AutoFACT: An Automatic Functional Annotation and Classification Tool

Affiliation: Centre Robert-Cedergren de l'Université de Montréal en bio-informatique et génomique & Département de biochimie, Université de Montréal

Automatic Detection and Classification of Glioma Tumors using Statistical Features

The characterization and grading of glioma tumors, via image derived features, for diagnosis, prognosis, and treatment response has been an active research area in medical image computing. This paper presents a novel method for automatic detection and classification of glioma from conventional T2 weighted MR images. Automatic detection of the tumor was established using newly developed method called Adaptive Gray level Algebraic set Segmentation Algorithm (AGASA).Statistical Features were extracted from the detected tumor texture using first order statistics and gray level co-occurrence matrix (GLCM) based second order statistical methods. Statistical significance of the features was determined by t-test and its corresponding p-value. A decision system was developed for the grade detection of glioma using these selected features and its p-value. The detection performance of the decision system was validated using the receiver operating characteristic (ROC) curve. The diagnosis and grading of glioma using this non-invasive method can contribute promising results in medical image computing

Microarray data classification using automatic SVM kernel selection

Microarray data classification is one of the most important emerging clinical applications in the medical community. Machine learning algorithms are most frequently used to complete this task. We selected one of the state-of-the-art kernel-based algorithms, the support vector machine (SVM), to classify microarray data. As a large number of kernels are available, a significant research question is what is the best kernel for patient diagnosis based on microarray data classification using SVM? We first suggest three solutions based on data visualization and quantitative measures. Different types of microarray problems then test the proposed solutions. Finally, we found that the rule-based approach is most useful for automatic kernel selection for SVM to classify microarray data.

Automatic network traffic classification

The thesis addresses a number of critical problems in regard to fully automating the process of network traffic classification and protocol identification. Several effective solutions based on statistical analysis and machine learning techniques are proposed, which significantly reduce the requirements for human interventions in network traffic classification systems.

Automatic microstructural characterization and classification using artificial intelligence techniques on ultrasound signals

Secondary phases such as Laves and carbides are formed during the final solidification stages of nickel based superalloy coatings deposited during the gas tungsten arc welding cold wire process. However, when aged at high temperatures, other phases can precipitate in the microstructure, like the γ″ and δ phases. This work presents a new application and evaluation of artificial intelligent techniques to classify (the background echo and backscattered) ultrasound signals in order to characterize the microstructure of a Ni-based alloy thermally aged at 650 and 950 °C for 10, 100 and 200 h. The background echo and backscattered ultrasound signals were acquired using transducers with frequencies of 4 and 5 MHz. Thus with the use of features extraction techniques, i.e.; detrended fluctuation analysis and the Hurst method, the accuracy and speed in the classification of the secondary phases from ultrasound signals could be studied. The classifiers under study were the recent optimum-path forest (OPF) and the more traditional support vector machines and Bayesian. The experimental results revealed that the OPF classifier was the fastest and most reliable. In addition, the OPF classifier revealed to be a valid and adequate tool for microstructure characterization through ultrasound signals classification due to its speed, sensitivity, accuracy and reliability. © 2013 Elsevier B.V. All rights reserved.

Automatic segmentation and classification of human intestinal parasites from microscopy images

Human intestinal parasites constitute a problem in most tropical countries, causing death or physical and mental disorders. Their diagnosis usually relies on the visual analysis of microscopy images, with error rates that may range from moderate to high. The problem has been addressed via computational image analysis, but only for a few species and images free of fecal impurities. In routine, fecal impurities are a real challenge for automatic image analysis. We have circumvented this problem by a method that can segment and classify, from bright field microscopy images with fecal impurities, the 15 most common species of protozoan cysts, helminth eggs, and larvae in Brazil. Our approach exploits ellipse matching and image foresting transform for image segmentation, multiple object descriptors and their optimum combination by genetic programming for object representation, and the optimum-path forest classifier for object recognition. The results indicate that our method is a promising approach toward the fully automation of the enteroparasitosis diagnosis. © 2012 IEEE.

Fusion of probabilistic knowledge-based classification rules and learning automata for automatic recognition of digital images

In this paper, the fusion of probabilistic knowledge-based classification rules and learning automata theory is proposed and as a result we present a set of probabilistic classification rules with self-learning capability. The probabilities of the classification rules change dynamically guided by a supervised reinforcement process aimed at obtaining an optimum classification accuracy. This novel classifier is applied to the automatic recognition of digital images corresponding to visual landmarks for the autonomous navigation of an unmanned aerial vehicle (UAV) developed by the authors. The classification accuracy of the proposed classifier and its comparison with well-established pattern recognition methods is finally reported.

Automatic blood glucose classification for gestational diabetes with feature selection: decision trees vs neural networks

Automatic blood glucose classification may help specialists to provide a better interpretation of blood glucose data, downloaded directly from patients glucose meter and will contribute in the development of decision support systems for gestational diabetes. This paper presents an automatic blood glucose classifier for gestational diabetes that compares 6 different feature selection methods for two machine learning algorithms: neural networks and decision trees. Three searching algorithms, Greedy, Best First and Genetic, were combined with two different evaluators, CSF and Wrapper, for the feature selection. The study has been made with 6080 blood glucose measurements from 25 patients. Decision trees with a feature set selected with the Wrapper evaluator and the Best first search algorithm obtained the best accuracy: 95.92%.

