Bayesian model averaging (BMA) is the state of the art approach for overcoming model uncertainty. Yet, especially on small data sets, the results yielded by BMA might be sensitive to the prior over the models. Credal Model Averaging (CMA) addresses this problem by substituting the single prior over the models by a set of priors (credal set). Such approach solves the problem of how to choose the prior over the models and automates sensitivity analysis. We discuss various CMA algorithms for building an ensemble of logistic regressors characterized by different sets of covariates. We show how CMA can be appropriately tuned to the case in which one is prior-ignorant and to the case in which instead domain knowledge is available. CMA detects prior-dependent instances, namely instances in which a different class is more probable depending on the prior over the models. On such instances CMA suspends the judgment, returning multiple classes. We thoroughly compare different BMA and CMA variants on a real case study, predicting presence of Alpine marmot burrows in an Alpine valley. We find that BMA is almost a random guesser on the instances recognized as prior-dependent by CMA.

This paper provides new insight into maximizing F1 scores in the context of binary classification and also in the context of multilabel classification. The harmonic mean of precision and recall, F1 score is widely used to measure the success of a binary classifier when one class is rare. Micro average, macro average, and per instance average F1 scores are used in multilabel classification. For any classifier that produces a real-valued output, we derive the relationship between the best achievable F1 score and the decision-making threshold that achieves this optimum. As a special case, if the classifier outputs are well-calibrated conditional probabilities, then the optimal threshold is half the optimal F1 score. As another special case, if the classifier is completely uninformative, then the optimal behavior is to classify all examples as positive. Since the actual prevalence of positive examples typically is low, this behavior can be considered undesirable. As a case study, we discuss the results, which can be surprising, of applying this procedure when predicting 26,853 labels for Medline documents.

We consider the infinite-horizon discounted optimal control problem formalized by Markov Decision Processes. We focus on several approximate variations of the Policy Iteration algorithm: Approximate Policy Iteration, Conservative Policy Iteration (CPI), a natural adaptation of the Policy Search by Dynamic Programming algorithm to the infinite-horizon case (PSDP$_\infty$), and the recently proposed Non-Stationary Policy iteration (NSPI(m)). For all algorithms, we describe performance bounds, and make a comparison by paying a particular attention to the concentrability constants involved, the number of iterations and the memory required. Our analysis highlights the following points: 1) The performance guarantee of CPI can be arbitrarily better than that of API/API($\alpha$), but this comes at the cost of a relative---exponential in $\frac{1}{\epsilon}$---increase of the number of iterations. 2) PSDP$_\infty$ enjoys the best of both worlds: its performance guarantee is similar to that of CPI, but within a number of iterations similar to that of API. 3) Contrary to API that requires a constant memory, the memory needed by CPI and PSDP$_\infty$ is proportional to their number of iterations, which may be problematic when the discount factor $\gamma$ is close to 1 or the approximation error $\epsilon$ is close to $0$; we show that the NSPI(m) algorithm allows to make an overall trade-off between memory and performance. Simulations with these schemes confirm our analysis.

A standard technique for understanding underlying dependency structures among a set of variables posits a shared conditional probability distribution for the variables measured on individuals within a group. This approach is often referred to as module networks, where individuals are represented by nodes in a network, groups are termed modules, and the focus is on estimating the network structure among modules. However, estimation solely from node-specific variables can lead to spurious dependencies, and unverifiable structural assumptions are often used for regularization. Here, we propose an extended model that leverages direct observations about the network in addition to node-specific variables. By integrating complementary data types, we avoid the need for structural assumptions. We illustrate theoretical and practical significance of the model and develop a reversible-jump MCMC learning procedure for learning modules and model parameters. We demonstrate the method accuracy in predicting modular structures from synthetic data and capability to learn influence structures in twitter data and regulatory modules in the Mycobacterium tuberculosis gene regulatory network.

