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An efficient method for the computation of Legendre moments

Yap PT, Paramesran R

IEEE Trans Pattern Anal Mach Intell, 2005 Dec;27(12):1996-2002.
PMID: 16355666

Legendre moments are continuous moments, hence, when applied to discrete-space images, numerical approximation is involved and error occurs. This paper proposes a method to compute the exact values of the moments by mathematically integrating the Legendre polynomials over the corresponding intervals of the image pixels. Experimental results show that the values obtained match those calculated theoretically, and the image reconstructed from these moments have lower error than that of the conventional methods for the same order. Although the same set of exact Legendre moments can be obtained indirectly from the set of geometric moments, the computation time taken is much longer than the proposed method.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Random multispace quantization as an analytic mechanism for BioHashing of biometric and random identity inputs

Teoh AB, Goh A, Ngo DC

IEEE Trans Pattern Anal Mach Intell, 2006 Dec;28(12):1892-901.
PMID: 17108365

Biometric analysis for identity verification is becoming a widespread reality. Such implementations necessitate large-scale capture and storage of biometric data, which raises serious issues in terms of data privacy and (if such data is compromised) identity theft. These problems stem from the essential permanence of biometric data, which (unlike secret passwords or physical tokens) cannot be refreshed or reissued if compromised. Our previously presented biometric-hash framework prescribes the integration of external (password or token-derived) randomness with user-specific biometrics, resulting in bitstring outputs with security characteristics (i.e., noninvertibility) comparable to cryptographic ciphers or hashes. The resultant BioHashes are hence cancellable, i.e., straightforwardly revoked and reissued (via refreshed password or reissued token) if compromised. BioHashing furthermore enhances recognition effectiveness, which is explained in this paper as arising from the Random Multispace Quantization (RMQ) of biometric and external random inputs.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext Intelligent color vision system for ripeness classification of oil palm fresh fruit bunch

Fadilah N, Mohamad-Saleh J, Abdul Halim Z, Ibrahim H, Syed Ali SS

Sensors (Basel), 2012;12(10):14179-95.
PMID: 23202043 DOI: 10.3390/s121014179

Ripeness classification of oil palm fresh fruit bunches (FFBs) during harvesting is important to ensure that they are harvested during optimum stage for maximum oil production. This paper presents the application of color vision for automated ripeness classification of oil palm FFB. Images of oil palm FFBs of type DxP Yangambi were collected and analyzed using digital image processing techniques. Then the color features were extracted from those images and used as the inputs for Artificial Neural Network (ANN) learning. The performance of the ANN for ripeness classification of oil palm FFB was investigated using two methods: training ANN with full features and training ANN with reduced features based on the Principal Component Analysis (PCA) data reduction technique. Results showed that compared with using full features in ANN, using the ANN trained with reduced features can improve the classification accuracy by 1.66% and is more effective in developing an automated ripeness classifier for oil palm FFB. The developed ripeness classifier can act as a sensor in determining the correct oil palm FFB ripeness category.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Computer-aided detection/diagnosis of breast cancer in mammography and ultrasound: a review

Jalalian A, Mashohor SB, Mahmud HR, Saripan MI, Ramli AR, Karasfi B

Clin Imaging, 2013 May-Jun;37(3):420-6.
PMID: 23153689 DOI: 10.1016/j.clinimag.2012.09.024

Breast cancer is the most common form of cancer among women worldwide. Early detection of breast cancer can increase treatment options and patients' survivability. Mammography is the gold standard for breast imaging and cancer detection. However, due to some limitations of this modality such as low sensitivity especially in dense breasts, other modalities like ultrasound and magnetic resonance imaging are often suggested to achieve additional information. Recently, computer-aided detection or diagnosis (CAD) systems have been developed to help radiologists in order to increase diagnosis accuracy. Generally, a CAD system consists of four stages: (a) preprocessing, (b) segmentation of regions of interest, (c) feature extraction and selection, and finally (d) classification. This paper presents the approaches which are applied to develop CAD systems on mammography and ultrasound images. The performance evaluation metrics of CAD systems are also reviewed.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Novel direct and self-regulating approaches to determine optimum growing multi-experts network structure

