Representing distributions over permutations can be a daunting task due to the fact that the number of permutations of $n$ objects scales factorially in $n$. One recent way that has been used to reduce storage complexity has been to exploit probabilistic independence, but as we argue, full independence assumptions impose strong sparsity constraints on distributions and are unsuitable for modeling rankings. We identify a novel class of independence structures, called \emph{riffled independence}, encompassing a more expressive family of distributions while retaining many of the properties necessary for performing efficient inference and reducing sample complexity. In riffled independence, one draws two permutations independently, then performs the \emph{riffle shuffle}, common in card games, to combine the two permutations to form a single permutation. Within the context of ranking, riffled independence corresponds to ranking disjoint sets of objects independently, then interleaving those rankings. In this paper, we provide a formal introduction to riffled independence and present algorithms for using riffled independence within Fourier-theoretic frameworks which have been explored by a number of recent papers. Additionally, we propose an automated method for discovering sets of items which are riffle independent from a training set of rankings. We show that our clustering-like algorithms can be used to discover meaningful latent coalitions from real preference ranking datasets and to learn the structure of hierarchically decomposable models based on riffled independence.

A semantic network is a directed labeled graph (Sowa, 1991). The thesis of this article is that the state of a computing machine, its low-level instructions, and the executing program can be represented as a semantic network. The computational model that is presented can be instantiated using any semantic network representation. However, given the existence of the Resource Description Framework (RDF) (Manola & Miller, 2004) and the popular Web Ontology Language (OWL) (McGuinness & Harmelen, 2004), this article presents the theory and the application in terms of these constructs. The computing model that is proposed is perhaps simple in theory, but in application, requires a relatively strong background in the computer sciences.

The basic unit of meaning on the Semantic Web is the RDF statement, or triple, which combines a distinct subject, predicate and object to make a definite assertion about the world. A set of triples constitutes a graph, to which they give a collective meaning. It is upon this simple foundation that the rich, complex knowledge structures of the Semantic Web are built. Yet the very expressiveness of RDF, by inviting comparison with real-world knowledge, highlights a fundamental shortcoming, in that RDF is limited to statements of absolute fact, independent of the context in which a statement is asserted. This is in stark contrast with the thoroughly context-sensitive nature of human thought. The model presented here provides a particularly simple means of contextualizing an RDF triple by associating it with related statements in the same graph. This approach, in combination with a notion of graph similarity, is sufficient to select only those statements from an RDF graph which are subjectively most relevant to the context of the requesting process.

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.

Class prediction is an important application of microarray gene expression data analysis. The high-dimensionality of microarray data, where number of genes (variables) is very large compared to the number of samples (obser- vations), makes the application of many prediction techniques (e.g., logistic regression, discriminant analysis) difficult. An efficient way to solve this prob- lem is by using dimension reduction statistical techniques. Increasingly used in psychology-related applications, Rasch model (RM) provides an appealing framework for handling high-dimensional microarray data. In this paper, we study the potential of RM-based modeling in dimensionality reduction with binarized microarray gene expression data and investigate its prediction ac- curacy in the context of class prediction using linear discriminant analysis. Two different publicly available microarray data sets are used to illustrate a general framework of the approach. Performance of the proposed method is assessed by re-randomization scheme using principal component analysis (PCA) as a benchmark method. Our results show that RM-based dimension reduction is as effective as PCA-based dimension reduction. The method is general and can be applied to the other high-dimensional data problems.

We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show that global consistency with the data can be achieved through purely local considerations, inferring the neighbourhood of each node in turn. The optimisation problem solved for each individual node can be reduced to a Set Covering Problem, which is known to be NP-hard but can be approximated well in practice. We then extend our approach to account for noisy data, based on the Minimum Description Length principle. We demonstrate our algorithms on synthetic data, generated by an SIR-like epidemiological model.

We introduce a framework for representing a variety of interesting problems as inference over the execution of probabilistic model programs. We represent a "solution" to such a problem as a guide program which runs alongside the model program and influences the model program's random choices, leading the model program to sample from a different distribution than from its priors. Ideally the guide program influences the model program to sample from the posteriors given the evidence. We show how the KL- divergence between the true posterior distribution and the distribution induced by the guided model program can be efficiently estimated (up to an additive constant) by sampling multiple executions of the guided model program. In addition, we show how to use the guide program as a proposal distribution in importance sampling to statistically prove lower bounds on the probability of the evidence and on the probability of a hypothesis and the evidence. We can use the quotient of these two bounds as an estimate of the conditional probability of the hypothesis given the evidence. We thus turn the inference problem into a heuristic search for better guide programs.

Standard hybrid learners that use domain knowledge require stronger knowledge that is hard and expensive to acquire. However, weaker domain knowledge can benefit from prior knowledge while being cost effective. Weak knowledge in the form of feature relative importance (FRI) is presented and explained. Feature relative importance is a real valued approximation of a feature's importance provided by experts. Advantage of using this knowledge is demonstrated by IANN, a modified multilayer neural network algorithm. IANN is a very simple modification of standard neural network algorithm but attains significant performance gains. Experimental results in the field of molecular biology show higher performance over other empirical learning algorithms including standard backpropagation and support vector machines. IANN performance is even comparable to a theory refinement system KBANN that uses stronger domain knowledge. This shows Feature relative importance can improve performance of existing empirical learning algorithms significantly with minimal effort.

Model selection in clustering requires (i) to specify a suitable clustering principle and (ii) to control the model order complexity by choosing an appropriate number of clusters depending on the noise level in the data. We advocate an information theoretic perspective where the uncertainty in the measurements quantizes the set of data partitionings and, thereby, induces uncertainty in the solution space of clusterings. A clustering model, which can tolerate a higher level of fluctuations in the measurements than alternative models, is considered to be superior provided that the clustering solution is equally informative. This tradeoff between \emph{informativeness} and \emph{robustness} is used as a model selection criterion. The requirement that data partitionings should generalize from one data set to an equally probable second data set gives rise to a new notion of structure induced information.