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.

Auctions are markets with strict regulations governing the information available to traders in the market and the possible actions they can take. Since well designed auctions achieve desirable economic outcomes, they have been widely used in solving real-world optimization problems, and in structuring stock or futures exchanges. Auctions also provide a very valuable testing-ground for economic theory, and they play an important role in computer-based control systems. Auction mechanism design aims to manipulate the rules of an auction in order to achieve specific goals. Economists traditionally use mathematical methods, mainly game theory, to analyze auctions and design new auction forms. However, due to the high complexity of auctions, the mathematical models are typically simplified to obtain results, and this makes it difficult to apply results derived from such models to market environments in the real world. As a result, researchers are turning to empirical approaches. This report aims to survey the theoretical and empirical approaches to designing auction mechanisms and trading strategies with more weights on empirical ones, and build the foundation for further research in the field.

We introduce a new tractable temporal constraint language, which strictly contains the Ord-Horn language of Buerkert and Nebel and the class of AND/OR precedence constraints. The algorithm we present for this language decides whether a given set of constraints is consistent in time that is quadratic in the input size. We also prove that (unlike Ord-Horn) this language cannot be solved by Datalog or by establishing local consistency.

This papers develops a logical language for representing probabilistic causal laws. Our interest in such a language is twofold. First, it can be motivated as a fundamental study of the representation of causal knowledge. Causality has an inherent dynamic aspect, which has been studied at the semantical level by Shafer in his framework of probability trees. In such a dynamic context, where the evolution of a domain over time is considered, the idea of a causal law as something which guides this evolution is quite natural. In our formalization, a set of probabilistic causal laws can be used to represent a class of probability trees in a concise, flexible and modular way. In this way, our work extends Shafer's by offering a convenient logical representation for his semantical objects. Second, this language also has relevance for the area of probabilistic logic programming. In particular, we prove that the formal semantics of a theory in our language can be equivalently defined as a probability distribution over the well-founded models of certain logic programs, rendering it formally quite similar to existing languages such as ICL or PRISM. Because we can motivate and explain our language in a completely self-contained way as a representation of probabilistic causal laws, this provides a new way of explaining the intuitions behind such probabilistic logic programs: we can say precisely which knowledge such a program expresses, in terms that are equally understandable by a non-logician. Moreover, we also obtain an additional piece of knowledge representation methodology for probabilistic logic programs, by showing how they can express probabilistic causal laws.

In this paper we apply computer learning methods to diagnosing ovarian cancer using the level of the standard biomarker CA125 in conjunction with information provided by mass-spectrometry. We are working with a new data set collected over a period of 7 years. Using the level of CA125 and mass-spectrometry peaks, our algorithm gives probability predictions for the disease. To estimate classification accuracy we convert probability predictions into strict predictions. Our algorithm makes fewer errors than almost any linear combination of the CA125 level and one peak's intensity (taken on the log scale). To check the power of our algorithm we use it to test the hypothesis that CA125 and the peaks do not contain useful information for the prediction of the disease at a particular time before the diagnosis. Our algorithm produces $p$-values that are better than those produced by the algorithm that has been previously applied to this data set. Our conclusion is that the proposed algorithm is more reliable for prediction on new data.

An intent expression system using eye robots is proposed for a mascot robot system from a viewpoint of humatronics. The eye robot aims at providing a basic interface method for an information terminal robot system. To achieve better understanding of the displayed information, the importance and the degree of certainty of the information should be communicated along with the main content. The proposed intent expression system aims at conveying this additional information using the eye robot system. Eye motions are represented as the states in a pleasure-arousal space model. Changes in the model state are calculated by fuzzy inference according to the importance and degree of certainty of the displayed information. These changes influence the arousal-sleep coordinates in the space that corresponds to levels of liveliness during communication. The eye robot provides a basic interface for the mascot robot system that is easy to be understood as an information terminal for home environments in a humatronics society.

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.

We propose an efficient algorithm for sparse signal reconstruction problems. The proposed algorithm is an augmented Lagrangian method based on the dual sparse reconstruction problem. It is efficient when the number of unknown variables is much larger than the number of observations because of the dual formulation. Moreover, the primal variable is explicitly updated and the sparsity in the solution is exploited. Numerical comparison with the state-of-the-art algorithms shows that the proposed algorithm is favorable when the design matrix is poorly conditioned or dense and very large.

A mechanism called Eligibility Propagation is proposed to speed up the Time Hopping technique used for faster Reinforcement Learning in simulations. Eligibility Propagation provides for Time Hopping similar abilities to what eligibility traces provide for conventional Reinforcement Learning. It propagates values from one state to all of its temporal predecessors using a state transitions graph. Experiments on a simulated biped crawling robot confirm that Eligibility Propagation accelerates the learning process more than 3 times.

The pace of progress in the fields of Evolutionary Computation and Machine Learning is currently limited -- in the former field, by the improbability of making advantageous extensions to evolutionary algorithms when their capacity for adaptation is poorly understood, and in the latter by the difficulty of finding effective semi-principled reductions of hard real-world problems to relatively simple optimization problems. In this paper we explain why a theory which can accurately explain the simple genetic algorithm's remarkable capacity for adaptation has the potential to address both these limitations. We describe what we believe to be the impediments -- historic and analytic -- to the discovery of such a theory and highlight the negative role that the building block hypothesis (BBH) has played. We argue based on experimental results that a fundamental limitation which is widely believed to constrain the SGA's adaptive ability (and is strongly implied by the BBH) is in fact illusionary and does not exist. The SGA therefore turns out to be more powerful than it is currently thought to be. We give conditions under which it becomes feasible to numerically approximate and study the multivariate marginals of the search distribution of an infinite population SGA over multiple generations even when its genomes are long, and explain why this analysis is relevant to the riddle of the SGA's remarkable adaptive abilities.