Finding structures in information networks using the affinity network

This thesis proposes a novel graphical model for inference called the Affinity Network,which displays the closeness between pairs of variables and is an alternative to Bayesian Networks and Dependency Networks. The Affinity Network shares some similarities with Bayesian Networks and Dependency Networks but avoids their heuristic and stochastic graph construction algorithms by using a message passing scheme. A comparison with the above two instances of graphical models is given for sparse discrete and continuous medical data and data taken from the UCI machine learning repository. The experimental study reveals that the Affinity Network graphs tend to be more accurate on the basis of an exhaustive search with the small datasets. Moreover, the graph construction algorithm is faster than the other two methods with huge datasets. The Affinity Network is also applied to data produced by a synchronised system. A detailed analysis and numerical investigation into this dynamical system is provided and it is shown that the Affinity Network can be used to characterise its emergent behaviour even in the presence of noise.

Biomedical events extraction using the hidden vector state model

Objective: Biomedical events extraction concerns about events describing changes on the state of bio-molecules from literature. Comparing to the protein-protein interactions (PPIs) extraction task which often only involves the extraction of binary relations between two proteins, biomedical events extraction is much harder since it needs to deal with complex events consisting of embedded or hierarchical relations among proteins, events, and their textual triggers. In this paper, we propose an information extraction system based on the hidden vector state (HVS) model, called HVS-BioEvent, for biomedical events extraction, and investigate its capability in extracting complex events. Methods and material: HVS has been previously employed for extracting PPIs. In HVS-BioEvent, we propose an automated way to generate abstract annotations for HVS training and further propose novel machine learning approaches for event trigger words identification, and for biomedical events extraction from the HVS parse results. Results: Our proposed system achieves an F-score of 49.57% on the corpus used in the BioNLP'09 shared task, which is only 2.38% lower than the best performing system by UTurku in the BioNLP'09 shared task. Nevertheless, HVS-BioEvent outperforms UTurku's system on complex events extraction with 36.57% vs. 30.52% being achieved for extracting regulation events, and 40.61% vs. 38.99% for negative regulation events. Conclusions: The results suggest that the HVS model with the hierarchical hidden state structure is indeed more suitable for complex event extraction since it could naturally model embedded structural context in sentences.

Exploring ant-based algorithms for gene expression data analysis

Objective: Recently, much research has been proposed using nature inspired algorithms to perform complex machine learning tasks. Ant colony optimization (ACO) is one such algorithm based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper investigates ant-based algorithms for gene expression data clustering and associative classification. Methods and material: An ant-based clustering (Ant-C) and an ant-based association rule mining (Ant-ARM) algorithms are proposed for gene expression data analysis. The proposed algorithms make use of the natural behavior of ants such as cooperation and adaptation to allow for a flexible robust search for a good candidate solution. Results: Ant-C has been tested on the three datasets selected from the Stanford Genomic Resource Database and achieved relatively high accuracy compared to other classical clustering methods. Ant-ARM has been tested on the acute lymphoblastic leukemia (ALL)/acute myeloid leukemia (AML) dataset and generated about 30 classification rules with high accuracy. Conclusions: Ant-C can generate optimal number of clusters without incorporating any other algorithms such as K-means or agglomerative hierarchical clustering. For associative classification, while a few of the well-known algorithms such as Apriori, FP-growth and Magnum Opus are unable to mine any association rules from the ALL/AML dataset within a reasonable period of time, Ant-ARM is able to extract associative classification rules.

Helicopter vibration sensor selection using data visualisation

The main objective of the project is to enhance the already effective health-monitoring system (HUMS) for helicopters by analysing structural vibrations to recognise different flight conditions directly from sensor information. The goal of this paper is to develop a new method to select those sensors and frequency bands that are best for detecting changes in flight conditions. We projected frequency information to a 2-dimensional space in order to visualise flight-condition transitions using the Generative Topographic Mapping (GTM) and a variant which supports simultaneous feature selection. We created an objective measure of the separation between different flight conditions in the visualisation space by calculating the Kullback-Leibler (KL) divergence between Gaussian mixture models (GMMs) fitted to each class: the higher the KL-divergence, the better the interclass separation. To find the optimal combination of sensors, they were considered in pairs, triples and groups of four sensors. The sensor triples provided the best result in terms of KL-divergence. We also found that the use of a variational training algorithm for the GMMs gave more reliable results.

Gaussian process quantile regression using expectation propagation

Direct quantile regression involves estimating a given quantile of a response variable as a function of input variables. We present a new framework for direct quantile regression where a Gaussian process model is learned, minimising the expected tilted loss function. The integration required in learning is not analytically tractable so to speed up the learning we employ the Expectation Propagation algorithm. We describe how this work relates to other quantile regression methods and apply the method on both synthetic and real data sets. The method is shown to be competitive with state of the art methods whilst allowing for the leverage of the full Gaussian process probabilistic framework.

Joint sentiment/topic model for sentiment analysis

Sentiment analysis or opinion mining aims to use automated tools to detect subjective information such as opinions, attitudes, and feelings expressed in text. This paper proposes a novel probabilistic modeling framework based on Latent Dirichlet Allocation (LDA), called joint sentiment/topic model (JST), which detects sentiment and topic simultaneously from text. Unlike other machine learning approaches to sentiment classification which often require labeled corpora for classifier training, the proposed JST model is fully unsupervised. The model has been evaluated on the movie review dataset to classify the review sentiment polarity and minimum prior information have also been explored to further improve the sentiment classification accuracy. Preliminary experiments have shown promising results achieved by JST.

