Remote protein homology detection and fold recognition refer to detection of structural homology in proteins where there are small or no similarities in the sequence. To detect protein structural classes from protein primary sequence information, homology-based methods have been developed, which can be divided to three types: discriminative classifiers, generative models for protein families and pairwise sequence comparisons. Support Vector Machines (SVM) and Neural Networks (NN) are two popular discriminative methods. Recent studies have shown that SVM has fast speed during training, more accurate and efficient compared to NN. We present a comprehensive method based on two-layer classifiers. The 1st layer is used to detect up to superfamily and family in SCOP hierarchy using optimized binary SVM classification rules. It used the kernel function known as the Bio-kernel, which incorporates the biological information in the classification process. The 2nd layer uses discriminative SVM algorithm with string kernel that will detect up to protein fold level in SCOP hierarchy. The results obtained were evaluated using mean ROC and mean MRFP and the significance of the result produced with pairwise t-test was tested. Experimental results show that our approaches significantly improve the performance of remote protein homology detection and fold recognition for all three different version SCOP datasets (1.53, 1.67 and 1.73). We achieved 4.19% improvements in term of mean ROC in SCOP 1.53, 4.75% in SCOP 1.67 and 4.03% in SCOP 1.73 datasets when compared to the result produced by well-known methods. The combination of first layer and second layer of BioSVM-2L performs well in remote homology detection and fold recognition even in three different versions of datasets.
Content-based image retrieval techniques have been extensively studied for the past few years. With the growth of digital medical image databases, the demand for content-based analysis and retrieval tools has been increasing remarkably. Blood cell image is a key diagnostic tool for hematologists. An automated system that can retrieved relevant blood cell images correctly and efficiently would save the effort and time of hematologists. The purpose of this work is to develop such a content-based image retrieval system. Global color histogram and wavelet-based methods are used in the prototype. The system allows users to search by providing a query image and select one of four implemented methods. The obtained results demonstrate the proposed extended query refinement has the potential to capture a user's high level query and perception subjectivity by dynamically giving better query combinations. Color-based methods performed better than wavelet-based methods with regard to precision, recall rate and retrieval time. Shape and density of blood cells are suggested as measurements for future improvement. The system developed is useful for undergraduate education.
This paper focuses on the detection of retinal blood vessels which play a vital role in reducing the proliferative diabetic retinopathy and for preventing the loss of visual capability. The proposed algorithm which takes advantage of the powerful preprocessing techniques such as the contrast enhancement and thresholding offers an automated segmentation procedure for retinal blood vessels. To evaluate the performance of the new algorithm, experiments are conducted on 40 images collected from DRIVE database. The results show that the proposed algorithm performs better than the other known algorithms in terms of accuracy. Furthermore, the proposed algorithm being simple and easy to implement, is best suited for fast processing applications.
Iris-based biometric systems identify individuals based on the characteristics of their iris, since they are proven to remain unique for a long time. An iris recognition system includes four phases, the most important of which is preprocessing in which the iris segmentation is performed. The accuracy of an iris biometric system critically depends on the segmentation system. In this paper, an iris segmentation system using edge detection techniques and Hough transforms is presented. The newly proposed edge detection system enhances the performance of the segmentation in a way that it performs much more efficiently than the other conventional iris segmentation methods.
The authors present a new method of recognizing different human facial gestures through their neural activities and muscle movements, which can be used in machine-interfacing applications. Human-machine interface (HMI) technology utilizes human neural activities as input controllers for the machine. Recently, much work has been done on the specific application of facial electromyography (EMG)-based HMI, which have used limited and fixed numbers of facial gestures. In this work, a multipurpose interface is suggested that can support 2-11 control commands that can be applied to various HMI systems. The significance of this work is finding the most accurate facial gestures for any application with a maximum of eleven control commands. Eleven facial gesture EMGs are recorded from ten volunteers. Detected EMGs are passed through a band-pass filter and root mean square features are extracted. Various combinations of gestures with a different number of gestures in each group are made from the existing facial gestures. Finally, all combinations are trained and classified by a Fuzzy c-means classifier. In conclusion, combinations with the highest recognition accuracy in each group are chosen. An average accuracy >90% of chosen combinations proved their ability to be used as command controllers.
Multistrategy Learning of Self-Organizing Map (SOM) and Particle Swarm Optimization (PSO) is commonly implemented in clustering domain due to its capabilities in handling complex data characteristics. However, some of these multistrategy learning architectures have weaknesses such as slow convergence time always being trapped in the local minima. This paper proposes multistrategy learning of SOM lattice structure with Particle Swarm Optimisation which is called ESOMPSO for solving various classification problems. The enhancement of SOM lattice structure is implemented by introducing a new hexagon formulation for better mapping quality in data classification and labeling. The weights of the enhanced SOM are optimised using PSO to obtain better output quality. The proposed method has been tested on various standard datasets with substantial comparisons with existing SOM network and various distance measurement. The results show that our proposed method yields a promising result with better average accuracy and quantisation errors compared to the other methods as well as convincing significant test.
