Speech Recognition with unknown partial feature corruption - a review of the union model

This paper provides a summary of our studies on robust speech recognition based on a new statistical approach – the probabilistic union model. We consider speech recognition given that part of the acoustic features may be corrupted by noise. The union model is a method for basing the recognition on the clean part of the features, thereby reducing the effect of the noise on recognition. To this end, the union model is similar to the missing feature method. However, the two methods achieve this end through different routes. The missing feature method usually requires the identity of the noisy data for noise removal, while the union model combines the local features based on the union of random events, to reduce the dependence of the model on information about the noise. We previously investigated the applications of the union model to speech recognition involving unknown partial corruption in frequency band, in time duration, and in feature streams. Additionally, a combination of the union model with conventional noise-reduction techniques was studied, as a means of dealing with a mixture of known or trainable noise and unknown unexpected noise. In this paper, a unified review, in the context of dealing with unknown partial feature corruption, is provided into each of these applications, giving the appropriate theory and implementation algorithms, along with an experimental evaluation.

Min-BDeu and Max-BDeu Scores for Learning Bayesian Networks

This work presents two new score functions based on the Bayesian Dirichlet equivalent uniform (BDeu) score for learning Bayesian network structures. They consider the sensitivity of BDeu to varying parameters of the Dirichlet prior. The scores take on the most adversary and the most beneficial priors among those within a contamination set around the symmetric one. We build these scores in such way that they are decomposable and can be computed efficiently. Because of that, they can be integrated into any state-of-the-art structure learning method that explores the space of directed acyclic graphs and allows decomposable scores. Empirical results suggest that our scores outperform the standard BDeu score in terms of the likelihood of unseen data and in terms of edge discovery with respect to the true network, at least when the training sample size is small. We discuss the relation between these new scores and the accuracy of inferred models. Moreover, our new criteria can be used to identify the amount of data after which learning is saturated, that is, additional data are of little help to improve the resulting model.

Decision Making by Credal Nets

Credal nets are probabilistic graphical models which extend Bayesian nets to cope with sets of distributions. This feature makes the model particularly suited for the implementation of classifiers and knowledge-based systems. When working with sets of (instead of single) probability distributions, the identification of the optimal option can be based on different criteria, some of them eventually leading to multiple choices. Yet, most of the inference algorithms for credal nets are designed to compute only the bounds of the posterior probabilities. This prevents some of the existing criteria from being used. To overcome this limitation, we present two simple transformations for credal nets which make it possible to compute decisions based on the maximality and E-admissibility criteria without any modification in the inference algorithms. We also prove that these decision problems have the same complexity of standard inference, being NP^PP-hard for general credal nets and NP-hard for polytrees.

Incorporating PGMs into a BDI Architecture

In this paper, we present a hybrid BDI-PGM framework, in which PGMs (Probabilistic Graphical Models) are incorporated into a BDI (belief-desire-intention) architecture. This work is motivated by the need to address the scalability and noisy sensing issues in SCADA (Supervisory Control And Data Acquisition) systems. Our approach uses the incorporated PGMs to model the uncertainty reasoning and decision making processes of agents situated in a stochastic environment. In particular, we use Bayesian networks to reason about an agent’s beliefs about the environment based on its sensory observations, and select optimal plans according to the utilities of actions defined in influence diagrams. This approach takes the advantage of the scalability of the BDI architecture and the uncertainty reasoning capability of PGMs. We present a prototype of the proposed approach using a transit scenario to validate its effectiveness.

Adaptive Probabilistic Topic Models for Social Networks

Thesis (Master's)--University of Washington, 2012

Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo

This article presents a statistical method for detecting recombination in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationship between the taxa, and (2) a site graph (hidden Markov model) representing interactions between different sites in the DNA sequence alignments. We adopt a Bayesian approach and sample the parameters of the model from the posterior distribution with Markov chain Monte Carlo, using a Metropolis-Hastings and Gibbs-within-Gibbs scheme. The proposed method is tested on various synthetic and real-world DNA sequence alignments, and we compare its performance with the established detection methods RECPARS, PLATO, and TOPAL, as well as with two alternative parameter estimation schemes.

What will affect software reuse: a causal model analysis

Software reuse is an important topic due to its potential benefits in increasing product quality and decreasing cost. Although more and more people are aware that not only technical issues, but also nontechnical issues are important to the success of software reuse, people are still not certain which factors will have direct effect on the success of reuse. In this paper, we applied a causal discovery algorithm to the software reuse survey data [2]. Ensemble strategy is incorporated to locate a probable causal model structure for software reuse, and find all those factors which have direct effect on the success of reuse. Our discovery results reinforced some conclusions of Morisio et al. and found some new conclusions which might significantly improve the odds of a reuse project succeeding.

Probabilistic models over ordered partitions with applications in document ranking and collaborative filtering

Ranking is an important task for handling a large amount of content. Ideally, training data for supervised ranking would include a complete rank of documents (or other objects such as images or videos) for a particular query. However, this is only possible for small sets of documents. In practice, one often resorts to document rating, in that a subset of documents is assigned with a small number indicating the degree of relevance. This poses a general problem of modelling and learning rank data with ties. In this paper, we propose a probabilistic generative model, that models the process as permutations over partitions. This results in super-exponential combinatorial state space with unknown numbers of partitions and unknown ordering among them. We approach the problem from the discrete choice theory, where subsets are chosen in a stagewise manner, reducing the state space per each stage significantly. Further, we show that with suitable parameterisation, we can still learn the models in linear time. We evaluate the proposed models on two application areas: (i) document ranking with the data from the recently held Yahoo! challenge, and (ii) collaborative filtering with movie data. The results demonstrate that the models are competitive against well-known rivals.

