Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of these methods also require an a priori matching of the variables (e.g., genes or metabolites) between the species. However, many experiments have a complicated multi-way experimental design often involving irregularly-sampled time-series measurements, and for instance metabolites do not always have known matchings between organisms. We introduce a Bayesian modelling framework for translating between multiple species the results from 'omics' experiments having a complex multi-way, time-series experimental design. The underlying assumption is that the unknown matching can be inferred from the response of the variables to multiple covariates including time.

A new distance function dist(A,B) for fuzzy sets A and B is introduced. It is based on the descriptive complexity, i.e., the number of bits (on average) that are needed to describe an element in the symmetric difference of the two sets. The distance gives the amount of additional information needed to describe any one of the two sets given the other. We prove its mathematical properties and perform pattern clustering on data based on this distance.

A learning algorithm based on primary school teaching and learning is presented. The methodology is to continuously evaluate a student and to give them training on the examples for which they repeatedly fail, until, they can correctly answer all types of questions. This incremental learning procedure produces better learning curves by demanding the student to optimally dedicate their learning time on the failed examples. When used in machine learning, the algorithm is found to train a machine on a data with maximum variance in the feature space so that the generalization ability of the network improves. The algorithm has interesting applications in data mining, model evaluations and rare objects discovery.

Rough set theory, a mathematical tool to deal with inexact or uncertain knowledge in information systems, has originally described the indiscernibility of elements by equivalence relations. Covering rough sets are a natural extension of classical rough sets by relaxing the partitions arising from equivalence relations to coverings. Recently, some topological concepts such as neighborhood have been applied to covering rough sets. In this paper, we further investigate the covering rough sets based on neighborhoods by approximation operations. We show that the upper approximation based on neighborhoods can be defined equivalently without using neighborhoods. To analyze the coverings themselves, we introduce unary and composition operations on coverings. A notion of homomorphismis provided to relate two covering approximation spaces. We also examine the properties of approximations preserved by the operations and homomorphisms, respectively.

There has been a long history of using fuzzy language equivalence to compare the behavior of fuzzy systems, but the comparison at this level is too coarse. Recently, a finer behavioral measure, bisimulation, has been introduced to fuzzy finite automata. However, the results obtained are applicable only to finite-state systems. In this paper, we consider bisimulation for general fuzzy systems which may be infinite-state or infinite-event, by modeling them as fuzzy transition systems. To help understand and check bisimulation, we characterize it in three ways by enumerating whole transitions, comparing individual transitions, and using a monotonic function. In addition, we address composition operations, subsystems, quotients, and homomorphisms of fuzzy transition systems and discuss their properties connected with bisimulation. The results presented here are useful for comparing the behavior of general fuzzy systems. In particular, this makes it possible to relate an infinite fuzzy system to a finite one, which is easier to analyze, with the same behavior.

Statistical models of natural stimuli provide an important tool for researchers in the fields of machine learning and computational neuroscience. A canonical way to quantitatively assess and compare the performance of statistical models is given by the likelihood. One class of statistical models which has recently gained increasing popularity and has been applied to a variety of complex data are deep belief networks. Analyses of these models, however, have been typically limited to qualitative analyses based on samples due to the computationally intractable nature of the model likelihood. Motivated by these circumstances, the present article provides a consistent estimator for the likelihood that is both computationally tractable and simple to apply in practice. Using this estimator, a deep belief network which has been suggested for the modeling of natural image patches is quantitatively investigated and compared to other models of natural image patches. Contrary to earlier claims based on qualitative results, the results presented in this article provide evidence that the model under investigation is not a particularly good model for natural images

The Monty Hall problem is the TV game scenario where you, the contestant, are presented with three doors, with a car hidden behind one and goats hidden behind the other two. After you select a door, the host (Monty Hall) opens a second door to reveal a goat. You are then invited to stay with your original choice of door, or to switch to the remaining unopened door, and claim whatever you find behind it. Assuming your objective is to win the car, is your best strategy to stay or switch, or does it not matter? Jason Rosenhouse has provided the definitive analysis of this game, along with several intriguing variations, and discusses some of its psychological and philosophical implications. This extended review examines several themes from the book in some detail from a Bayesian perspective, and points out one apparently inadvertent error.

The problem of maximum-likelihood (ML) estimation of discrete tree-structured distributions is considered. Chow and Liu established that ML-estimation reduces to the construction of a maximum-weight spanning tree using the empirical mutual information quantities as the edge weights. Using the theory of large-deviations, we analyze the exponent associated with the error probability of the event that the ML-estimate of the Markov tree structure differs from the true tree structure, given a set of independently drawn samples. By exploiting the fact that the output of ML-estimation is a tree, we establish that the error exponent is equal to the exponential rate of decay of a single dominant crossover event. We prove that in this dominant crossover event, a non-neighbor node pair replaces a true edge of the distribution that is along the path of edges in the true tree graph connecting the nodes in the non-neighbor pair. Using ideas from Euclidean information theory, we then analyze the scenario of ML-estimation in the very noisy learning regime and show that the error exponent can be approximated as a ratio, which is interpreted as the signal-to-noise ratio (SNR) for learning tree distributions. We show via numerical experiments that in this regime, our SNR approximation is accurate.

Online offerings such as web search, news portals, and e-commerce applications face the challenge of providing high-quality service to a large, heterogeneous user base. Recent efforts have highlighted the potential to improve performance by introducing methods to personalize services based on special knowledge about users and their context. For example, a user's demographics, location, and past search and browsing may be useful in enhancing the results offered in response to web search queries. However, reasonable concerns about privacy by both users, providers, and government agencies acting on behalf of citizens, may limit access by services to such information. We introduce and explore an economics of privacy in personalization, where people can opt to share personal information, in a standing or on-demand manner, in return for expected enhancements in the quality of an online service. We focus on the example of web search and formulate realistic objective functions for search efficacy and privacy. We demonstrate how we can find a provably near-optimal optimization of the utility-privacy tradeoff in an efficient manner. We evaluate our methodology on data drawn from a log of the search activity of volunteer participants. We separately assess users preferences about privacy and utility via a large-scale survey, aimed at eliciting preferences about peoples willingness to trade the sharing of personal data in returns for gains in search efficiency. We show that a significant level of personalization can be achieved using a relatively small amount of information about users.

Often we wish to predict a large number of variables that depend on each other as well as on other observed variables. Structured prediction methods are essentially a combination of classification and graphical modeling, combining the ability of graphical models to compactly model multivariate data with the ability of classification methods to perform prediction using large sets of input features. This tutorial describes conditional random fields, a popular probabilistic method for structured prediction. CRFs have seen wide application in natural language processing, computer vision, and bioinformatics. We describe methods for inference and parameter estimation for CRFs, including practical issues for implementing large scale CRFs. We do not assume previous knowledge of graphical modeling, so this tutorial is intended to be useful to practitioners in a wide variety of fields.