Loo CK, Rajeswari M, Rao MV

IEEE Trans Neural Netw, 2004 Nov;15(6):1378-95.
PMID: 15565767

This paper presents two novel approaches to determine optimum growing multi-experts network (GMN) structure. The first method called direct method deals with expertise domain and levels in connection with local experts. The growing neural gas (GNG) algorithm is used to cluster the local experts. The concept of error distribution is used to apportion error among the local experts. After reaching the specified size of the network, redundant experts removal algorithm is invoked to prune the size of the network based on the ranking of the experts. However, GMN is not ergonomic due to too many network control parameters. Therefore, a self-regulating GMN (SGMN) algorithm is proposed. SGMN adopts self-adaptive learning rates for gradient-descent learning rules. In addition, SGMN adopts a more rigorous clustering method called fully self-organized simplified adaptive resonance theory in a modified form. Experimental results show SGMN obtains comparative or even better performance than GMN in four benchmark examples, with reduced sensitivity to learning parameters setting. Moreover, both GMN and SGMN outperform the other neural networks and statistical models. The efficacy of SGMN is further justified in three industrial applications and a control problem. It provides consistent results besides holding out a profound potential and promise for building a novel type of nonlinear model consisting of several local linear models.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext Development and mining of a volatile organic compound database

Abdullah AA, Altaf-Ul-Amin M, Ono N, Sato T, Sugiura T, Morita AH, et al.

Biomed Res Int, 2015;2015:139254.
PMID: 26495281 DOI: 10.1155/2015/139254

Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases. Information on VOCs is scattered in the literature until now; however, there is still no available database describing VOCs and their biological activities. To attain this purpose, we have developed KNApSAcK Metabolite Ecology Database, which contains the information on the relationships between VOCs and their emitting organisms. The KNApSAcK Metabolite Ecology is also linked with the KNApSAcK Core and KNApSAcK Metabolite Activity Database to provide further information on the metabolites and their biological activities. The VOC database can be accessed online.

Matched MeSH terms: Pattern Recognition, Automated/methods
Fulltext Invariant Feature Matching for Image Registration Application Based on New Dissimilarity of Spatial Features

Mousavi Kahaki SM, Nordin MJ, Ashtari AH, J Zahra S

PLoS One, 2016;11(3):e0149710.
PMID: 26985996 DOI: 10.1371/journal.pone.0149710

An invariant feature matching method is proposed as a spatially invariant feature matching approach. Deformation effects, such as affine and homography, change the local information within the image and can result in ambiguous local information pertaining to image points. New method based on dissimilarity values, which measures the dissimilarity of the features through the path based on Eigenvector properties, is proposed. Evidence shows that existing matching techniques using similarity metrics--such as normalized cross-correlation, squared sum of intensity differences and correlation coefficient--are insufficient for achieving adequate results under different image deformations. Thus, new descriptor's similarity metrics based on normalized Eigenvector correlation and signal directional differences, which are robust under local variation of the image information, are proposed to establish an efficient feature matching technique. The method proposed in this study measures the dissimilarity in the signal frequency along the path between two features. Moreover, these dissimilarity values are accumulated in a 2D dissimilarity space, allowing accurate corresponding features to be extracted based on the cumulative space using a voting strategy. This method can be used in image registration applications, as it overcomes the limitations of the existing approaches. The output results demonstrate that the proposed technique outperforms the other methods when evaluated using a standard dataset, in terms of precision-recall and corner correspondence.

