On relationship of Z-curve and Fourier approaches for DNA coding sequence classification

Z-curve features are one of the popular features used in exon/intron classification. We showed that although both Z-curve and Fourier approaches are based on detecting 3-periodicity in coding regions, there are significant differences in their spectral formulation. From the spectral formulation of the Z-curve, we obtained three modified sequences that characterize different biological properties. Spectral analysis on the modified sequences showed a much more prominent 3-periodicity peak in coding regions than the Fourier approach. For long sequences, prominent peaks at 2Π/3 are observed at coding regions, whereas for short sequences, clearly discernible peaks are still visible. Better classification can be obtained using spectral features derived from the modified sequences

Cross chromosomal similarity for DNA sequence compression

Current DNA compression algorithms work by finding similar repeated regions within the DNA sequence and then encoding these regions together to achieve compression. Our study on chromosome sequence similarity reveals that the length of similar repeated regions within one chromosome is about 4.5% of the total sequence length. The compression gain is often not high because of these short lengths. It is well known that similarity exist among different regions of chromosome sequences. This implies that similar repeated sequences are found among different regions of chromosome sequences. Here, we study cross-chromosomal similarity for DNA sequence compression. The length and location of similar repeated regions among the sixteen chromosomes of S. cerevisiae are studied. It is found that the average percentage of similar subsequences found between two chromosome sequences is about 10% in which 8% comes from cross-chromosomal prediction and 2% from self-chromosomal prediction. The percentage of similar subsquences is about 18% in which only 1.2% comes from self-chromosomal prediction while the rest is from cross-chromosomal prediction among the 16 chromosomes studied. This suggests the importance of cross-chromosomal similarities in addition to self-chromosomal similarities in DNA sequence compression. An additional 23% of storage space could be reduced on average using self-chromosomal and cross-chromosomal predictions in compressing the 16 chromosomes of S. cerevisiae

Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization

<p>Abstract</p> <p>Background</p> <p>The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens/hundreds of different conditions. In microarray data, genes with similar functions usually co-express under certain conditions only <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. Thus, biclustering which clusters genes and conditions simultaneously is preferred over the traditional clustering technique in discovering these coherent genes. Various biclustering algorithms have been developed using different bicluster formulations. Unfortunately, many useful formulations result in NP-complete problems. In this article, we investigate an efficient method for identifying a popular type of biclusters called additive model. Furthermore, parallel coordinate (PC) plots are used for bicluster visualization and analysis.</p> <p>Results</p> <p>We develop a novel and efficient biclustering algorithm which can be regarded as a greedy version of an existing algorithm known as pCluster algorithm. By relaxing the constraint in homogeneity, the proposed algorithm has polynomial-time complexity in the worst case instead of exponential-time complexity as in the pCluster algorithm. Experiments on artificial datasets verify that our algorithm can identify both additive-related and multiplicative-related biclusters in the presence of overlap and noise. Biologically significant biclusters have been validated on the yeast cell-cycle expression dataset using Gene Ontology annotations. Comparative study shows that the proposed approach outperforms several existing biclustering algorithms. We also provide an interactive exploratory tool based on PC plot visualization for determining the parameters of our biclustering algorithm.</p> <p>Conclusion</p> <p>We have proposed a novel biclustering algorithm which works with PC plots for an interactive exploratory analysis of gene expression data. Experiments show that the biclustering algorithm is efficient and is capable of detecting co-regulated genes. The interactive analysis enables an optimum parameter determination in the biclustering algorithm so as to achieve the best result. In future, we will modify the proposed algorithm for other bicluster models such as the coherent evolution model.</p

Use of subword tokenization for domain generation algorithm classification

Abstract Domain name generation algorithm (DGA) classification is an essential but challenging problem. Both feature-extracting machine learning (ML) methods and deep learning (DL) models such as convolutional neural networks and long short-term memory have been developed. However, the performance of these approaches varies with different types of DGAs. Most features in the ML methods can characterize random-looking DGAs better than word-looking DGAs. To improve the classification performance on word-looking DGAs, subword tokenization is employed for the DL models. Our experimental results proved that the subword tokenization can provide excellent classification performance on the word-looking DGAs. We then propose an integrated scheme that chooses an appropriate method for DGA classification depending on the nature of the DGAs. Results show that the integrated scheme outperformed existing ML and DL methods, and also the subword DL methods

IMGCAT: An approach to dismantle the anonymity of a source camera using correlative features and an integrated 1D convolutional neural network

With the proliferation of smartphones, digital data collection has become trivial. The ability to analyze images has increased, but source authentication has stagnated. Editing and tampering of images has become more common with advancements in signal processing technology. Recent developments have introduced the use of seam carving (insertion and deletion) techniques to disguise the identity of the camera, specifically in the child pornography market. In this article, we focus on the available features in the image based on PRNU (photo response nonuniformity). The forced-seam sculpting technique is a well-known method to create occlusion for camera attribution by injecting seams into each 50 × 50 pixel block. To counter this, we perform camera identification using a 1D CNN integrated with feature extractions on 20 × 20 pixel blocks. We achieve state-of-the-art performance for our proposed IMGCAT (image categorization) in three-class classification over the baselines (original, seam removed, seam inserted). Based on our experimental findings, our model is robust when dealing with blind facts related to the questionable camera