Much recent research has been conducted in the area of Bayesian learning, particularly with regard to the optimization of hyper-parameters via Gaussian process regression. The methodologies rely chiefly on the method of maximizing the expected improvement of a score function with respect to adjustments in the hyper-parameters. In this work, we present a novel algorithm that exploits notions of confidence intervals and uncertainties to enable the discovery of the best optimal within a targeted region of the parameter space. We demonstrate the efficacy of our algorithm with respect to machine learning problems and show cases where our algorithm is competitive with the method of maximizing expected improvement.

Our winning submission to the 2014 Kaggle competition for Large Scale Hierarchical Text Classification (LSHTC) consists mostly of an ensemble of sparse generative models extending Multinomial Naive Bayes. The base-classifiers consist of hierarchically smoothed models combining document, label, and hierarchy level Multinomials, with feature pre-processing using variants of TF-IDF and BM25. Additional diversification is introduced by different types of folds and random search optimization for different measures. The ensemble algorithm optimizes macroFscore by predicting the documents for each label, instead of the usual prediction of labels per document. Scores for documents are predicted by weighted voting of base-classifier outputs with a variant of Feature-Weighted Linear Stacking. The number of documents per label is chosen using label priors and thresholding of vote scores. This document describes the models and software used to build our solution. Reproducing the results for our solution can be done by running the scripts included in the Kaggle package. A package omitting precomputed result files is also distributed. All code is open source, released under GNU GPL 2.0, and GPL 3.0 for Weka and Meka dependencies.

Translation rule selection is a task of selecting appropriate translation rules for an ambiguous source-language segment. As translation ambiguities are pervasive in statistical machine translation, we introduce two topic-based models for translation rule selection which incorporates global topic information into translation disambiguation. We associate each synchronous translation rule with source- and target-side topic distributions.With these topic distributions, we propose a topic dissimilarity model to select desirable (less dissimilar) rules by imposing penalties for rules with a large value of dissimilarity of their topic distributions to those of given documents. In order to encourage the use of non-topic specific translation rules, we also present a topic sensitivity model to balance translation rule selection between generic rules and topic-specific rules. Furthermore, we project target-side topic distributions onto the source-side topic model space so that we can benefit from topic information of both the source and target language. We integrate the proposed topic dissimilarity and sensitivity model into hierarchical phrase-based machine translation for synchronous translation rule selection. Experiments show that our topic-based translation rule selection model can substantially improve translation quality.

Today most of the information in all areas is available over the web. It increases the web utilization as well as attracts the interest of researchers to improve the effectiveness of web access and web utilization. As the number of web clients gets increased, the bandwidth sharing is performed that decreases the web access efficiency. Web page prefetching improves the effectiveness of web access by availing the next required web page before the user demand. It is an intelligent predictive mining that analyze the user web access history and predict the next page. In this work, vague improved markov model is presented to perform the prediction. In this work, vague rules are suggested to perform the pruning at different levels of markov model. Once the prediction table is generated, the association mining will be implemented to identify the most effective next page. In this paper, an integrated model is suggested to improve the prediction accuracy and effectiveness.

Non-linear systems of differential equations have attracted the interest in fields like system biology, ecology or biochemistry, due to their flexibility and their ability to describe dynamical systems. Despite the importance of such models in many branches of science they have not been the focus of systematic statistical analysis until recently. In this work we propose a general approach to estimate the parameters of systems of differential equations measured with noise. Our methodology is based on the maximization of the penalized likelihood where the system of differential equations is used as a penalty. To do so, we use a Reproducing Kernel Hilbert Space approach that allows to formulate the estimation problem as an unconstrained numeric maximization problem easy to solve. The proposed method is tested with synthetically simulated data and it is used to estimate the unobserved transcription factor CdaR in Steptomyes coelicolor using gene expression data of the genes it regulates.

The increasing demand of world wide web raises the need of predicting the user's web page request.The most widely used approach to predict the web pages is the pattern discovery process of Web usage mining. This process involves inevitability of many techniques like Markov model, association rules and clustering. Fuzzy theory with different techniques has been introduced for the better results. Our focus is on Markov models. This paper is introducing the vague Rules with Markov models for more accuracy using the vague set theory.