Relation discovery from web data for competency management

In current organizations, valuable enterprise knowledge is often buried under rapidly expanding huge amount of unstructured information in the form of web pages, blogs, and other forms of human text communications. We present a novel unsupervised machine learning method called CORDER (COmmunity Relation Discovery by named Entity Recognition) to turn these unstructured data into structured information for knowledge management in these organizations. CORDER exploits named entity recognition and co-occurrence data to associate individuals in an organization with their expertise and associates. We discuss the problems associated with evaluating unsupervised learners and report our initial evaluation experiments in an expert evaluation, a quantitative benchmarking, and an application of CORDER in a social networking tool called BuddyFinder.

Community relation discovery by named entities

Discovering who works with whom, on which projects and with which customers is a key task in knowledge management. Although most organizations keep models of organizational structures, these models do not necessarily accurately reflect the reality on the ground. In this paper we present a text mining method called CORDER which first recognizes named entities (NEs) of various types from Web pages, and then discovers relations from a target NE to other NEs which co-occur with it. We evaluated the method on our departmental Website. We used the CORDER method to first find related NEs of four types (organizations, people, projects, and research areas) from Web pages on the Website and then rank them according to their co-occurrence with each of the people in our department. 20 representative people were selected and each of them was presented with ranked lists of each type of NE. Each person specified whether these NEs were related to him/her and changed or confirmed their rankings. Our results indicate that the method can find the NEs with which these people are closely related and provide accurate rankings.

Mining web data for competency management

We present CORDER (COmmunity Relation Discovery by named Entity Recognition) an un-supervised machine learning algorithm that exploits named entity recognition and co-occurrence data to associate individuals in an organization with their expertise and associates. We discuss the problems associated with evaluating unsupervised learners and report our initial evaluation experiments.

How weak categorizers based upon different principles strengthen performance

Combining the results of classifiers has shown much promise in machine learning generally. However, published work on combining text categorizers suggests that, for this particular application, improvements in performance are hard to attain. Explorative research using a simple voting system is presented and discussed in the light of a probabilistic model that was originally developed for safety critical software. It was found that typical categorization approaches produce predictions which are too similar for combining them to be effective since they tend to fail on the same records. Further experiments using two less orthodox categorizers are also presented which suggest that combining text categorizers can be successful, provided the essential element of ‘difference’ is considered.

Visual data mining using principled projection algorithms and information visualization techniques

We introduce a flexible visual data mining framework which combines advanced projection algorithms from the machine learning domain and visual techniques developed in the information visualization domain. The advantage of such an interface is that the user is directly involved in the data mining process. We integrate principled projection algorithms, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates and billboarding, to provide a visual data mining framework. Results on a real-life chemoinformatics dataset using GTM are promising and have been analytically compared with the results from the traditional projection methods. It is also shown that the HGTM algorithm provides additional value for large datasets. The computational complexity of these algorithms is discussed to demonstrate their suitability for the visual data mining framework. Copyright 2006 ACM.

Adaptive electrical signal post-processing in optical communications systems

Improving bit error rates in optical communication systems is a difficult and important problem. The error correction must take place at high speed and be extremely accurate. We show the feasibility of using hardware implementable machine learning techniques. This may enable some error correction at the speed required.

Proteomic applications of automated GPCR classification

The G-protein coupled receptor (GPCR) superfamily fulfils various metabolic functions and interacts with a diverse range of ligands. There is a lack of sequence similarity between the six classes that comprise the GPCR superfamily. Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of their amino acid sequences. This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area.

Evolving ambiguous images

This work explores the creation of ambiguous images, i.e., images that may induce multistable perception, by evolutionary means. Ambiguous images are created using a general purpose approach, composed of an expression-based evolutionary engine and a set of object detectors, which are trained in advance using Machine Learning techniques. Images are evolved using Genetic Programming and object detectors are used to classify them. The information gathered during classification is used to assign fitness. In a first stage, the system is used to evolve images that resemble a single object. In a second stage, the discovery of ambiguous images is promoted by combining pairs of object detectors. The analysis of the results highlights the ability of the system to evolve ambiguous images and the differences between computational and human ambiguous images.

Guiding local regression using visualisation

Solving many scientific problems requires effective regression and/or classification models for large high-dimensional datasets. Experts from these problem domains (e.g. biologists, chemists, financial analysts) have insights into the domain which can be helpful in developing powerful models but they need a modelling framework that helps them to use these insights. Data visualisation is an effective technique for presenting data and requiring feedback from the experts. A single global regression model can rarely capture the full behavioural variability of a huge multi-dimensional dataset. Instead, local regression models, each focused on a separate area of input space, often work better since the behaviour of different areas may vary. Classical local models such as Mixture of Experts segment the input space automatically, which is not always effective and it also lacks involvement of the domain experts to guide a meaningful segmentation of the input space. In this paper we addresses this issue by allowing domain experts to interactively segment the input space using data visualisation. The segmentation output obtained is then further used to develop effective local regression models.