Stratification bias in low signal microarray studies

BACKGROUND: When analysing microarray and other small sample size biological datasets, care is needed to avoid various biases. We analyse a form of bias, stratification bias, that can substantially affect analyses using sample-reuse validation techniques and lead to inaccurate results. This bias is due to imperfect stratification of samples in the training and test sets and the dependency between these stratification errors, i.e. the variations in class proportions in the training and test sets are negatively correlated. RESULTS: We show that when estimating the performance of classifiers on low signal datasets (i.e. those which are difficult to classify), which are typical of many prognostic microarray studies, commonly used performance measures can suffer from a substantial negative bias. For error rate this bias is only severe in quite restricted situations, but can be much larger and more frequent when using ranking measures such as the receiver operating characteristic (ROC) curve and area under the ROC (AUC). Substantial biases are shown in simulations and on the van 't Veer breast cancer dataset. The classification error rate can have large negative biases for balanced datasets, whereas the AUC shows substantial pessimistic biases even for imbalanced datasets. In simulation studies using 10-fold cross-validation, AUC values of less than 0.3 can be observed on random datasets rather than the expected 0.5. Further experiments on the van 't Veer breast cancer dataset show these biases exist in practice. CONCLUSION: Stratification bias can substantially affect several performance measures. In computing the AUC, the strategy of pooling the test samples from the various folds of cross-validation can lead to large biases; computing it as the average of per-fold estimates avoids this bias and is thus the recommended approach. As a more general solution applicable to other performance measures, we show that stratified repeated holdout and a modified version of k-fold cross-validation, balanced, stratified cross-validation and balanced leave-one-out cross-validation, avoids the bias. Therefore for model selection and evaluation of microarray and other small biological datasets, these methods should be used and unstratified versions avoided. In particular, the commonly used (unbalanced) leave-one-out cross-validation should not be used to estimate AUC for small datasets

Improving "bag-of-keypoints" image categorisation: Generative Models and PDF-Kernels

In this paper we propose two distinct enhancements to the basic ''bag-of-keypoints" image categorisation scheme proposed in [4]. In this approach images are represented as a variable sized set of local image features (keypoints). Thus, we require machine learning tools which can operate on sets of vectors. In [4] this is achieved by representing the set as a histogram over bins found by k-means. We show how this approach can be improved and generalised using Gaussian Mixture Models (GMMs). Alternatively, the set of keypoints can be represented directly as a probability density function, over which a kernel can be de ned. This approach is shown to give state of the art categorisation performance

Evaluation and analysis of hybrid intelligent pattern recognition techniques for speaker identification

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The rapid momentum of the technology progress in the recent years has led to a tremendous rise in the use of biometric authentication systems. The objective of this research is to investigate the problem of identifying a speaker from its voice regardless of the content (i.e. text-independent), and to design efficient methods of combining face and voice in producing a robust authentication system. A novel approach towards speaker identification is developed using wavelet analysis, and multiple neural networks including Probabilistic Neural Network (PNN), General Regressive Neural Network (GRNN)and Radial Basis Function-Neural Network (RBF NN) with the AND voting scheme. This approach is tested on GRID and VidTIMIT cor-pora and comprehensive test results have been validated with state- of-the-art approaches. The system was found to be competitive and it improved the recognition rate by 15% as compared to the classical Mel-frequency Cepstral Coe±cients (MFCC), and reduced the recognition time by 40% compared to Back Propagation Neural Network (BPNN), Gaussian Mixture Models (GMM) and Principal Component Analysis (PCA). Another novel approach using vowel formant analysis is implemented using Linear Discriminant Analysis (LDA). Vowel formant based speaker identification is best suitable for real-time implementation and requires only a few bytes of information to be stored for each speaker, making it both storage and time efficient. Tested on GRID and Vid-TIMIT, the proposed scheme was found to be 85.05% accurate when Linear Predictive Coding (LPC) is used to extract the vowel formants, which is much higher than the accuracy of BPNN and GMM. Since the proposed scheme does not require any training time other than creating a small database of vowel formants, it is faster as well. Furthermore, an increasing number of speakers makes it di±cult for BPNN and GMM to sustain their accuracy, but the proposed score-based methodology stays almost linear. Finally, a novel audio-visual fusion based identification system is implemented using GMM and MFCC for speaker identi¯cation and PCA for face recognition. The results of speaker identification and face recognition are fused at different levels, namely the feature, score and decision levels. Both the score-level and decision-level (with OR voting) fusions were shown to outperform the feature-level fusion in terms of accuracy and error resilience. The result is in line with the distinct nature of the two modalities which lose themselves when combined at the feature-level. The GRID and VidTIMIT test results validate that the proposed scheme is one of the best candidates for the fusion of face and voice due to its low computational time and high recognition accuracy