Segmentation is the most crucial part in the computer-aided bone age assessment. A well-known type of segmentation performed in the system is adaptive segmentation. While providing better result than global thresholding method, the adaptive segmentation produces a lot of unwanted noise that could affect the latter process of epiphysis extraction.
Automating the detection of lesions in liver CT scans requires a high performance and robust solution. With CT-scan start to become the norm in emergency department, the need for a fast and efficient liver lesions detection method is arising. In this paper, we propose a fast and evolvable method to profile the features of pre-segmented healthy liver and use it to detect the presence of liver lesions in emergency scenario. Our preliminary experiment with the MICCAI 2007 grand challenge datasets shows promising results of a fast training time, ability to evolve the produced healthy liver profiles, and accurate detection of the liver lesions. Lastly, the future work directions are also presented.
An intelligent gait-phase detection algorithm based on kinematic and kinetic parameters is presented in this paper. The gait parameters do not vary distinctly for each gait phase; therefore, it is complex to differentiate gait phases with respect to a threshold value. To overcome this intricacy, the concept of fuzzy logic was applied to detect gait phases with respect to fuzzy membership values. A real-time data-acquisition system was developed consisting of four force-sensitive resistors and two inertial sensors to obtain foot-pressure patterns and knee flexion/extension angle, respectively. The detected gait phases could be further analyzed to identify abnormality occurrences, and hence, is applicable to determine accurate timing for feedback. The large amount of data required for quality gait analysis necessitates the utilization of information technology to store, manage, and extract required information. Therefore, a software application was developed for real-time acquisition of sensor data, data processing, database management, and a user-friendly graphical-user interface as a tool to simplify the task of clinicians. The experiments carried out to validate the proposed system are presented along with the results analysis for normal and pathological walking patterns.
This paper presents a new application of the Particle Swarm Optimization (PSO) algorithm to optimize Mel Frequency Cepstrum Coefficients (MFCC) parameters, in order to extract an optimal feature set for diagnosis of hypothyroidism in infants using Multi-Layer Perceptrons (MLP) neural network. MFCC features is influenced by the number of filter banks (f(b)) and the number of coefficients (n(c)) used. These parameters are critical in representation of the features as they affect the resolution and dimensionality of the features. In this paper, the PSO algorithm was used to optimize the values of f(b) and n(c). The MFCC features based on the PSO optimization were extracted from healthy and unhealthy infant cry signals and used to train MLP in the classification of hypothyroid infant cries. The results indicate that the PSO algorithm could determine the optimum combination of f(b) and n(c) that produce the best classification accuracy of the MLP.
Load shedding is some of the essential requirement for maintaining security of modern power systems, particularly in competitive energy markets. This paper proposes an intelligent scheme for fast and accurate load shedding using neural networks for predicting the possible loss of load at the early stage and neuro-fuzzy for determining the amount of load shed in order to avoid a cascading outage. A large scale electrical power system has been considered to validate the performance of the proposed technique in determining the amount of load shed. The proposed techniques can provide tools for improving the reliability and continuity of power supply. This was confirmed by the results obtained in this research of which sample results are given in this paper.
The detection of bright objects such as optic disc (OD) and exudates in color fundus images is an important step in the diagnosis of eye diseases such as diabetic retinopathy and glaucoma. In this paper, a novel approach to automatically segment the OD and exudates is proposed. The proposed algorithm makes use of the green component of the image and preprocessing steps such as average filtering, contrast adjustment, and thresholding. The other processing techniques used are morphological opening, extended maxima operator, minima imposition, and watershed transformation. The proposed algorithm is evaluated using the test images of STARE and DRIVE databases with fixed and variable thresholds. The images drawn by human expert are taken as the reference images. The proposed method yields sensitivity values as high as 96.7%, which are better than the results reported in the literature.
An intelligent prediction system has been developed to discriminate drug-like and non drug-like molecules pattern. The system is constructed by using the application of advanced version of standard multilayer perceptron (MLP) neural network called Hybrid Multilayer Perceptron (HMLP) neural network and trained using Modified Recursive Prediction Error (MRPE) training algorithm. In this work, a well understood and easy excess Rule of Five + Veber filter properties are selected as the topological descriptor. The main idea behind the selection of this simple descriptor is to assure that the system could be used widely, beneficial and more advantageous regardless at all user level within a drug discovery organization.
In this brief, a new neural network model called generalized adaptive resonance theory (GART) is introduced. GART is a hybrid model that comprises a modified Gaussian adaptive resonance theory (MGA) and the generalized regression neural network (GRNN). It is an enhanced version of the GRNN, which preserves the online learning properties of adaptive resonance theory (ART). A series of empirical studies to assess the effectiveness of GART in classification, regression, and time series prediction tasks is conducted. The results demonstrate that GART is able to produce good performances as compared with those of other methods, including the online sequential extreme learning machine (OSELM) and sequential learning radial basis function (RBF) neural network models.
