In order to better protect and conserve biodiversity, ecologists use machine learning and statistics to understand how species respond to their environment and to predict how they will respond to future climate change, habitat loss and other threats. A fundamental modeling task is to estimate the probability that a given species is present in (or uses) a site, conditional on environmental variables such as precipitation and temperature. For a limited number of species, survey data consisting of both presence and absence records are available, and can be used to fit a variety of conventional classification and regression models. For most species, however, the available data consist only of occurrence records --- locations where the species has been observed. In two closely-related but separate bodies of ecological literature, diverse special-purpose models have been developed that contrast occurrence data with a random sample of available environmental conditions. The most widespread statistical approaches involve either fitting an exponential model of species' conditional probability of presence, or fitting a naive logistic model in which the random sample of available conditions is treated as absence data; both approaches have well-known drawbacks, and do not necessarily produce valid probabilities. After summarizing existing methods, we overcome their drawbacks by introducing a new scaled binomial loss function for estimating an underlying logistic model of species presence/absence. Like the Expectation-Maximization approach of Ward et al. and the method of Steinberg and Cardell, our approach requires an estimate of population prevalence, $\Pr(y=1)$, since prevalence is not identifiable from occurrence data alone. In contrast to the latter two methods, our loss function is straightforward to integrate into a variety of existing modeling frameworks such as generalized linear and additive models and boosted regression trees. We also demonstrate that approaches by Lele and Keim and by Lancaster and Imbens that surmount the identifiability issue by making parametric data assumptions do not typically produce valid probability estimates.

We describe a memory-efficient implementation of a dynamic programming algorithm for learning the optimal structure of a Bayesian network from training data. The algorithm leverages the layered structure of the dynamic programming graphs representing the recursive decomposition of the problem to reduce the memory requirements of the algorithm from O(n2 n ) to O(C(n, n/2)), where C(n, n/2) is the binomial coefficient. Experimental results show that the approach runs up to an order of magnitude faster and scales to datasets with more variables than previous approaches.

A key problem in statistical modeling is model selection, how to choose a model at an appropriate level of complexity. This problem appears in many settings, most prominently in choosing the number ofclusters in mixture models or the number of factors in factor analysis. In this tutorial we describe Bayesian nonparametric methods, a class of methods that side-steps this issue by allowing the data to determine the complexity of the model. This tutorial is a high-level introduction to Bayesian nonparametric methods and contains several examples of their application.

In this paper, a methodology for the automated detection and classification of Tuberculosis(TB) is presented. Tuberculosis is a disease caused by mycobacterium which spreads through the air and attacks low immune bodies easily. Our methodology is based on clustering and classification that classifies TB into two categories, Pulmonary Tuberculosis(PTB) and retroviral PTB(RPTB) that is those with Human Immunodeficiency Virus (HIV) infection. Initially K-means clustering is used to group the TB data into two clusters and assigns classes to clusters. Subsequently multiple different classification algorithms are trained on the result set to build the final classifier model based on K-fold cross validation method. This methodology is evaluated using 700 raw TB data obtained from a city hospital. The best obtained accuracy was 98.7% from support vector machine (SVM) compared to other classifiers. The proposed approach helps doctors in their diagnosis decisions and also in their treatment planning procedures for different categories.

We address the issue of knots selection for Gaussian predictive process methodology. Predictive process approximation provides an effective solution to the cubic order computational complexity of Gaussian process models. This approximation crucially depends on a set of points, called knots, at which the original process is retained, while the rest is approximated via a deterministic extrapolation. Knots should be few in number to keep the computational complexity low, but provide a good coverage of the process domain to limit approximation error. We present theoretical calculations to show that coverage must be judged by the canonical metric of the Gaussian process. This necessitates having in place a knots selection algorithm that automatically adapts to the changes in the canonical metric affected by changes in the parameter values controlling the Gaussian process covariance function. We present an algorithm toward this by employing an incomplete Cholesky factorization with pivoting and dynamic stopping. Although these concepts already exist in the literature, our contribution lies in unifying them into a fast algorithm and in using computable error bounds to finesse implementation of the predictive process approximation. The resulting adaptive predictive process offers a substantial automatization of Guassian process model fitting, especially for Bayesian applications where thousands of values of the covariance parameters are to be explored.

Many widely studied graphical models with latent variables lead to nontrivial constraints on the distribution of the observed variables. Inspired by the Bell inequalities in quantum mechanics, we refer to any linear inequality whose violation rules out some latent variable model as a "hidden variable test" for that model. Our main contribution is to introduce a sequence of relaxations which provides progressively tighter hidden variable tests. We demonstrate applicability to mixtures of sequences of i.i.d. variables, Bell inequalities, and homophily models in social networks. For the last, we demonstrate that our method provides a test that is able to rule out latent homophily as the sole explanation for correlations on a real social network that are known to be due to influence.

We propose a new additive decomposition of probability tables that preserves equivalence of the joint distribution while reducing the size of potentials, without extra variables. We formulate the Most Probable Explanation (MPE) problem in belief networks as a Weighted Constraint Satisfaction Problem (WCSP). Our pairwise decomposition allows to replace a cost function with smaller-arity functions. The resulting pairwise decomposed WCSP is then easier to solve using state-of-the-art WCSP techniques. Although testing pairwise decomposition is equivalent to testing pairwise independence in the original belief network, we show how to efficiently test and enforce it, even in the presence of hard constraints. Furthermore, we infer additional information from the resulting nonbinary cost functions by projecting and subtracting them on binary functions. We observed huge improvements by preprocessing with pairwise decomposition and project&subtract compared to the current state-of-the-art solvers on two difficult sets of benchmark.

Many applications of causal inference, such as finding the relationship between stock prices and news reports, involve both discrete and continuous variables observed over time. Inference with these complex sets of temporal data, though, has remained difficult and required a number of simplifications. We show that recent approaches for inferring temporal relationships (represented as logical formulas) can be adapted for inference with continuous valued effects. Building on advances in logic, PCTLc (an extension of PCTL with numerical constraints) is introduced here to allow representation and inference of relationships with a mixture of discrete and continuous components. Then, finding significant relationships in the continuous case can be done using the conditional expectation of an effect, rather than its conditional probability. We evaluate this approach on both synthetically generated and actual financial market data, demonstrating that it can allow us to answer different questions than the discrete approach can.

This paper presents new results for the (partial) maximum a posteriori (MAP) problem in Bayesian networks, which is the problem of querying the most probable state configuration of some of the network variables given evidence. It is demonstrated that the problem remains hard even in networks with very simple topology, such as binary polytrees and simple trees (including the Naive Bayes structure), which extends previous complexity results. Furthermore, a Fully Polynomial Time Approximation Scheme for MAP in networks with bounded treewidth and bounded number of states per variable is developed. Approximation schemes were thought to be impossible, but here it is shown otherwise under the assumptions just mentioned, which are adopted in most applications.

In this paper, we tackle the challenges of multi-label classification by developing a general conditional dependency network model. The proposed model is a cyclic directed graphical model, which provides an intuitive representation for the dependencies among multiple label variables, and a well integrated framework for efficient model training using binary classifiers and label predictions using Gibbs sampling inference. Our experiments show the proposed conditional model can effectively exploit the label dependency to improve multi-label classification performance.