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families.

Intelligent Search and Automatic Document Classification and Cataloging Based on Ontology Approach

This paper presents an approach to development of intelligent search system and automatic document classification and cataloging tools for CASE-system based on metadata. The described method uses advantages of ontology approach and traditional approach based on keywords. The method has powerful intelligent means and it can be integrated with existing document search systems.

Classification of Airborne LIDAR Intensity Data Using Statistical Analysis and Hough Transform with Application to Power Line Corridors

Light Detection and Ranging (LIDAR) has great potential to assist vegetation management in power line corridors by providing more accurate geometric information of the power line assets and vegetation along the corridors. However, the development of algorithms for the automatic processing of LIDAR point cloud data, in particular for feature extraction and classification of raw point cloud data, is in still in its infancy. In this paper, we take advantage of LIDAR intensity and try to classify ground and non-ground points by statistically analyzing the skewness and kurtosis of the intensity data. Moreover, the Hough transform is employed to detected power lines from the filtered object points. The experimental results show the effectiveness of our methods and indicate that better results were obtained by using LIDAR intensity data than elevation data.

Design of automatic vision-based inspection system for solder joint segmentation

Purpose: Computer vision has been widely used in the inspection of electronic components. This paper proposes a computer vision system for the automatic detection, localisation, and segmentation of solder joints on Printed Circuit Boards (PCBs) under different illumination conditions. Design/methodology/approach: An illumination normalization approach is applied to an image, which can effectively and efficiently eliminate the effect of uneven illumination while keeping the properties of the processed image the same as in the corresponding image under normal lighting conditions. Consequently special lighting and instrumental setup can be reduced in order to detect solder joints. These normalised images are insensitive to illumination variations and are used for the subsequent solder joint detection stages. In the segmentation approach, the PCB image is transformed from an RGB color space to a YIQ color space for the effective detection of solder joints from the background. Findings: The segmentation results show that the proposed approach improves the performance significantly for images under varying illumination conditions. Research limitations/implications: This paper proposes a front-end system for the automatic detection, localisation, and segmentation of solder joint defects. Further research is required to complete the full system including the classification of solder joint defects. Practical implications: The methodology presented in this paper can be an effective method to reduce cost and improve quality in production of PCBs in the manufacturing industry. Originality/value: This research proposes the automatic location, identification and segmentation of solder joints under different illumination conditions.

Improving automatic speaker verification using SVM techniques

Automatic recognition of people is an active field of research with important forensic and security applications. In these applications, it is not always possible for the subject to be in close proximity to the system. Voice represents a human behavioural trait which can be used to recognise people in such situations. Automatic Speaker Verification (ASV) is the process of verifying a persons identity through the analysis of their speech and enables recognition of a subject at a distance over a telephone channel { wired or wireless. A significant amount of research has focussed on the application of Gaussian mixture model (GMM) techniques to speaker verification systems providing state-of-the-art performance. GMM's are a type of generative classifier trained to model the probability distribution of the features used to represent a speaker. Recently introduced to the field of ASV research is the support vector machine (SVM). An SVM is a discriminative classifier requiring examples from both positive and negative classes to train a speaker model. The SVM is based on margin maximisation whereby a hyperplane attempts to separate classes in a high dimensional space. SVMs applied to the task of speaker verification have shown high potential, particularly when used to complement current GMM-based techniques in hybrid systems. This work aims to improve the performance of ASV systems using novel and innovative SVM-based techniques. Research was divided into three main themes: session variability compensation for SVMs; unsupervised model adaptation; and impostor dataset selection. The first theme investigated the differences between the GMM and SVM domains for the modelling of session variability | an aspect crucial for robust speaker verification. Techniques developed to improve the robustness of GMMbased classification were shown to bring about similar benefits to discriminative SVM classification through their integration in the hybrid GMM mean supervector SVM classifier. Further, the domains for the modelling of session variation were contrasted to find a number of common factors, however, the SVM-domain consistently provided marginally better session variation compensation. Minimal complementary information was found between the techniques due to the similarities in how they achieved their objectives. The second theme saw the proposal of a novel model for the purpose of session variation compensation in ASV systems. Continuous progressive model adaptation attempts to improve speaker models by retraining them after exploiting all encountered test utterances during normal use of the system. The introduction of the weight-based factor analysis model provided significant performance improvements of over 60% in an unsupervised scenario. SVM-based classification was then integrated into the progressive system providing further benefits in performance over the GMM counterpart. Analysis demonstrated that SVMs also hold several beneficial characteristics to the task of unsupervised model adaptation prompting further research in the area. In pursuing the final theme, an innovative background dataset selection technique was developed. This technique selects the most appropriate subset of examples from a large and diverse set of candidate impostor observations for use as the SVM background by exploiting the SVM training process. This selection was performed on a per-observation basis so as to overcome the shortcoming of the traditional heuristic-based approach to dataset selection. Results demonstrate the approach to provide performance improvements over both the use of the complete candidate dataset and the best heuristically-selected dataset whilst being only a fraction of the size. The refined dataset was also shown to generalise well to unseen corpora and be highly applicable to the selection of impostor cohorts required in alternate techniques for speaker verification.