Matched MeSH terms: Pattern Recognition, Automated/methods
Fulltext The Role of Serotype Interactions and Seasonality in Dengue Model Selection and Control: Insights from a Pattern Matching Approach

Ten Bosch QA, Singh BK, Hassan MR, Chadee DD, Michael E

PLoS Negl Trop Dis, 2016 05;10(5):e0004680.
PMID: 27159023 DOI: 10.1371/journal.pntd.0004680

The epidemiology of dengue fever is characterized by highly seasonal, multi-annual fluctuations, and the irregular circulation of its four serotypes. It is believed that this behaviour arises from the interplay between environmental drivers and serotype interactions. The exact mechanism, however, is uncertain. Constraining mathematical models to patterns characteristic to dengue epidemiology offers a means for detecting such mechanisms. Here, we used a pattern-oriented modelling (POM) strategy to fit and assess a range of dengue models, driven by combinations of temporary cross protective-immunity, cross-enhancement, and seasonal forcing, on their ability to capture the main characteristics of dengue dynamics. We show that all proposed models reproduce the observed dengue patterns across some part of the parameter space. Which model best supports the dengue dynamics is determined by the level of seasonal forcing. Further, when tertiary and quaternary infections are allowed, the inclusion of temporary cross-immunity alone is strongly supported, but the addition of cross-enhancement markedly reduces the parameter range at which dengue dynamics are produced, irrespective of the strength of seasonal forcing. The implication of these structural uncertainties on predicted vulnerability to control is also discussed. With ever expanding spread of dengue, greater understanding of dengue dynamics and control efforts (e.g. a near-future vaccine introduction) has become critically important. This study highlights the capacity of multi-level pattern-matching modelling approaches to offer an analytic tool for deeper insights into dengue epidemiology and control.

Matched MeSH terms: Pattern Recognition, Automated*
Automated extraction of retinal vasculature

Tan JH, Acharya UR, Chua KC, Cheng C, Laude A

Med Phys, 2016 May;43(5):2311.
PMID: 27147343 DOI: 10.1118/1.4945413

The authors propose an algorithm that automatically extracts retinal vasculature and provides a simple measure to correct the extraction. The output of the method is a network of salient points, and blood vessels are drawn by connecting the salient points using a centripetal parameterized Catmull-Rom spline.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext A Robust and Fast Computation Touchless Palm Print Recognition System Using LHEAT and the IFkNCN Classifier

Jaafar H, Ibrahim S, Ramli DA

Comput Intell Neurosci, 2015;2015:360217.
PMID: 26113861 DOI: 10.1155/2015/360217

Mobile implementation is a current trend in biometric design. This paper proposes a new approach to palm print recognition, in which smart phones are used to capture palm print images at a distance. A touchless system was developed because of public demand for privacy and sanitation. Robust hand tracking, image enhancement, and fast computation processing algorithms are required for effective touchless and mobile-based recognition. In this project, hand tracking and the region of interest (ROI) extraction method were discussed. A sliding neighborhood operation with local histogram equalization, followed by a local adaptive thresholding or LHEAT approach, was proposed in the image enhancement stage to manage low-quality palm print images. To accelerate the recognition process, a new classifier, improved fuzzy-based k nearest centroid neighbor (IFkNCN), was implemented. By removing outliers and reducing the amount of training data, this classifier exhibited faster computation. Our experimental results demonstrate that a touchless palm print system using LHEAT and IFkNCN achieves a promising recognition rate of 98.64%.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext A Unified Framework for Brain Segmentation in MR Images

Yazdani S, Yusof R, Karimian A, Riazi AH, Bennamoun M

Comput Math Methods Med, 2015;2015:829893.
PMID: 26089978 DOI: 10.1155/2015/829893

Brain MRI segmentation is an important issue for discovering the brain structure and diagnosis of subtle anatomical changes in different brain diseases. However, due to several artifacts brain tissue segmentation remains a challenging task. The aim of this paper is to improve the automatic segmentation of brain into gray matter, white matter, and cerebrospinal fluid in magnetic resonance images (MRI). We proposed an automatic hybrid image segmentation method that integrates the modified statistical expectation-maximization (EM) method and the spatial information combined with support vector machine (SVM). The combined method has more accurate results than what can be achieved with its individual techniques that is demonstrated through experiments on both real data and simulated images. Experiments are carried out on both synthetic and real MRI. The results of proposed technique are evaluated against manual segmentation results and other methods based on real T1-weighted scans from Internet Brain Segmentation Repository (IBSR) and simulated images from BrainWeb. The Kappa index is calculated to assess the performance of the proposed framework relative to the ground truth and expert segmentations. The results demonstrate that the proposed combined method has satisfactory results on both simulated MRI and real brain datasets.