Utilizing the multiple degrees of freedom offered by the data glove for each finger and the hand, a novel on-line signature verification system using the Singular Value Decomposition (SVD) numerical tool for signature classification and verification is presented. The proposed technique is based on the Singular Value Decomposition in finding r singular vectors sensing the maximal energy of glove data matrix A, called principal subspace, so the effective dimensionality of A can be reduced. Having modeled the data glove signature through its r-principal subspace, signature authentication is performed by finding the angles between the different subspaces. A demonstration of the data glove is presented as an effective high-bandwidth data entry device for signature verification. This SVD-based signature verification technique is tested and its performance is shown to be able to recognize forgery signatures with a false acceptance rate of less than 1.2%.
A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search space of the Gene Ontology graph. The genetic similarity algorithm is implemented in the Gene Ontology browser named basic UTMGO to overcome the weaknesses of the existing Gene Ontology browsers which use a conventional approach based on keyword matching. To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO. The objective of developing the extended UTMGO is to provide a simple and practical tool that is capable of producing better results and requires a reasonable amount of running time with low computing cost specifically for offline usage. The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools.
This paper proposes to develop an automated diagnostic system for cervical pre-cancerous. METHODS AND DATA SAMPLES: The proposed automated diagnostic system consists of two parts; an automatic feature extraction and an intelligent diagnostic. In the automatic feature extraction, the system automatically extracts four cervical cells features (i.e. nucleus size, nucleus grey level, cytoplasm size and cytoplasm grey level). A new features extraction algorithm called region-growing-based features extraction (RGBFE) is proposed to extract the cervical cells features. The extracted features will then be fed as input data to the intelligent diagnostic part. A new artificial neural network (ANN) architecture called hierarchical hybrid multilayered perceptron (H(2)MLP) network is proposed to predict the cervical pre-cancerous stage into three classes, namely normal, low grade intra-epithelial squamous lesion (LSIL) and high grade intra-epithelial squamous lesion (HSIL). We empirically assess the capability of the proposed diagnostic system using 550 reported cases (211 normal cases, 143 LSIL cases and 196 HSIL cases).
Skin colour is vital information in dermatological diagnosis. It reflects pathological condition beneath the skin and commonly being used to indicate the extent of a disease. Psoriasis is a skin disease which is indicated by the appearance of red plaques. Although there is no cure for psoriasis, there are many treatment modalities to help control the disease. To evaluate treatment efficacy, PASI (Psoriasis Area and Severity Index) which is the current gold standard method is used to determine severity of psoriasis lesion. Erythema (redness) is one parameter in PASI. Commonly, the erythema is assessed visually, thus leading to subjective and inconsistent result. In this work, we proposed an objective assessment of psoriasis erythema for PASI scoring. The colour of psoriasis lesion is analyzed by DeltaL, Deltahue, and Deltachroma of CIELAB colour space. References of lesion with different scores are obtained from the selected lesions by two dermatologists. Results based on 38 lesions from 22 patients with various level of skin pigmentation show that PASI erythema score can be determined objectively and consistent with dermatology scoring.
For a given DNA sequence, it is well known that pair wise alignment schemes are used to determine the similarity with the DNA sequences available in the databanks. The efficiency of the alignment decides the type of amino acids and its corresponding proteins. In order to evaluate the given DNA sequence for its proteomic identity, a pattern matching approach is proposed in this paper. A block based semi-global alignment scheme is introduced to determine the similarity between the DNA sequences (known and given). The two DNA sequences are divided into blocks of equal length and alignment is performed which minimizes the computational complexity. The efficiency of the alignment scheme is evaluated using the parameter, percentage of similarity (POS). Four essential DNA version of the amino acids that emphasize the importance of proteomic functionalities are chosen as patterns and matching is performed with the known and given DNA sequences to determine the similarity between them. The ratio of amino acid counts between the two sequences is estimated and the results are compared with that of the POS value. It is found from the experimental results that higher the POS value and the pattern matching higher are the similarity between the two DNA sequences. The optimal block is also identified based on the POS value and amino acids count.
Information about retinal vasculature morphology is used in grading the severity and progression of diabetic retinopathy. An image analysis system can help ophthalmologists make accurate and efficient diagnoses. This paper presents the development of an image processing algorithm for detecting and reconstructing retinal vasculature. The detection of the vascular structure is achieved by image enhancement using contrast limited adaptive histogram equalization followed by the extraction of the vessels using bottom-hat morphological transformation. For reconstruction of the complete retinal vasculature, a region growing technique based on first-order Gaussian derivative is developed. The technique incorporates both gradient magnitude change and average intensity as the homogeneity criteria that enable the process to adapt to intensity changes and intensity spread over the vasculature region. The reconstruction technique reduces the required number of seeds to near optimal for the region growing process. It also overcomes poor performance of current seed-based methods, especially with low and inconsistent contrast images as normally seen in vasculature regions of fundus images. Simulations of the algorithm on 20 test images from the DRIVE database show that it outperforms many other published methods and achieved an accuracy range (ability to detect both vessel and non-vessel pixels) of 0.91 - 0.95, a sensitivity range (ability to detect vessel pixels) of 0.91 - 0.95 and a specificity range (ability to detect non-vessel pixels) of 0.88 - 0.94.