Graph-induced restricted Boltzmann machines for document modeling

Discovering knowledge from unstructured texts is a central theme in data mining and machine learning. We focus on fast discovery of thematic structures from a corpus. Our approach is based on a versatile probabilistic formulation – the restricted Boltzmann machine (RBM) –where the underlying graphical model is an undirected bipartite graph. Inference is efficient document representation can be computed with a single matrix projection, making RBMs suitable for massive text corpora available today. Standard RBMs, however, operate on bag-of-words assumption, ignoring the inherent underlying relational structures among words. This results in less coherent word thematic grouping. We introduce graph-based regularization schemes that exploit the linguistic structures, which in turn can be constructed from either corpus statistics or domain knowledge. We demonstrate that the proposed technique improves the group coherence, facilitates visualization, provides means for estimation of intrinsic dimensionality, reduces overfitting, and possibly leads to better classification accuracy.

The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients

The success of combination antiretroviral therapy is limited by the evolutionary escape dynamics of HIV-1. We used Isotonic Conjunctive Bayesian Networks (I-CBNs), a class of probabilistic graphical models, to describe this process. We employed partial order constraints among viral resistance mutations, which give rise to a limited set of mutational pathways, and we modeled phenotypic drug resistance as monotonically increasing along any escape pathway. Using this model, the individualized genetic barrier (IGB) to each drug is derived as the probability of the virus not acquiring additional mutations that confer resistance. Drug-specific IGBs were combined to obtain the IGB to an entire regimen, which quantifies the virus' genetic potential for developing drug resistance under combination therapy. The IGB was tested as a predictor of therapeutic outcome using between 2,185 and 2,631 treatment change episodes of subtype B infected patients from the Swiss HIV Cohort Study Database, a large observational cohort. Using logistic regression, significant univariate predictors included most of the 18 drugs and single-drug IGBs, the IGB to the entire regimen, the expert rules-based genotypic susceptibility score (GSS), several individual mutations, and the peak viral load before treatment change. In the multivariate analysis, the only genotype-derived variables that remained significantly associated with virological success were GSS and, with 10-fold stronger association, IGB to regimen. When predicting suppression of viral load below 400 cps/ml, IGB outperformed GSS and also improved GSS-containing predictors significantly, but the difference was not significant for suppression below 50 cps/ml. Thus, the IGB to regimen is a novel data-derived predictor of treatment outcome that has potential to improve the interpretation of genotypic drug resistance tests.

Learning Bayesian networks from data by the incremental compilation of new network polynomials

Probabilistic graphical models are a huge research field in artificial intelligence nowadays. The scope of this work is the study of directed graphical models for the representation of discrete distributions. Two of the main research topics related to this area focus on performing inference over graphical models and on learning graphical models from data. Traditionally, the inference process and the learning process have been treated separately, but given that the learned models structure marks the inference complexity, this kind of strategies will sometimes produce very inefficient models. With the purpose of learning thinner models, in this master thesis we propose a new model for the representation of network polynomials, which we call polynomial trees. Polynomial trees are a complementary representation for Bayesian networks that allows an efficient evaluation of the inference complexity and provides a framework for exact inference. We also propose a set of methods for the incremental compilation of polynomial trees and an algorithm for learning polynomial trees from data using a greedy score+search method that includes the inference complexity as a penalization in the scoring function.

Expressive power of binary relevance and chain classifiers based on Bayesian Networks for multi-label classification

Bayesian network classifiers are widely used in machine learning because they intuitively represent causal relations. Multi-label classification problems require each instance to be assigned a subset of a defined set of h labels. This problem is equivalent to finding a multi-valued decision function that predicts a vector of h binary classes. In this paper we obtain the decision boundaries of two widely used Bayesian network approaches for building multi-label classifiers: Multi-label Bayesian network classifiers built using the binary relevance method and Bayesian network chain classifiers. We extend our previous single-label results to multi-label chain classifiers, and we prove that, as expected, chain classifiers provide a more expressive model than the binary relevance method.

Distributed Estimation of Distribution Algorithms for continuous optimization: how does the exchanged information influence their behavior?

One of the most promising areas in which probabilistic graphical models have shown an incipient activity is the field of heuristic optimization and, in particular, in Estimation of Distribution Algorithms. Due to their inherent parallelism, different research lines have been studied trying to improve Estimation of Distribution Algorithms from the point of view of execution time and/or accuracy. Among these proposals, we focus on the so-called distributed or island-based models. This approach defines several islands (algorithms instances) running independently and exchanging information with a given frequency. The information sent by the islands can be either a set of individuals or a probabilistic model. This paper presents a comparative study for a distributed univariate Estimation of Distribution Algorithm and a multivariate version, paying special attention to the comparison of two alternative methods for exchanging information, over a wide set of parameters and problems ? the standard benchmark developed for the IEEE Workshop on Evolutionary Algorithms and other Metaheuristics for Continuous Optimization Problems of the ISDA 2009 Conference. Several analyses from different points of view have been conducted to analyze both the influence of the parameters and the relationships between them including a characterization of the configurations according to their behavior on the proposed benchmark.

Statistical Hurdle Models for Single Cell Gene Expression: Differential Expression and Graphical Modeling

Thesis (Ph.D.)--University of Washington, 2016-06

Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.