We apply belief propagation to a Bayesian bipartite graph composed of discrete independent hidden variables and discrete visible variables. The network is the Discrete counterpart of Independent Component Analysis (DICA) and it is manipulated in a factor graph form for inference and learning. A full set of simulations is reported for character images from the MNIST dataset. The results show that the factorial code implemented by the sources contributes to build a good generative model for the data that can be used in various inference modes.

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. While standard alignment-based methods provide state-of-the-art performance, compositional approaches that assign a taxonomic class to a DNA read based on the k-mers it contains have the potential to provide faster solutions. In this work, we investigate the potential of modern, large-scale machine learning implementations for taxonomic affectation of next-generation sequencing reads based on their k-mers profile. We show that machine learning-based compositional approaches benefit from increasing the number of fragments sampled from reference genome to tune their parameters, up to a coverage of about 10, and from increasing the k-mer size to about 12. Tuning these models involves training a machine learning model on about 10 8 samples in 10 7 dimensions, which is out of reach of standard soft-wares but can be done efficiently with modern implementations for large-scale machine learning. The resulting models are competitive in terms of accuracy with well-established alignment tools for problems involving a small to moderate number of candidate species, and for reasonable amounts of sequencing errors. We show, however, that compositional approaches are still limited in their ability to deal with problems involving a greater number of species, and more sensitive to sequencing errors. We finally confirm that compositional approach achieve faster prediction times, with a gain of 3 to 15 times with respect to the BWA-MEM short read mapper, depending on the number of candidate species and the level of sequencing noise.

Much of the data being created on the web contains interactions between users and items. Stochastic blockmodels, and other methods for community detection and clustering of bipartite graphs, can infer latent user communities and latent item clusters from this interaction data. These methods, however, typically ignore the items' contents and the information they provide about item clusters, despite the tendency of items in the same latent cluster to share commonalities in content. We introduce content-augmented stochastic blockmodels (CASB), which use item content together with user-item interaction data to enhance the user communities and item clusters learned. Comparisons to several state-of-the-art benchmark methods, on datasets arising from scientists interacting with scientific articles, show that content-augmented stochastic blockmodels provide highly accurate clusters with respect to metrics representative of the underlying community structure.

We empirically evaluate a stochastic annealing strategy for Bayesian posterior optimization with variational inference. Variational inference is a deterministic approach to approximate posterior inference in Bayesian models in which a typically non-convex objective function is locally optimized over the parameters of the approximating distribution. We investigate an annealing method for optimizing this objective with the aim of finding a better local optimal solution and compare with deterministic annealing methods and no annealing. We show that stochastic annealing can provide clear improvement on the GMM and HMM, while performance on LDA tends to favor deterministic annealing methods.

We treat the problem of estimation of orientation parameters whose values are invariant to transformations from a spherical symmetry group. Previous work has shown that any such group-invariant distribution must satisfy a restricted finite mixture representation, which allows the orientation parameter to be estimated using an Expectation Maximization (EM) maximum likelihood (ML) estimation algorithm. In this paper, we introduce two parametric models for this spherical symmetry group estimation problem: 1) the hyperbolic Von Mises Fisher (VMF) mixture distribution and 2) the Watson mixture distribution. We also introduce a new EM-ML algorithm for clustering samples that come from mixtures of group-invariant distributions with different parameters. We apply the models to the problem of mean crystal orientation estimation under the spherically symmetric group associated with the crystal form, e.g., cubic or octahedral or hexahedral. Simulations and experiments establish the advantages of the extended EM-VMF and EM-Watson estimators for data acquired by Electron Backscatter Diffraction (EBSD) microscopy of a polycrystalline Nickel alloy sample.

Model-based clustering imposes a finite mixture modelling structure on data for clustering. Finite mixture models assume that the population is a convex combination of a finite number of densities, the distribution within each population is a basic assumption of each particular model. Among all distributions that have been tried, the generalized hyperbolic distribution has the advantage that is a generalization of several other methods, such as the Gaussian distribution, the skew t-distribution, etc. With specific parameters, it can represent either a symmetric or a skewed distribution. While its inherent flexibility is an advantage in many ways, it means the estimation of more parameters than its special and limiting cases. The aim of this work is to propose a mixture of generalized hyperbolic factor analyzers to introduce parsimony and extend the method to high dimensional data. This work can be seen as an extension of the mixture of factor analyzers model to generalized hyperbolic mixtures. The performance of our generalized hyperbolic factor analyzers is illustrated on real data, where it performs favourably compared to its Gaussian analogue.

Most work in heuristic search focused on path finding problems in which the cost of a path in the state space is the sum of its edges' weights. This paper addresses a different class of path finding problems in which the cost of a path is the product of its weights. We present reductions from different classes of multiplicative path finding problems to suitable classes of additive path finding problems. As a case study, we consider the problem of finding least and most probable paths in a Markov Chain, where path cost corresponds to the probability of traversing it. The importance of this problem is demonstrated in an anomaly detection application for cyberspace security. Three novel anomaly detection metrics for Markov Chains are presented, where computing these metrics require finding least and most probable paths. The underlying Markov Chain is dynamically changing, and so fast methods for computing least and most probable paths are needed. We propose such methods based on the proposed reductions and using heuristic search algorithms.

This paper provides a novel POMDP planning method, called Palm LEAf SEarch (PLEASE), which allows the selection of more than one outcome when their potential impacts are close to the highest one during its forward exploration. Compared with existing trial-based algorithms, PLEASE can save considerable time to propagate the bound improvements of beliefs in deep levels of the search tree to the root belief because of fewer backup operations. Experiments showed that PLEASE scales up SARSOP, one of the fastest algorithms, by orders of magnitude on some POMDP tasks with large observation spaces.

We introduce an approximate search algorithm for fast maximum a posteriori probability estimation in probabilistic programs, which we call Bayesian ascent Monte Carlo (BaMC). Probabilistic programs represent probabilistic models with varying number of mutually dependent finite, countable, and continuous random variables. BaMC is an anytime MAP search algorithm applicable to any combination of random variables and dependencies. We compare BaMC to other MAP estimation algorithms and show that BaMC is faster and more robust on a range of probabilistic models.

Monte-Carlo Tree Search (MCTS) algorithms estimate the value of MDP states based on rewards received by performing multiple random simulations. MCTS algorithms can use different strategies to aggregate these rewards and provide an estimation for the states’ values. The most common aggregation method is to store the mean reward of all simulations. Another common approach stores the best observed reward from each state. Both of these methods have complementary benefits and drawbacks. In this paper, we show that both of these methods are biased estimators for the real expected value of MDP states. We propose an hybrid approach that uses the best reward for states with low noise, and otherwise uses the mean. Experimental results on the Sailing MDP domain show that our method has a considerable advantage when the rewards are drawn from a noisy distribution.