We present a new statistical framework called hidden Markov Dirichlet process (HMDP) to jointly model the genetic recombinations among possibly infinite number of founders and the coalescence-with-mutation events in the resulting genealogies. The HMDP posits that a haplotype of genetic markers is generated by a sequence of recombination events that select an ancestor for each locus from an unbounded set of founders according to a 1st-order Markov transition process. Conjoining this process with a mutation model, our method accommodates both between-lineage recombination and within-lineage sequence variations, and leads to a compact and natural interpretation of the population structure and inheritance process underlying haplotype data. We have developed an efficient sampling algorithm for HMDP based on a two-level nested Pólya urn scheme. On both simulated and real SNP haplotype data, our method performs competitively or significantly better than extant methods in uncovering the recombination hotspots along chromosomal loci; and in addition it also infers the ancestral genetic patterns and offers a highly accurate map of ancestral compositions of modern populations.

The additive clustering model is widely used to infer the features of a set of stimuli from their similarities, on the assumption that similarity is a weighted linear function of common features. This paper develops a fully Bayesian formulation of the additive clustering model, using methods from nonparametric Bayesian statistics to allow the number of features to vary. We use this to explore several approaches to parameter estimation, showing that the nonparametric Bayesian approach provides a straightforward way to obtain estimates of both the number of features used in producing similarity judgments and their importance.

We present a generalization of dynamic Bayesian networks to concisely describe complex probability distributions such as in problems with multiple interacting variable-length streams of random variables. Our framework incorporates recent graphical model constructs to account for existence uncertainty, value-specific independence, aggregation relationships, and local and global constraints, while still retaining a Bayesian network interpretation and efficient inference and learning techniques. We introduce one such general technique, which is an extension of Value Elimination, a backtracking search inference algorithm. Multi-dynamic Bayesian networks are motivated by our work on Statistical Machine Translation (MT). We present results on MT word alignment in support of our claim that MDBNs are a promising framework for the rapid prototyping of new MT systems.

This has been made possible by advancements in satellite sensor technology thus enabling the acquisition of land cover information over large areas at various spatial, temporal spectral and radiometric resolutions. The process of relating pixels in a satellite image to known land cover is called image classification and the algorithms used to effect the classification process are called image classifiers (Mather, 1987). The extraction of land cover information from satellite images using image classifiers has been the subject of intense interest and research in the remote sensing community (Foody and Mathur, 2004b). Some of the traditional classifiers that have been in use in remote sensing studies include the maximum likelihood, minimum distance to means and the box classifier. As technology has advanced, new classification algorithms have become part of the main stream image classifiers such as decision trees and artificial neural networks. Studies have been made to compare these new techniques with the traditional ones and they have been observed to post improved classification accuracies (Peddle et al. 1994; Rogan et al. 2002; Li et al. 2003; Mahesh and Mather, 2003).

Data collection often results in records that have missing values or variables. This investigation compares 3 different data imputation models and identifies their merits by using accuracy measures. Autoencoder Neural Networks, Principal components and Support Vector regression are used for prediction and combined with a genetic algorithm to then impute missing variables. The use of PCA improves the overall performance of the autoencoder network while the use of support vector regression shows promising potential for future investigation. Accuracies of up to 97.4 % on imputation of some of the variables were achieved.

In this paper, we present a method to optimise rough set partition sizes, to which rule extraction is performed on HIV data. The genetic algorithm optimisation technique is used to determine the partition sizes of a rough set in order to maximise the rough sets prediction accuracy. The proposed method is tested on a set of demographic properties of individuals obtained from the South African antenatal survey. Six demographic variables were used in the analysis, these variables are; race, age of mother, education, gravidity, parity, and age of father, with the outcome or decision being either HIV positive or negative. Rough set theory is chosen based on the fact that it is easy to interpret the extracted rules. The prediction accuracy of equal width bin partitioning is 57.7% while the accuracy achieved after optimising the partitions is 72.8%. Several other methods have been used to analyse the HIV data and their results are stated and compared to that of rough set theory (RST).

The QXOR-SAT problem is the quantified version of the satisfiability problem XOR-SAT in which the connective exclusive-or is used instead of the usual or. We study the phase transition associated with random QXOR-SAT instances. We give a description of this phase transition in the case of one alternation of quantifiers, thus performing an advanced practical and theoretical study on the phase transition of a quantified problem.

In this paper we present the creation of an Arabic version of Automated Speech Recognition System (ASR). This system is based on the open source Sphinx-4, from the Carnegie Mellon University. Which is a speech recognition system based on discrete hidden Markov models (HMMs). We investigate the changes that must be made to the model to adapt Arabic voice recognition.

In this paper Arabic was investigated from the speech recognition problem point of view. We propose a novel approach to build an Arabic Automated Speech Recognition System (ASR). This system is based on the open source CMU Sphinx-4, from the Carnegie Mellon University. CMU Sphinx is a large-vocabulary; speaker-independent, continuous speech recognition system based on discrete Hidden Markov Models (HMMs). We build a model using utilities from the OpenSource CMU Sphinx. We will demonstrate the possible adaptability of this system to Arabic voice recognition.

Sets", we consider the problem of retrieving items from a concept or cluster, given a query consisting of a few items from that cluster. We formulate this as a Bayesian inference problem and describe a very simple algorithm for solving it. Our algorithm uses a modelbased concept of a cluster and ranks items using a score which evaluates the marginal probability that each item belongs to a cluster containing the query items. For exponential family models with conjugate priors this marginal probability is a simple function of sufficient statistics. We focus on sparse binary data and show that our score can be evaluated exactly using a single sparse matrix multiplication, making it possible to apply our algorithm to very large datasets. We evaluate our algorithm on three datasets: retrieving movies from EachMovie, finding completions of author sets from the NIPS dataset, and finding completions of sets of words appearing in the Grolier encyclopedia.