Wavelet methods in speech recognition

In this thesis, novel wavelet techniques are developed to improve parametrization of speech signals prior to classification. It is shown that non-linear operations carried out in the wavelet domain improve the performance of a speech classifier and consistently outperform classical Fourier methods. This is because of the localised nature of the wavelet, which captures correspondingly well-localised time-frequency features within the speech signal. Furthermore, by taking advantage of the approximation ability of wavelets, efficient representation of the non-stationarity inherent in speech can be achieved in a relatively small number of expansion coefficients. This is an attractive option when faced with the so-called 'Curse of Dimensionality' problem of multivariate classifiers such as Linear Discriminant Analysis (LDA) or Artificial Neural Networks (ANNs). Conventional time-frequency analysis methods such as the Discrete Fourier Transform either miss irregular signal structures and transients due to spectral smearing or require a large number of coefficients to represent such characteristics efficiently. Wavelet theory offers an alternative insight in the representation of these types of signals. As an extension to the standard wavelet transform, adaptive libraries of wavelet and cosine packets are introduced which increase the flexibility of the transform. This approach is observed to be yet more suitable for the highly variable nature of speech signals in that it results in a time-frequency sampled grid that is well adapted to irregularities and transients. They result in a corresponding reduction in the misclassification rate of the recognition system. However, this is necessarily at the expense of added computing time. Finally, a framework based on adaptive time-frequency libraries is developed which invokes the final classifier to choose the nature of the resolution for a given classification problem. The classifier then performs dimensionaIity reduction on the transformed signal by choosing the top few features based on their discriminant power. This approach is compared and contrasted to an existing discriminant wavelet feature extractor. The overall conclusions of the thesis are that wavelets and their relatives are capable of extracting useful features for speech classification problems. The use of adaptive wavelet transforms provides the flexibility within which powerful feature extractors can be designed for these types of application

Exploiting Domain Knowledge for Cross-domain Text Classification in Heterogeneous Data Sources

With the growing amount of data generated in large heterogeneous repositories (such as the Word Wide Web, corporate repositories, citation databases), there is an increased need for the end users to locate relevant information efficiently. Text Classification (TC) techniques provide automated means for classifying fragments of text (phrases, paragraphs or documents) into predefined semantic types, allowing an efficient way for organising and analysing such large document collections. Current approaches to TC rely on supervised learning, which perform well on the domains on which the TC system is built, but tend to adapt poorly to different domains. This thesis presents a body of work for exploring adaptive TC techniques across hetero- geneous corpora in large repositories with the goal of finding novel ways of bridging the gap across domains. The proposed approaches rely on the exploitation of domain knowledge for the derivation of stable cross-domain features. This thesis also investigates novel ways of estimating the performance of a TC classifier, by means of domain similarity measures. For this purpose, two novel knowledge-based similarity measures are proposed that capture the usefulness of the selected cross-domain features for cross-domain TC. The evaluation of these approaches and measures is presented on real world datasets against various strong baseline methods and content-based measures used in transfer learning. This thesis explores how domain knowledge can be used to enhance the representation of documents to address the lexical gap across the domains. Given that the effectiveness of a text classifier largely depends on the availability of annotated data, this thesis explores techniques which can leverage data from social knowledge sources (such as DBpedia and Freebase). Techniques are further presented, which explore the feasibility of exploiting different semantic graph structures from knowledge sources in order to create novel cross- domain features and domain similarity metrics. The methodologies presented provide a novel representation of documents, and exploit four wide coverage knowledge sources: DBpedia, Freebase, SNOMED-CT and MeSH. The contribution of this thesis demonstrates the feasibility of exploiting domain knowl- edge for adaptive TC and domain similarity, providing an enhanced representation of docu- ments with semantic information about entities, that can indeed reduce the lexical differences between domains

Physically inspired methods and development of data-driven predictive systems.

