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Journal articles on the topic 'Read overlap graph'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Baaijens, Jasmijn A., and Alexander Schönhuth. "Overlap graph-based generation of haplotigs for diploids and polyploids." Bioinformatics 35, no. 21 (2019): 4281–89. http://dx.doi.org/10.1093/bioinformatics/btz255.

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Abstract Motivation Haplotype-aware genome assembly plays an important role in genetics, medicine and various other disciplines, yet generation of haplotype-resolved de novo assemblies remains a major challenge. Beyond distinguishing between errors and true sequential variants, one needs to assign the true variants to the different genome copies. Recent work has pointed out that the enormous quantities of traditional NGS read data have been greatly underexploited in terms of haplotig computation so far, which reflects that methodology for reference independent haplotig computation has not yet

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Liu, Yuansheng, and Jinyan Li. "Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression." PLOS Computational Biology 17, no. 7 (2021): e1009229. http://dx.doi.org/10.1371/journal.pcbi.1009229.

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Graphs such as de Bruijn graphs and OLC (overlap-layout-consensus) graphs have been widely adopted for the de novo assembly of genomic short reads. This work studies another important problem in the field: how graphs can be used for high-performance compression of the large-scale sequencing data. We present a novel graph definition named Hamming-Shifting graph to address this problem. The definition originates from the technological characteristics of next-generation sequencing machines, aiming to link all pairs of distinct reads that have a small Hamming distance or a small shifting offset or

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Dida, Firaol, and Gangman Yi. "Empirical evaluation of methods for de novo genome assembly." PeerJ Computer Science 7 (July 9, 2021): e636. http://dx.doi.org/10.7717/peerj-cs.636.

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Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms. A drastic reduction in the costs of generating short reads on the genomes of new organisms is attributable to recent advances in NGS technologies such as Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for several organisms, and de novo assembly is a key initiative that has facilitated gene discovery and other studies. More powerful analytical alg

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McNair, Katelyn, Carol Zhou, Elizabeth A. Dinsdale, Brian Souza, and Robert A. Edwards. "PHANOTATE: a novel approach to gene identification in phage genomes." Bioinformatics 35, no. 22 (2019): 4537–42. http://dx.doi.org/10.1093/bioinformatics/btz265.

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Abstract Motivation Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene c

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Nazarie, Fahmi W., Barbara Shih, Tim Angus, et al. "Visualization and analysis of RNA-Seq assembly graphs." Nucleic Acids Research 47, no. 14 (2019): 7262–75. http://dx.doi.org/10.1093/nar/gkz599.

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AbstractRNA-Seq is a powerful transcriptome profiling technology enabling transcript discovery and quantification. Whilst most commonly used for gene-level quantification, the data can be used for the analysis of transcript isoforms. However, when the underlying transcript assemblies are complex, current visualization approaches can be limiting, with splicing events a challenge to interpret. Here, we report on the development of a graph-based visualization method as a complementary approach to understanding transcript diversity from short-read RNA-Seq data. Following the mapping of reads to a

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Lin, Yu, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, and Pavel A. Pevzner. "Assembly of long error-prone reads using de Bruijn graphs." Proceedings of the National Academy of Sciences 113, no. 52 (2016): E8396—E8405. http://dx.doi.org/10.1073/pnas.1604560113.

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The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the

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Beaufays, Françoise, and Eric A. Wan. "Relating Real-Time Backpropagation and Backpropagation-Through-Time: An Application of Flow Graph Interreciprocity." Neural Computation 6, no. 2 (1994): 296–306. http://dx.doi.org/10.1162/neco.1994.6.2.296.

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We show that signal flow graph theory provides a simple way to relate two popular algorithms used for adapting dynamic neural networks, real-time backpropagation and backpropagation-through-time. Starting with the flow graph for real-time backpropagation, we use a simple transposition to produce a second graph. The new graph is shown to be interreciprocal with the original and to correspond to the backpropagation-through-time algorithm. Interreciprocity provides a theoretical argument to verify that both flow graphs implement the same overall weight update.

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Kusuma, Wisnu Ananta, and Albert Adrianus. "Pengkontruksian Bidirected Overlap Graph untuk Perakitan Sekuens DNA." Jurnal Teknologi Informasi dan Ilmu Komputer 7, no. 2 (2020): 407. http://dx.doi.org/10.25126/jtiik.2020722070.

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<p><em>De novo DNA </em>(<em>Deoxyribonucleic Acid</em>)<em> sequence assembly</em> atau perakitan sekuens DNA secara <em>De novo </em>adalah tahapan yang sangat penting dalam analisis sekuens DNA. Tahapan ini diperlukan untuk merakit atau menyambungkan kembali fragmen-fragmen DNA (<em>reads</em>) yang dihasilkan oleh <em>Next Generation Sequencing</em> menjadi genom yang utuh. Masalah perakitan DNA ini dapat direpresentasikan sebagai masalah Shortest Common Superstring (SCS). Perakitan ini memerlukan bantuan perangk

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Shomorony, Ilan, Samuel H. Kim, Thomas A. Courtade, and David N. C. Tse. "Information-optimal genome assembly via sparse read-overlap graphs." Bioinformatics 32, no. 17 (2016): i494—i502. http://dx.doi.org/10.1093/bioinformatics/btw450.