Matched MeSH terms: Pattern Recognition, Automated/statistics & numerical data
Automated Detection of Alzheimer's Disease Using Brain MRI Images- A Study with Various Feature Extraction Techniques

Acharya UR, Fernandes SL, WeiKoh JE, Ciaccio EJ, Fabell MKM, Tanik UJ, et al.

J Med Syst, 2019 Aug 09;43(9):302.
PMID: 31396722 DOI: 10.1007/s10916-019-1428-9

The aim of this work is to develop a Computer-Aided-Brain-Diagnosis (CABD) system that can determine if a brain scan shows signs of Alzheimer's disease. The method utilizes Magnetic Resonance Imaging (MRI) for classification with several feature extraction techniques. MRI is a non-invasive procedure, widely adopted in hospitals to examine cognitive abnormalities. Images are acquired using the T2 imaging sequence. The paradigm consists of a series of quantitative techniques: filtering, feature extraction, Student's t-test based feature selection, and k-Nearest Neighbor (KNN) based classification. Additionally, a comparative analysis is done by implementing other feature extraction procedures that are described in the literature. Our findings suggest that the Shearlet Transform (ST) feature extraction technique offers improved results for Alzheimer's diagnosis as compared to alternative methods. The proposed CABD tool with the ST + KNN technique provided accuracy of 94.54%, precision of 88.33%, sensitivity of 96.30% and specificity of 93.64%. Furthermore, this tool also offered an accuracy, precision, sensitivity and specificity of 98.48%, 100%, 96.97% and 100%, respectively, with the benchmark MRI database.

Matched MeSH terms: Pattern Recognition, Automated/methods*
A Two Layer Sparse Autoencoder for Glaucoma Identification with Fundus Images

Raghavendra U, Gudigar A, Bhandary SV, Rao TN, Ciaccio EJ, Acharya UR

J Med Syst, 2019 Jul 30;43(9):299.
PMID: 31359230 DOI: 10.1007/s10916-019-1427-x

Glaucoma is a type of eye condition which may result in partial or consummate vision loss. Higher intraocular pressure is the leading cause for this condition. Screening for glaucoma and early detection can avert vision loss. Computer aided diagnosis (CAD) is an automated process with the potential to identify glaucoma early through quantitative analysis of digital fundus images. Preparing an effective model for CAD requires a large database. This study presents a CAD tool for the precise detection of glaucoma using a machine learning approach. An autoencoder is trained to determine effective and important features from fundus images. These features are used to develop classes of glaucoma for testing. The method achieved an F - measure value of 0.95 utilizing 1426 digital fundus images (589 control and 837 glaucoma). The efficacy of the system is evident, and is suggestive of its possible utility as an additional tool for verification of clinical decisions.

Matched MeSH terms: Pattern Recognition, Automated/methods
Objective assessment of psoriasis erythema for PASI scoring

Ahmad Fadzil MH, Ihtatho D, Affandi AM, Hussein SH

Annu Int Conf IEEE Eng Med Biol Soc, 2008;2008:4070-3.
PMID: 19163606 DOI: 10.1109/IEMBS.2008.4650103

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.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext Bleeding detection in wireless capsule endoscopy videos - Color versus texture features

Pogorelov K, Suman S, Azmadi Hussin F, Saeed Malik A, Ostroukhova O, Riegler M, et al.

J Appl Clin Med Phys, 2019 Aug;20(8):141-154.
PMID: 31251460 DOI: 10.1002/acm2.12662

