A Time-Series-Based Feature Extraction Approach for Prediction of Protein Structural Class

This paper presents a novel feature vector based on physicochemical property of amino acids for prediction protein structural classes. The proposed method is divided into three different stages. First, a discrete time series representation to protein sequences using physicochemical scale is provided. Later on, a wavelet-based time-series technique is proposed for extracting features from mapped amino acid sequence and a fixed length feature vector for classification is constructed. The proposed feature space summarizes the variance information of ten different biological properties of amino acids. Finally, an optimized support vector machine model is constructed for prediction of each protein structural class. The proposed approach is evaluated using leave-one-out cross-validation tests on two standard datasets. Comparison of our result with existing approaches shows that overall accuracy achieved by our approach is better than exiting methods

Post Event Investigation of Multi-stream Video Data Utilizing Hadoop Cluster

Rapid advancement in technology and in-expensive camera has raised the necessity of monitoring systems for surveillance applications. As a result data acquired from numerous cameras deployed for surveillance is tremendous. When an event is triggered then, manually investigating such a massive data is a complex task. Thus it is essential to explore an approach that, can store massive multi-stream video data as well as, process them to find useful information. To address the challenge of storing and processing multi-stream video data, we have used Hadoop, which has grown into a leading computing model for data intensive applications. In this paper we propose a novel technique for performing post event investigation on stored surveillance video data. Our algorithm stores video data in HDFS in such a way that it efficiently identifies the location of data from HDFS based on the time of occurrence of event and perform further processing. To prove efficiency of our proposed work, we have performed event detection in the video based on the time period provided by the user. In order to estimate the performance of our approach, we evaluated the storage and processing of video data by varying (i) pixel resolution of video frame (ii) size of video data (iii) number of reducers (workers) executing the task (iv) the number of nodes in the cluster. The proposed framework efficiently achieve speed up of 5.9 for large files of 1024X1024 pixel resolution video frames thus makes it appropriate for the feasible practical deployment in any applications

Real-Time Implementation and Performance Optimization of Local Derivative Pattern Algorithm on GPUs

Pattern based texture descriptors are widely used in Content Based Image Retrieval (CBIR) for efficient retrieval of matching images. Local Derivative Pattern (LDP), a higher order local pattern operator, originally proposed for face recognition, encodes the distinctive spatial relationships contained in a local region of an image as the feature vector. LDP efficiently extracts finer details and provides efficient retrieval however, it was proposed for images of limited resolution. Over the period of time the development in the digital image sensors had paid way for capturing images at a very high resolution. LDP algorithm though very efficient in content-based image retrieval did not scale well when capturing features from such high-resolution images as it becomes computationally very expensive. This paper proposes how to efficiently extract parallelism from the LDP algorithm and strategies for optimally implementing it by exploiting some inherent General-Purpose Graphics Processing Unit (GPGPU) characteristics. By optimally configuring the GPGPU kernels, image retrieval was performed at a much faster rate. The LDP algorithm was ported on to Compute Unified Device Architecture (CUDA) supported GPGPU and a maximum speed up of around 240x was achieved as compared to its sequential counterpart

Identifying Inverted Repeat Structure in DNA Sequences using Correlation Framework

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 200

A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeats are linked to over a dozen major neurodegenerative genetic disorders. In this paper, we present an algorithm to identify the exact and inexact repeat patterns in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. Using the new measure our algorithm resolves the problems like whether the repeat pattern is of period P or its multiple (i.e., 2P, 3P, etc.), and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of O(NLw logLw), where N is the length of DNA sequence and Lw is the window length, for identifying repeats. The algorithm operates in two stages. In the first stage, each nucleotide is analyzed separately for periodicity, and in the second stage, the periodic information of each nucleotide is combined together to identify the tandem repeats. Datasets having exact and inexact repeats were taken up for the experimental purpose. The experimental result shows the effectiveness of the approach

Question Processing and Clustering in INDOC: A Biomedical Question Answering System

The exponential growth in the volume of publications in the biomedical domain has made it impossible for an individual to keep pace with the advances. Even though evidence-based medicine has gained wide acceptance, the physicians are unable to access the relevant information in the required time, leaving most of the questions unanswered. This accentuates the need for fast and accurate biomedical question answering systems. In this paper we introduce INDOC—a biomedical question answering system based on novel ideas of indexing and extracting the answer to the questions posed. INDOC displays the results in clusters to help the user arrive the most relevant set of documents quickly. Evaluation was done against the standard OHSUMED test collection. Our system achieves high accuracy and minimizes user effort

An Efficient Coding Method for Teleconferencing Video and Confocal Microscopic Image Sequences

In this paper we propose a three-dimensional vector quantization based video coding scheme. The algorithm uses a 3D vector quantization pyramidal code book based model with adaptive code book pyramidal codebook for compression. The pyramidal code book based model helps in getting high compression in case of modest motion. The adaptive vector quantization algorithm is used to train the code book for optimal performance with time. Some of the distinguished features of our algorithm are its excellent performance due to its adaptive behavior to the video composition and excellent compression due to codebook approach. We also propose an efficient codebook based post processing technique which enables the vector quantizer to possess higher correlation preservation property. Based on the special pattern of the codebook imposed by post-processing technique, a window based fast search (WBFS) algorithm is proposed. The WBFS algorithm not only accelerates the vector quantization processing, but also results in better rate-distortion performance. The proposed approach can be used for both teleconferencing videos and to compress images obtained from confocal laser scanning microscopy (CLSM). The results show that the proposed method gave higher subjective and objective image quality of reconstructed images at a better compression ratio and presented more acceptable results when applying image processing filters such as edge detection on reconstructed images. The experimental results demonstrate that the proposed method outperforms the teleconferencing compression standards H.261 and LBG based vector quantization technique