Traditionally building of predictive models is perceived as a combination of both science and art. Although the designer of a predictive system effectively follows a prescribed procedure, his domain knowledge as well as expertise and intuition in the field of machine learning are often irreplaceable. However, in many practical situations it is possible to build well–performing predictive systems by following a rigorous methodology and offsetting not only the lack of domain knowledge but also partial lack of expertise and intuition, by computational power. The generalised predictive model development cycle discussed in this thesis is an example of such methodology, which despite being computationally expensive, has been successfully applied to real–world problems. The proposed predictive system design cycle is a purely data–driven approach. The quality of data used to build the system is thus of crucial importance. In practice however, the data is rarely perfect. Common problems include missing values, high dimensionality or very limited amount of labelled exemplars. In order to address these issues, this work investigated and exploited inspirations coming from physics. The novel use of well–established physical models in the form of potential fields, has resulted in derivation of a comprehensive Electrostatic Field Classification Framework for supervised and semi–supervised learning from incomplete data. Although the computational power constantly becomes cheaper and more accessible, it is not infinite. Therefore efficient techniques able to exploit finite amount of predictive information content of the data and limit the computational requirements of the resource–hungry predictive system design procedure are very desirable. In designing such techniques this work once again investigated and exploited inspirations coming from physics. By using an analogy with a set of interacting particles and the resulting Information Theoretic Learning framework, the Density Preserving Sampling technique has been derived. This technique acts as a computationally efficient alternative for cross–validation, which fits well within the proposed methodology. All methods derived in this thesis have been thoroughly tested on a number of benchmark datasets. The proposed generalised predictive model design cycle has been successfully applied to two real–world environmental problems, in which a comparative study of Density Preserving Sampling and cross–validation has also been performed confirming great potential of the proposed methods

Knowledge Base Enrichment by Relation Learning from Social Tagging Data

There has been considerable interest in transforming unstructured social tagging data into structured knowledge for semantic-based retrieval and recommendation. Research in this line mostly exploits data co-occurrence and often overlooks the complex and ambiguous meanings of tags. Furthermore, there have been few comprehensive evaluation studies regarding the quality of the discovered knowledge. We propose a supervised learning method to discover subsumption relations from tags. The key to this method is quantifying the probabilistic association among tags to better characterise their relations. We further develop an algorithm to organise tags into hierarchies based on the learned relations. Experiments were conducted using a large, publicly available dataset, Bibsonomy, and three popular, human-engineered or data-driven knowledge bases: DBpedia, Microsoft Concept Graph, and ACM Computing Classification System. We performed a comprehensive evaluation using different strategies: relation-level, ontology-level, and knowledge base enrichment based evaluation. The results clearly show that the proposed method can extract knowledge of better quality than the existing methods against the gold standard knowledge bases. The proposed approach can also enrich knowledge bases with new subsumption relations, having the potential to significantly reduce time and human effort for knowledge base maintenance and ontology evolution

Effective denoising and classification of hyperspectral images using curvelet transform and singular spectrum analysis

Hyperspectral imaging (HSI) classification has become a popular research topic in recent years, and effective feature extraction is an important step before the classification task. Traditionally, spectral feature extraction techniques are applied to the HSI data cube directly. This paper presents a novel algorithm for HSI feature extraction by exploiting the curvelet transformed domain via a relatively new spectral feature processing technique – singular spectrum analysis (SSA). Although the wavelet transform has been widely applied for HSI data analysis, the curvelet transform is employed in this paper since it is able to separate image geometric details and background noise effectively. Using the support vector machine (SVM) classifier, experimental results have shown that features extracted by SSA on curvelet coefficients have better performance in terms of classification accuracies over features extracted on wavelet coefficients. Since the proposed approach mainly relies on SSA for feature extraction on the spectral dimension, it actually belongs to the spectral feature extraction category. Therefore, the proposed method has also been compared with some state-of-the-art spectral feature extraction techniques to show its efficacy. In addition, it has been proven that the proposed method is able to remove the undesirable artefacts introduced during the data acquisition process as well. By adding an extra spatial post-processing step to the classified map achieved using the proposed approach, we have shown that the classification performance is comparable with several recent spectral-spatial classification methods