We report recent research on computing with biology-based neural network models by means of physics-based opto-electronic hardware. New technology provides opportunities for very-high-speed computation and uncovers problems obstructing the wide-spread use of this new capability. The Computation Modeling community may be able to offer solutions to these cross-boundary research problems.

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.

The Lady Maisry ballads afford us a framework within which to segment a storyline into its major components. Segments and as a consequence nodal points are discussed for nine different variants of the Lady Maisry story of a (young) woman being burnt to death by her family, on account of her becoming pregnant by a foreign personage. We motivate the importance of nodal points in textual and literary analysis. We show too how the openings of the nine variants can be analyzed comparatively, and also the conclusions of the ballads.

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.

This article presents a model of general-purpose computing on a semantic network substrate. The concepts presented are applicable to any semantic network representation. However, due to the standards and technological infrastructure devoted to the Semantic Web effort, this article is presented from this point of view. In the proposed model of computing, the application programming interface, the run-time program, and the state of the computing virtual machine are all represented in the Resource Description Framework (RDF). The implementation of the concepts presented provides a practical computing paradigm that leverages the highly-distributed and standardized representational-layer of the Semantic Web.

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.

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.

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.

Pac-Bayes bounds are among the most accurate generalization bounds for classifiers learned from independently and identically distributed (IID) data, and it is particularly so for margin classifiers: there have been recent contributions showing how practical these bounds can be either to perform model selection (Ambroladze et al., 2007) or even to directly guide the learning of linear classifiers (Germain et al., 2009). However, there are many practical situations where the training data show some dependencies and where the traditional IID assumption does not hold. Stating generalization bounds for such frameworks is therefore of the utmost interest, both from theoretical and practical standpoints. In this work, we propose the first - to the best of our knowledge - Pac-Bayes generalization bounds for classifiers trained on data exhibiting interdependencies. The approach undertaken to establish our results is based on the decomposition of a so-called dependency graph that encodes the dependencies within the data, in sets of independent data, thanks to graph fractional covers. Our bounds are very general, since being able to find an upper bound on the fractional chromatic number of the dependency graph is sufficient to get new Pac-Bayes bounds for specific settings. We show how our results can be used to derive bounds for ranking statistics (such as Auc) and classifiers trained on data distributed according to a stationary {\ss}-mixing process. In the way, we show how our approach seemlessly allows us to deal with U-processes. As a side note, we also provide a Pac-Bayes generalization bound for classifiers learned on data from stationary $\varphi$-mixing distributions.