Electrical and Electronic Engineering - Research Publications

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Subject: Artificial Intelligence and Image Processing × Author: Palaniswami, Marimuthu × Author: GUBBI LAKSHMINARASIMHA, JAYAVARDHANA ×

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    PROTEIN SECONDARY STRUCTURE PREDICTION USING SUPPORT VECTOR MACHINES AND A NEW FEATURE REPRESENTATION
    Gubbi, J ; Lai, DTH ; Palaniswami, M ; Parker, M (WORLD SCIENTIFIC PUBL CO PTE LTD, 2006-12)
    Knowledge of the secondary structure and solvent accessibility of a protein plays a vital role in the prediction of fold, and eventually the tertiary structure of the protein. A challenging issue of predicting protein secondary structure from sequence alone is addressed. Support vector machines (SVM) are employed for the classification and the SVM outputs are converted to posterior probabilities for multi-class classification. The effect of using Chou–Fasman parameters and physico-chemical parameters along with evolutionary information in the form of position specific scoring matrix (PSSM) is analyzed. These proposed methods are tested on the RS126 and CB513 datasets. A new dataset is curated (PSS504) using recent release of CATH. On the CB513 dataset, sevenfold cross-validation accuracy of 77.9% was obtained using the proposed encoding method. A new method of calculating the reliability index based on the number of votes and the Support Vector Machine decision value is also proposed. A blind test on the EVA dataset gives an average Q3accuracy of 74.5% and ranks in top five protein structure prediction methods. Supplementary material including datasets are available on .
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    Automated Scoring of Obstructive Sleep Apnea and Hypopnea Events Using Short-Term Electrocardiogram Recordings
    Khandoker, AH ; Gubbi, J ; Palaniswami, M (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2009-11)
    Obstructive sleep apnea or hypopnea causes a pause or reduction in airflow with continuous breathing effort. The aim of this study is to identify individual apnea and hypopnea events from normal breathing events using wavelet-based features of 5-s ECG signals (sampling rate = 250 Hz) and estimate the surrogate apnea index (AI)/hypopnea index (HI) (AHI). Total 82,535 ECG epochs (each of 5-s duration) from normal breathing during sleep, 1638 ECG epochs from 689 hypopnea events, and 3151 ECG epochs from 1862 apnea events were collected from 17 patients in the training set. Two-staged feedforward neural network model was trained using features from ECG signals with leave-one-patient-out cross-validation technique. At the first stage of classification, events (apnea and hypopnea) were classified from normal breathing events, and at the second stage, hypopneas were identified from apnea. Independent test was performed on 16 subjects' ECGs containing 483 hypopnea and 1352 apnea events. The cross-validation and independent test accuracies of apnea and hypopnea detection were found to be 94.84% and 76.82%, respectively, for training set, and 94.72% and 79.77%, respectively, for test set. The Bland-Altman plots showed unbiased estimations with standard deviations of +/- 2.19, +/- 2.16, and +/- 3.64 events/h for AI, HI, and AHI, respectively. Results indicate the possibility of recognizing apnea/hypopnea events based on shorter segments of ECG signals.