Wireless capsule endoscopy (WCE) is an effective technology that can be used to make a gastrointestinal (GI) tract diagnosis of various lesions and abnormalities. Due to a long time required to pass through the GI tract, the resulting WCE data stream contains a large number of frames which leads to a tedious job for clinical experts to perform a visual check of each and every frame of a complete patient's video footage. In this paper, an automated technique for bleeding detection based on color and texture features is proposed. The approach combines the color information which is an essential feature for initial detection of frame with bleeding. Additionally, it uses the texture which plays an important role to extract more information from the lesion captured in the frames and allows the system to distinguish finely between borderline cases. The detection algorithm utilizes machine-learning-based classification methods, and it can efficiently distinguish between bleeding and nonbleeding frames and perform pixel-level segmentation of bleeding areas in WCE frames. The performed experimental studies demonstrate the performance of the proposed bleeding detection method in terms of detection accuracy, where we are at least as good as the state-of-the-art approaches. In this research, we have conducted a broad comparison of a number of different state-of-the-art features and classification methods that allows building an efficient and flexible WCE video processing system.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Classification of ankle joint movements based on surface electromyography signals for rehabilitation robot applications

Al-Quraishi MS, Ishak AJ, Ahmad SA, Hasan MK, Al-Qurishi M, Ghapanchizadeh H, et al.

Med Biol Eng Comput, 2017 May;55(5):747-758.
PMID: 27484411 DOI: 10.1007/s11517-016-1551-4

Electromyography (EMG)-based control is the core of prostheses, orthoses, and other rehabilitation devices in recent research. Nonetheless, EMG is difficult to use as a control signal given the complex nature of the signal. To overcome this problem, the researchers employed a pattern recognition technique. EMG pattern recognition mainly involves four stages: signal detection, preprocessing feature extraction, dimensionality reduction, and classification. In particular, the success of any pattern recognition technique depends on the feature extraction stage. In this study, a modified time-domain features set and logarithmic transferred time-domain features (LTD) were evaluated and compared with other traditional time-domain features set (TTD). Three classifiers were employed to assess the two feature sets, namely linear discriminant analysis (LDA), k nearest neighborhood, and Naïve Bayes. Results indicated the superiority of the new time-domain feature set LTD, on conventional time-domain features TTD with the average classification accuracy of 97.23 %. In addition, the LDA classifier outperformed the other two classifiers considered in this study.

Matched MeSH terms: Pattern Recognition, Automated/methods
Fulltext Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches

Yousef Kalafi E, Tan WB, Town C, Dhillon SK

BMC Bioinformatics, 2016 Dec 22;17(Suppl 19):511.
PMID: 28155722 DOI: 10.1186/s12859-016-1376-z

BACKGROUND: Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body surface and feed on skin and gill debris. Haptoral attachment organs consist of sclerotized hard parts such as hooks, anchors and marginal hooks. Monogenean species are differentiated based on their haptoral bars, anchors, marginal hooks, reproductive parts' (male and female copulatory organs) morphological characters and soft anatomical parts. The complex structure of these diagnostic organs and also their overlapping in microscopic digital images are impediments for developing fully automated identification system for monogeneans (LNCS 7666:256-263, 2012), (ISDA; 457-462, 2011), (J Zoolog Syst Evol Res 52(2): 95-99. 2013;). In this study images of hard parts of the haptoral organs such as bars and anchors are used to develop a fully automated identification technique for monogenean species identification by implementing image processing techniques and machine learning methods.
RESULT: Images of four monogenean species namely Sinodiplectanotrema malayanus, Trianchoratus pahangensis, Metahaliotrema mizellei and Metahaliotrema sp. (undescribed) were used to develop an automated technique for identification. K-nearest neighbour (KNN) was applied to classify the monogenean specimens based on the extracted features. 50% of the dataset was used for training and the other 50% was used as testing for system evaluation. Our approach demonstrated overall classification accuracy of 90%. In this study Leave One Out (LOO) cross validation is used for validation of our system and the accuracy is 91.25%.
CONCLUSIONS: The methods presented in this study facilitate fast and accurate fully automated classification of monogeneans at the species level. In future studies more classes will be included in the model, the time to capture the monogenean images will be reduced and improvements in extraction and selection of features will be implemented.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext Real-Time Human Detection for Aerial Captured Video Sequences via Deep Models

AlDahoul N, Md Sabri AQ, Mansoor AM

Comput Intell Neurosci, 2018;2018:1639561.
PMID: 29623089 DOI: 10.1155/2018/1639561

