustering algorithm that is scalable to massive datasets, capable of discovering twig clusters and identifying negative as well as positive correlations. We extensively validate KiWi using relevant biological datasets and show that KiWi correctly assigns redundant probes to the same cluster, groups experiments with common clinical annotations, differentiates real promoter sequences from negative control sequences, and shows good association with cis-regulatory motif predictions.

This paper applies machine learning techniques to student modeling. It presents a method for discovering high-level student behaviors from a very large set of low-level traces corresponding to problem-solving actions in a learning environment. Basic actions are encoded into sets of domain-dependent attribute-value patterns called cases. Then a domain-independent hierarchical clustering identifies what we call general attitudes, yielding automatic diagnosis expressed in natural language, addressed in principle to teachers. The method can be applied to individual students or to entire groups, like a class. We exhibit examples of this system applied to thousands of students' actions in the domain of algebraic transformations.

The task of identifying synonymous relations and objects, or synonym resolution, is critical for high-quality information extraction. This paper investigates synonym resolution in the context of unsupervised information extraction, where neither hand-tagged training examples nor domain knowledge is available. The paper presents a scalable, fully-implemented system that runs in O(KN log N) time in the number of extractions, N, and the maximum number of synonyms per word, K. The system, called Resolver , introduces a probabilistic relational model for predicting whether two strings are co-referential based on the similarity of the assertions containing them. On a set of two million assertions extracted from the Web, Resolver resolves objects with 78% precision and 68% recall, and resolves relations with 90% precision and 35% recall. Several variations of resolver's probabilistic model are explored, and experiments demonstrate that under appropriate conditions these variations can improve F1 by 5%. An extension to the basic Resolver system allows it to handle polysemous names with 97% precision and 95% recall on a data set from the TREC corpus.

1-Nearest Neighbor with the Dynamic Time Warping (DTW) distance is one of the most effective classifiers on time series domain. Since the global constraint has been introduced in speech community, many global constraint models have been proposed including Sakoe-Chiba (S-C) band, Itakura Parallelogram, and Ratanamahatana-Keogh (R-K) band. The R-K band is a general global constraint model that can represent any global constraints with arbitrary shape and size effectively. However, we need a good learning algorithm to discover the most suitable set of R-K bands, and the current R-K band learning algorithm still suffers from an 'overfitting' phenomenon. In this paper, we propose two new learning algorithms, i.e., band boundary extraction algorithm and iterative learning algorithm. The band boundary extraction is calculated from the bound of all possible warping paths in each class, and the iterative learning is adjusted from the original R-K band learning. We also use a Silhouette index, a well-known clustering validation technique, as a heuristic function, and the lower bound function, LB_Keogh, to enhance the prediction speed. Twenty datasets, from the Workshop and Challenge on Time Series Classification, held in conjunction of the SIGKDD 2007, are used to evaluate our approach.

Domain experts should provide relevant domain knowledge to an Intelligent Tutoring System (ITS) so that it can guide a learner during problemsolving learning activities. However, for many ill-defined domains, the domain knowledge is hard to define explicitly. In previous works, we showed how sequential pattern mining can be used to extract a partial problem space from logged user interactions, and how it can support tutoring services during problem-solving exercises. This article describes an extension of this approach to extract a problem space that is richer and more adapted for supporting tutoring services. We combined sequential pattern mining with (1) dimensional pattern mining (2) time intervals, (3) the automatic clustering of valued actions and (4) closed sequences mining. Some tutoring services have been implemented and an experiment has been conducted in a tutoring system.

The problem of Hybrid Linear Modeling (HLM) is to model and segment data using a mixture of affine subspaces. Different strategies have been proposed to solve this problem, however, rigorous analysis justifying their performance is missing. This paper suggests the Theoretical Spectral Curvature Clustering (TSCC) algorithm for solving the HLM problem, and provides careful analysis to justify it. The TSCC algorithm is practically a combination of Govindu's multi-way spectral clustering framework (CVPR 2005) and Ng et al.'s spectral clustering algorithm (NIPS 2001). The main result of this paper states that if the given data is sampled from a mixture of distributions concentrated around affine subspaces, then with high sampling probability the TSCC algorithm segments well the different underlying clusters. The goodness of clustering depends on the within-cluster errors, the between-clusters interaction, and a tuning parameter applied by TSCC. The proof also provides new insights for the analysis of Ng et al. (NIPS 2001).

We present a simple new criterion for classification, based on principles from lossy data compression. The criterion assigns a test sample to the class that uses the minimum number of additional bits to code the test sample, subject to an allowable distortion. We prove asymptotic optimality of this criterion for Gaussian data and analyze its relationships to classical classifiers. Theoretical results provide new insights into relationships among popular classifiers such as MAP and RDA, as well as unsupervised clustering methods based on lossy compression [13]. Minimizing the lossy coding length induces a regularization effect which stabilizes the (implicit) density estimate in a small-sample setting. Compression also provides a uniform means of handling classes of varying dimension. This simple classification criterion and its kernel and local versions perform competitively against existing classifiers on both synthetic examples and real imagery data such as handwritten digits and human faces, without requiring domain-specific information.

We consider the ensemble clustering problem where the task is to'aggregate' multiple clustering solutions into a single consolidated clustering that maximizes the shared information among given clustering solutions. We obtain several new results for this problem. First, we note that the notion of agreement under such circumstances can be better captured using an agreement measure based on a 2D string encoding rather than voting strategy based methods proposed in literature. Using this generalization, we first derive a nonlinear optimization model to maximize the new agreement measure. We then show that our optimization problem can be transformed into a strict 0-1 Semidefinite Program (SDP) via novel convexification techniques which can subsequently be relaxed to a polynomial time solvable SDP. Our experiments indicate improvements not only in terms of the proposed agreement measure but also the existing agreement measures based on voting strategies. We discuss evaluations on clustering and image segmentation databases.

We describe a new algorithm, Relaxed Survey Propagation (RSP), for finding MAP configurations in Markov random fields. We compare its performance with state-of-the-art algorithms including the max-product belief propagation, its sequential tree-reweighted variant, residual (sum-product) belief propagation, and tree-structured expectation propagation. We show that it outperforms all approaches for Ising models with mixed couplings, as well as on a web person disambiguation task formulated as a supervised clustering problem.

We introduce a new Bayesian model for hierarchical clustering based on a prior over trees called Kingman's coalescent. We develop novel greedy and sequential Monte Carlo inferences which operate in a bottom-up agglomerative fashion. We show experimentally the superiority of our algorithms over the state-of-the-art, and demonstrate our approach in document clustering and phylolinguistics.