Alokanand Sharma

Fast principal component analysis using fixed-point algorithm

In this paper we present an efficient way of computing principal component analysis (PCA). The algorithm finds the desired number of leading eigenvectors with a computational cost that is much less than that from the eigenvalue decomposition (EVD) based PCA method. The mean squared error generated by the proposed method is very similar to the EVD based PCA method.

Intrusion detection using text processing techniques with a kernel based similarity measure

This paper focuses on intrusion detection based on system call sequences using text processing techniques. It introduces kernel based similarity measure for the detection of host-based intrusions. The k-nearest neighbour (kNN) classifier is used to classify a process as either normal or abnormal. The proposed technique is evaluated on the DARPA-1998 database and its performance is compared with other existing techniques available in the literature. It is shown that this technique is significantly better than the other techniques in achieving lower false positive rates at 100% detection rate.

Class-dependent PCA, MDC and LDA: A combined classifier for pattern classification

Several pattern classifiers give high classification accuracy but their storage requirements and processing time are severely expensive. On the other hand, some classifiers require very low storage requirement and processing time but their classification accuracy is not satisfactory. In either of the cases the performance of the classifier is poor. In this paper, we have presented a technique based on the combination of minimum distance classifier (MDC), class-dependent principal component analysis (PCA) and linear discriminant analysis (LDA) which gives improved performance as compared with other standard techniques when experimented on several machine learning corpuses.

Rapid and Brief Communication: Subspace independent component analysis using vector kurtosis

This discussion presents a new perspective of subspace independent component analysis (ICA). The notion of a function of cumulants (kurtosis) is generalized to vector kurtosis. This vector kurtosis is utilized in the subspace ICA algorithm to estimate subspace independent components. One of the main advantages of the presented approach is its computational simplicity. The experiments have shown promising results in estimating subspace independent components.

SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids

Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles and local structure conformations were incorporated. We used the k-nearest neighbors cleaning treatment for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred to as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathews correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively.

Detecting masquerades using a combination of Naïve Bayes and weighted RBF approach

Masquerade detection by automated means is gaining widespread interest due to the serious impact of masquerades on computer system or network. Several techniques have been introduced in an effort to minimize up to some extent the risk associated with masquerade attack. In this respect, we have developed a novel technique which comprises of Naïve Bayes approach and weighted radial basis function similarity approach. The proposed scheme exhibits very promising results in comparison with many earlier techniques while experimenting on SEA dataset in detecting masquerades.

Improving protein fold recognition and structural class prediction accuracies using physicochemical properties of amino acids

Predicting the three-dimensional (3-D) structure of a protein is an important task in the field of bioinformatics and biological sciences. However, directly predicting the 3-D structure from the primary structure is hard to achieve. Therefore, predicting the fold or structural class of a protein sequence is generally used as an intermediate step in determining the proteins 3-D structure. For protein fold recognition (PFR) and structural class prediction (SCP), two steps are required - feature extraction step and classification step. Feature extraction techniques generally utilize syntactical-based information, evolutionary-based information and physicochemical-based information to extract features. In this study, we explore the importance of utilizing the physicochemical properties of amino acids for improving PFR and SCP accuracies. For this, we propose a Forward Consecutive Search (FCS) scheme which aims to strategically select physicochemical attributes that will supplement the existing feature extraction techniques for PFR and SCP. An exhaustive search is conducted on all the existing 544 physicochemical attributes using the proposed FCS scheme and a subset of physicochemical attributes is identified. Features extracted from these selected attributes are then combined with existing syntactical-based and evolutionary-based features, to show an improvement in the recognition and prediction performance on benchmark datasets.

CSP-TSM: Optimizing the performance of Riemannian tangent space mapping using common spatial pattern for MI-BCI

BACKGROUND Classification of electroencephalography (EEG) signals for motor imagery based brain computer interface (MI-BCI) is an exigent task and common spatial pattern (CSP) has been extensively explored for this purpose. In this work, we focused on developing a new framework for classification of EEG signals for MI-BCI. METHOD We propose a single band CSP framework for MI-BCI that utilizes the concept of tangent space mapping (TSM) in the manifold of covariance matrices. The proposed method is named CSP-TSM. Spatial filtering is performed on the bandpass filtered MI EEG signal. Riemannian tangent space is utilized for extracting features from the spatial filtered signal. The TSM features are then fused with the CSP variance based features and feature selection is performed using Lasso. Linear discriminant analysis (LDA) is then applied to the selected features and finally classification is done using support vector machine (SVM) classifier. RESULTS The proposed framework gives improved performance for MI EEG signal classification in comparison with several competing methods. Experiments conducted shows that the proposed framework reduces the overall classification error rate for MI-BCI by 3.16%, 5.10% and 1.70% (for BCI Competition III dataset IVa, BCI Competition IV Dataset I and BCI Competition IV Dataset IIb, respectively) compared to the conventional CSP method under the same experimental settings. CONCLUSION The proposed CSP-TSM method produces promising results when compared with several competing methods in this paper. In addition, the computational complexity is less compared to that of TSM method. Our proposed CSP-TSM framework can be potentially used for developing improved MI-BCI systems.

HMMBinder: DNA-Binding Protein Prediction Using HMM Profile Based Features

DNA-binding proteins often play important role in various processes within the cell. Over the last decade, a wide range of classification algorithms and feature extraction techniques have been used to solve this problem. In this paper, we propose a novel DNA-binding protein prediction method called HMMBinder. HMMBinder uses monogram and bigram features extracted from the HMM profiles of the protein sequences. To the best of our knowledge, this is the first application of HMM profile based features for the DNA-binding protein prediction problem. We applied Support Vector Machines (SVM) as a classification technique in HMMBinder. Our method was tested on standard benchmark datasets. We experimentally show that our method outperforms the state-of-the-art methods found in the literature.

Remote patient physical condition monitoring service module for iWARD hospital robots

In this paper an intelligent system for remote patient physical condition monitoring service module for an Intelligent Robot Swarm for Attendance, Recognition, Cleaning and Delivery (iWARD) [1] is reported. The system algorithm and module software is implemented in C/C++, and the Orca robotics [2] components use the OpenCV[3] image analysis and processing library. The system is successfully tested on Linux (Ubuntu) platform as well as on a web server. The patient condition monitoring system can remotely measure the following body conditions: body temperature (BTemp), heart rate (HR), electrocardiogram (ECG), respiration rate (RR), body acceleration (BA) using sensors attached to the patients body. The system also includes an RGB video camera and a 3D laser sensor, which monitor the environment in order to find any patient lying on the floor. The system deals with various image-processing and sensor fusion techniques. The iWARD patient condition monitoring module evaluation tests were carried out in front of thirty healthcare professionals (doctors, nurses, nursing lecturers and healthcare assistances etc) during the final review meeting of the consortium and in two teaching hospitals (in Newcastle and San Sebastian, 2009) in Europe. The post iWARD system improved upon the prototype by adding a 3D laser sensor and replacing the original camera with a high quality Pan-Tilt-Zoom (PTZ) camera and implementing the identity detection methods. This allowed for the use of more robust patient condition monitoring algorithms. The outcomes of this research have significant contribution to the robotics application area in the hospital environment.