Linear-Time Algorithms for Computing Maximum-Density Sequence Segments with Bioinformatics Applications

We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with index j. The width of A(i,j) is w(i,j) = sum_{i <= k <= j} w_k, and the density is (sum_{i<= k <= j} a_k)/ w(i,j). The maximum-density segment problem takes A and two values L and U as input and asks for a segment of A with the largest possible density among those of width at least L and at most U. When U is unbounded, we provide a relatively simple, O(n)-time algorithm, improving upon the O(n \log L)-time algorithm by Lin, Jiang and Chao. When both L and U are specified, there are no previous nontrivial results. We solve the problem in O(n) time if w_i=1 for all i, and more generally in O(n+n\log(U-L+1)) time when w_i>=1 for all i.Comment: 23 pages, 13 figures. A significant portion of these results appeared under the title, "Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics," in Proceedings of the Second Workshop on Algorithms in Bioinformatics (WABI), volume 2452 of Lecture Notes in Computer Science (Springer-Verlag, Berlin), R. Guigo and D. Gusfield editors, 2002, pp. 157--17

Extraction of Projection Profile, Run-Histogram and Entropy Features Straight from Run-Length Compressed Text-Documents

Document Image Analysis, like any Digital Image Analysis requires identification and extraction of proper features, which are generally extracted from uncompressed images, though in reality images are made available in compressed form for the reasons such as transmission and storage efficiency. However, this implies that the compressed image should be decompressed, which indents additional computing resources. This limitation induces the motivation to research in extracting features directly from the compressed image. In this research, we propose to extract essential features such as projection profile, run-histogram and entropy for text document analysis directly from run-length compressed text-documents. The experimentation illustrates that features are extracted directly from the compressed image without going through the stage of decompression, because of which the computing time is reduced. The feature values so extracted are exactly identical to those extracted from uncompressed images.Comment: Published by IEEE in Proceedings of ACPR-2013. arXiv admin note: text overlap with arXiv:1403.778

Detecting Irregular Patterns in IoT Streaming Data for Fall Detection

Detecting patterns in real time streaming data has been an interesting and challenging data analytics problem. With the proliferation of a variety of sensor devices, real-time analytics of data from the Internet of Things (IoT) to learn regular and irregular patterns has become an important machine learning problem to enable predictive analytics for automated notification and decision support. In this work, we address the problem of learning an irregular human activity pattern, fall, from streaming IoT data from wearable sensors. We present a deep neural network model for detecting fall based on accelerometer data giving 98.75 percent accuracy using an online physical activity monitoring dataset called "MobiAct", which was published by Vavoulas et al. The initial model was developed using IBM Watson studio and then later transferred and deployed on IBM Cloud with the streaming analytics service supported by IBM Streams for monitoring real-time IoT data. We also present the systems architecture of the real-time fall detection framework that we intend to use with mbientlabs wearable health monitoring sensors for real time patient monitoring at retirement homes or rehabilitation clinics.Comment: 7 page

Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae

Verticillium nonalfalfae is a fungal plant pathogen that causes wilt disease by colonizing the vascular tissues of host plants. The disease induced by hop isolates of V. nonalfalfae manifests in two different forms, ranging from mild symptoms to complete plant dieback, caused by mild and lethal pathotypes, respectively. Pathogenicity variations between the causal strains have been attributed to differences in genomic sequences and perhaps also to differences in their mitochondrial genomes. We used data from our recent Illumina NGS-based project of genome sequencing V. nonalfalfae to study the mitochondrial genomes of its different strains. The aim of the research was to prepare a V. nonalfalfae reference mitochondrial genome and to determine its phylogenetic placement in the fungal kingdom. The resulting 26,139 bp circular DNA molecule contains a full complement of the 14 "standard" fungal mitochondrial protein-coding genes of the electron transport chain and ATP synthase subunits, together with a small rRNA subunit, a large rRNA subunit, which contains ribosomal protein S3 encoded within a type IA-intron and 26 tRNAs. Phylogenetic analysis of this mitochondrial genome placed it in the Verticillium spp. lineage in the Glomerellales group, which is also supported by previous phylogenetic studies based on nuclear markers. The clustering with the closely related Verticillium dahliae mitochondrial genome showed a very conserved synteny and a high sequence similarity. Two distinguishing mitochondrial genome features were also found-a potential long non-coding RNA (orf414) contained only in the Verticillium spp. of the fungal kingdom, and a specific fragment length polymorphism observed only in V. dahliae and V. nubilum of all the Verticillium spp., thus showing potential as a species specific biomarker