Electrical and Electronic Engineering - Research Publications
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ItemComplex Correlation Measure: a novel descriptor for Poincare plot(BMC, 2009-08-13)BACKGROUND: Poincaré plot is one of the important techniques used for visually representing the heart rate variability. It is valuable due to its ability to display nonlinear aspects of the data sequence. However, the problem lies in capturing temporal information of the plot quantitatively. The standard descriptors used in quantifying the Poincaré plot (SD1, SD2) measure the gross variability of the time series data. Determination of advanced methods for capturing temporal properties pose a significant challenge. In this paper, we propose a novel descriptor "Complex Correlation Measure (CCM)" to quantify the temporal aspect of the Poincaré plot. In contrast to SD1 and SD2, the CCM incorporates point-to-point variation of the signal. METHODS: First, we have derived expressions for CCM. Then the sensitivity of descriptors has been shown by measuring all descriptors before and after surrogation of the signal. For each case study, lag-1 Poincaré plots were constructed for three groups of subjects (Arrhythmia, Congestive Heart Failure (CHF) and those with Normal Sinus Rhythm (NSR)), and the new measure CCM was computed along with SD1 and SD2. ANOVA analysis distribution was used to define the level of significance of mean and variance of SD1, SD2 and CCM for different groups of subjects. RESULTS: CCM is defined based on the autocorrelation at different lags of the time series, hence giving an in depth measurement of the correlation structure of the Poincaré plot. A surrogate analysis was performed, and the sensitivity of the proposed descriptor was found to be higher as compared to the standard descriptors. Two case studies were conducted for recognizing arrhythmia and congestive heart failure (CHF) subjects from those with NSR, using the Physionet database and demonstrated the usefulness of the proposed descriptors in biomedical applications. CCM was found to be a more significant (p = 6.28E-18) parameter than SD1 and SD2 in discriminating arrhythmia from NSR subjects. In case of assessing CHF subjects also against NSR, CCM was again found to be the most significant (p = 9.07E-14). CONCLUSION: Hence, CCM can be used as an additional Poincaré plot descriptor to detect pathology.
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ItemIdentifying diabetic patients with cardiac autonomic neuropathy by heart rate complexity analysis(BMC, 2009-01-29)BACKGROUND: Cardiac autonomic neuropathy (CAN) in diabetes has been called a "silent killer", because so few patients realize that they suffer from it, and yet its effect can be lethal. Early sub clinical detection of CAN and intervention are of prime importance for risk stratification in preventing sudden death due to silent myocardial infarction. This study presents the usefulness of heart rate variability (HRV) and complexity analyses from short term ECG recordings as a screening tool for CAN. METHODS: A total of 17 sets of ECG recordings during supine rest were acquired from diabetic subjects with CAN (CAN+) and without CAN (CAN-) and analyzed. Poincaré plot indexes as well as traditional time and frequency, and the sample entropy (SampEn) measure were used for analyzing variability (short and long term) and complexity of HRV respectively. RESULTS: Reduced (p > 0.05)_Poincaré plot patterns and lower (p < 0.05) SampEn values were found in CAN+ group, which could be a practical diagnostic and prognostic marker. Classification Trees methodology generated a simple decision tree for CAN+ prediction including SampEn and Poincaré plot indexes with a sensitivity reaching 100% and a specificity of 75% (percentage of agreement 88.24%). CONCLUSION: Our results demonstrate the potential utility of SampEn (a complexity based estimator) of HRV in identifying asymptomatic CAN.
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ItemA comparative study on approximate entropy measure and poincare plot indexes of minimum foot clearance variability in the elderly during walking(BMC, 2008-02-02)BACKGROUND: Trip-related falls which is a major problem in the elderly population, might be linked to declines in the balance control function due to ageing. Minimum foot clearance (MFC) which provides a more sensitive measure of the motor function of the locomotor system, has been identified as a potential gait parameter associated with trip-related falls in older population. This paper proposes nonlinear indexes (approximate entropy (ApEn) and Poincaré plot indexes) of MFC variability and investigates the relationship of MFC with derived indexes of elderly gait patterns. The main aim is to find MFC variability indexes that well correlate with balance impairments. METHODS: MFC data during treadmill walking for 14 healthy elderly and 10 elderly participants with balance problems and a history of falls (falls risk) were analysed using a PEAK-2D motion analysis system. ApEn and Poincaré plot indexes of all MFC data sets were calculated and compared. RESULTS: Significant relationships of mean MFC with Poincaré plot indexes (SD1, SD2) and ApEn (r = 0.70, p < 0.05; r = 0.86, p < 0.01; r = 0.74, p < 0.05) were found in the falls-risk elderly group. On the other hand, such relationships were absent in the healthy elderly group. In contrast, the ApEn values of MFC data series were significantly (p < 0.05) correlated with Poincaré plot indexes of MFC in the healthy elderly group, whereas correlations were absent in the falls-risk group. The ApEn values in the falls-risk group (mean ApEn = 0.18 +/- 0.03) was significantly (p < 0.05) higher than that in the healthy group (mean ApEn = 0.13 +/- 0.13). The higher ApEn values in the falls-risk group might indicate increased irregularities and randomness in their gait patterns and an indication of loss of gait control mechanism. ApEn values of randomly shuffled MFC data of falls risk subjects did not show any significant relationship with mean MFC. CONCLUSION: Results have implication for quantifying gait dynamics in normal and pathological conditions, thus could be useful for the early diagnosis of at-risk gait. Further research should provide important information on whether falls prevention intervention can improve the gait performance of falls risk elderly by monitoring the change in MFC variability indexes.