Human detection in videos plays an important role in various real life applications. Most of traditional approaches depend on utilizing handcrafted features which are problem-dependent and optimal for specific tasks. Moreover, they are highly susceptible to dynamical events such as illumination changes, camera jitter, and variations in object sizes. On the other hand, the proposed feature learning approaches are cheaper and easier because highly abstract and discriminative features can be produced automatically without the need of expert knowledge. In this paper, we utilize automatic feature learning methods which combine optical flow and three different deep models (i.e., supervised convolutional neural network (S-CNN), pretrained CNN feature extractor, and hierarchical extreme learning machine) for human detection in videos captured using a nonstatic camera on an aerial platform with varying altitudes. The models are trained and tested on the publicly available and highly challenging UCF-ARG aerial dataset. The comparison between these models in terms of training, testing accuracy, and learning speed is analyzed. The performance evaluation considers five human actions (digging, waving, throwing, walking, and running). Experimental results demonstrated that the proposed methods are successful for human detection task. Pretrained CNN produces an average accuracy of 98.09%. S-CNN produces an average accuracy of 95.6% with soft-max and 91.7% with Support Vector Machines (SVM). H-ELM has an average accuracy of 95.9%. Using a normal Central Processing Unit (CPU), H-ELM's training time takes 445 seconds. Learning in S-CNN takes 770 seconds with a high performance Graphical Processing Unit (GPU).

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext Geometric feature descriptor and dissimilarity-based registration of remotely sensed imagery

Kahaki SMM, Arshad H, Nordin MJ, Ismail W

PLoS One, 2018;13(7):e0200676.
PMID: 30024921 DOI: 10.1371/journal.pone.0200676

Image registration of remotely sensed imagery is challenging, as complex deformations are common. Different deformations, such as affine and homogenous transformation, combined with multimodal data capturing can emerge in the data acquisition process. These effects, when combined, tend to compromise the performance of the currently available registration methods. A new image transform, known as geometric mean projection transform, is introduced in this work. As it is deformation invariant, it can be employed as a feature descriptor, whereby it analyzes the functions of all vertical and horizontal signals in local areas of the image. Moreover, an invariant feature correspondence method is proposed as a point matching algorithm, which incorporates new descriptor's dissimilarity metric. Considering the image as a signal, the proposed approach utilizes a square Eigenvector correlation (SEC) based on the Eigenvector properties. In our experiments on standard test images sourced from "Featurespace" and "IKONOS" datasets, the proposed method achieved higher average accuracy relative to that obtained from other state of the art image registration techniques. The accuracy of the proposed method was assessed using six standard evaluation metrics. Furthermore, statistical analyses, including t-test and Friedman test, demonstrate that the method developed as a part of this study is superior to the existing methods.

Matched MeSH terms: Pattern Recognition, Automated/methods*
Fulltext QuaBingo: A Prediction System for Protein Quaternary Structure Attributes Using Block Composition

Tung CH, Chen CW, Guo RC, Ng HF, Chu YW

Biomed Res Int, 2016;2016:9480276.
PMID: 27610389 DOI: 10.1155/2016/9480276

Background. Quaternary structures of proteins are closely relevant to gene regulation, signal transduction, and many other biological functions of proteins. In the current study, a new method based on protein-conserved motif composition in block format for feature extraction is proposed, which is termed block composition. Results. The protein quaternary assembly states prediction system which combines blocks with functional domain composition, called QuaBingo, is constructed by three layers of classifiers that can categorize quaternary structural attributes of monomer, homooligomer, and heterooligomer. The building of the first layer classifier uses support vector machines (SVM) based on blocks and functional domains of proteins, and the second layer SVM was utilized to process the outputs of the first layer. Finally, the result is determined by the Random Forest of the third layer. We compared the effectiveness of the combination of block composition, functional domain composition, and pseudoamino acid composition of the model. In the 11 kinds of functional protein families, QuaBingo is 23% of Matthews Correlation Coefficient (MCC) higher than the existing prediction system. The results also revealed the biological characterization of the top five block compositions. Conclusions. QuaBingo provides better predictive ability for predicting the quaternary structural attributes of proteins.

Matched MeSH terms: Pattern Recognition, Automated/methods

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