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ItemJeeva: Enterprise Grid Enabled Web Portal for Protein Secondary Structure Prediction(IEEE, 2008)This paper presents a Grid portal for protein secondary structure prediction developed by using services of Aneka, a .NET-based enterprise Grid technology. The portal is used by research scientists to discover new prediction structures in a parallel manner. An SVM (Support Vector Machine)-based prediction algorithm is used with 64 sample protein sequences as a case study to demonstrate the potential of enterprise Grids.
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ItemA monomial ν-SV method for regression( 2007)In the present paper we describe a new formulation for Support Vector regression (SVR), namely monomial ν-SVR. Like the standard ν-SVR, the monomial ν-SVR method automatically adjusts the radius of insensitivity (the tube width, epsilon) to suit the training data. However, by replacing Vapnik’s epsilon-insensitive cost with a more general monomial epsilon-insensitive cost (and likewise replacing the linear tube shrinking term with a monomial tube shrinking term), the performance of the monomial ν-SVR is improved for data corrupted by a wider range of noise distributions. We focus on the quadric form of monomial ν-SVR and show that the dual form of this is simpler than the standard ν-SVR. We show that, like Suykens’ Least-Squares SVR (LS-SVR) method (and unlike standard ν-SVR), the quadric ν-SVR dual has a unique global solution. Comparisons are made between the asymptotic efficiency of our method and that of standard ν-SVR and LS-SVR which demonstrate the superiority of our method for the special case of higher order polynomial noise. These theoretical predictions are validated using experimental comparisons with the alternative approaches of standard ν-SVR, LS-SVR and weighted LS-SVR.
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ItemProtein topology classification using two-stage support vector machines.(Universal Academy Press, 2006)The determination of the first 3-D model of a protein from its sequence alone is a non-trivial problem. The first 3-D model is the key to the molecular replacement method of solving phase problem in x-ray crystallography. If the sequence identity is more than 30%, homology modelling can be used to determine the correct topology (as defined by CATH) or fold (as defined by SCOP). If the sequence identity is less than 25%, however, the task is very challenging. In this paper we address the topology classification of proteins with sequence identity of less than 25%. The input information to the system is amino acid sequence, the predicted secondary structure and the predicted real value relative solvent accessibility. A two stage support vector machine (SVM) approach is proposed for classifying the sequences to three different structural classes (alpha, beta, alpha+beta) in the first stage and 39 topologies in the second stage. The method is evaluated using a newly curated dataset from CATH with maximum pairwise sequence identity less than 25%. An impressive overall accuracy of 87.44% and 83.15% is reported for class and topology prediction, respectively. In the class prediction stage, a sensitivity of 0.77 and a specificity of 0.91 is obtained. Data file, SVM implementation (SVMHEAVY) and result files can be downloaded from http://www.ee.unimelb.edu.au/ISSNIP/downloads/.
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ItemStability Analysis of the Decomposition Method for solving Support Vector Machines( 2005)In situations where processing memory is limited, the Support Vector Machine quadratic program can be decomposed into smaller sub-problems and solved sequentially. The convergence of this method has been proven previously through the use of a counting method. In this initial investigation, we approach the convergence analysis by treating the decomposed sub-problems as subsystems of a general system. The gradients of the subproblems and the inequality constraints are explicitly modelled as system variables. The change in these variables during optimization form a dynamic system modelled by vector differential equations. We show that the change in the objective function can be written as the energy in the system. This makes it a natural Lyapunov function which has an asymptotically stable point at the origin. The asymptotic stability of the whole system then follows under certain assumptions.
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ItemDisulphide Bridge Prediction using Fuzzy Support Vector Machines( 2005)One of the major contributors to the native form of protien is cystines forming covalent bonds in oxidized state. The Prediction of such bridges from the sequence is a very challenging task given that the number of bridges will rise exponentially as the number of cystines increases. We propose a novel technique for disulphide bridge prediction based on Fuzzy Support Vector Machines. We call the system DIzzy. In our investigation, we look at disulphide bond connectivity given two Cystines with and without a priori knowledge of the bonding state. We make use of a new encoding scheme based on physico-chemical properties and statistical features such as the probability of occurrence of each amino acid in different secondary structure states along with psiblast profiles. The performance is compared with normal support vector machines. We evaluate our method and compare it with the existing method using SPX dataset.
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ItemPrediction of cystine connectivity using SVM(BIOMEDICAL INFORMATICS, 2005)One of the major contributors to protein structures is the formation of disulphide bonds between selected pairs of cysteines at oxidized state. Prediction of such disulphide bridges from sequence is challenging given that the possible combination of cysteine pairs as the number of cysteines increases in a protein. Here, we describe a SVM (support vector machine) model for the prediction of cystine connectivity in a protein sequence with and without a priori knowledge on their bonding state. We make use of a new encoding scheme based on physico-chemical properties and statistical features (probability of occurrence of each amino acid residue in different secondary structure states along with PSI-blast profiles). We evaluate our method in SPX (an extended dataset of SP39 (swiss-prot 39) and SP41 (swiss-prot 41) with known disulphide information from PDB) dataset and compare our results with the recursive neural network model described for the same dataset.
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