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Best, Lisa A., Laurence D. Smith, and D. Alan Stubbs. "Perception of Linear and Nonlinear Trends: Using Slope and Curvature Information to Make Trend Discriminations." Perceptual and Motor Skills 104, no. 3 (2007): 707–21. http://dx.doi.org/10.2466/pms.104.3.707-721.

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This study investigated several factors influencing the perception of nonlinear relationships in time series graphs. To model real-world data, the graphed data represented different underlying trends and included different sample sizes and amounts of variability. Six trends (increasing and decreasing linear, exponential, asymptotic) were presented on four graph types (histogram, line graph, scatterplot, suspended bar graph). The experiment assessed how these factors affect trend discrimination, with the overall goal of judging what types of graphs lead to better discrimination. Six participant

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Ben-Bassat, Ilan, and Benny Chor. "CRISPR Detection From Short Reads Using Partial Overlap Graphs." Journal of Computational Biology 23, no. 6 (2016): 461–71. http://dx.doi.org/10.1089/cmb.2015.0226.

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Kovács, Tibor, Gábor Simon, and Gergely Mezei. "Benchmarking Graph Database Backends—What Works Well with Wikidata?" Acta Cybernetica 24, no. 1 (2019): 43–60. http://dx.doi.org/10.14232/actacyb.24.1.2019.5.

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Knowledge bases often utilize graphs as logical model. RDF-based knowledge bases (KB) are prime examples, as RDF (Resource Description Framework) does use graph as logical model. Graph databases are an emerging breed of NoSQL-type databases, offering graph as the logical model. Although there are specialized databases, the so-called triple stores, for storing RDF data, graph databases can also be promising candidates for storing knowledge. In this paper, we benchmark different graph database implementations loaded with Wikidata, a real-life, large-scale knowledge base. Graph databases come in

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Purwana, Unang, Dadi Rusdiana, and Winny Liliawati. "PENGUJIAN KEMAMPUAN MENGINTERPRETASIKAN GRAFIK KINEMATIKA CALON GURU FISIKA: THE POLYTOMOUS RASCH ANALYSIS." ORBITA: Jurnal Kajian, Inovasi dan Aplikasi Pendidikan Fisika 6, no. 2 (2020): 259. http://dx.doi.org/10.31764/orbita.v6i2.3264.

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ABSTRAKKemampuan interpretasi grafik merupakan kemampuan yang sangat penting dan kunci utama dalam memahami materi kinematika dan materi fisika lanjutan. Namun kemampuan interpretasi grafik materi kinematika mahasiswa calon guru masih rendah. Tujuan penelitian ini menguji kemampuan membaca dan menginterpretasikan grafik kinematika calon guru dengan analisis polytomous rasch model. Instrumen terdiri dari empat soal uraian menyajikan grafik kinematika. Tes diberikan ke 20 mahasiswa calon guru, terdiri dari 14 perempuan dan 6 laki-laki. Metode yang digunakan survei deskriptif kuantitatif dengan a

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Li, Yan, Tingjian Ge, and Cindy Chen. "Data stream event prediction based on timing knowledge and state transitions." Proceedings of the VLDB Endowment 13, no. 10 (2020): 1779–92. http://dx.doi.org/10.14778/3401960.3401973.

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We study a practical problem of predicting the upcoming events in data streams using a novel approach. Treating event time orders as relationship types between event entities, we build a dynamic knowledge graph and use it to predict future event timing. A unique aspect of this knowledge graph embedding approach for prediction is that we enhance conventional knowledge graphs with the notion of "states"---in what we call the ephemeral state nodes---to characterize the state of a data stream over time. We devise a complete set of methods for learning relevant events, for building the event-order

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Pacher, Dominic, Robert Binna, and Günther Specht. "Optimizing large knowledge networks in spatial computers." Knowledge Engineering Review 31, no. 4 (2016): 367–90. http://dx.doi.org/10.1017/s0269888916000187.

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AbstractThis paper presents a novel concept of a Spatially Aware Graph Store, which realizes a Graph Store on top of a spatial computer architecture to manage graphs in one, two or three physical dimensions. In this environment, the physical distance between graph nodes strongly affects graph traversal performance. Consequently, a Spatially Aware Graph Store needs to minimize these distances to operate efficiently. We show that this minimization can be achieved in two ways. First, by increasing the dimensionality of the spatial computer and second by applying optimization methods. For the latt

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Mallawaarachchi, Vijini, Anuradha Wickramarachchi, and Yu Lin. "GraphBin: refined binning of metagenomic contigs using assembly graphs." Bioinformatics 36, no. 11 (2020): 3307–13. http://dx.doi.org/10.1093/bioinformatics/btaa180.

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Abstract Motivation The field of metagenomics has provided valuable insights into the structure, diversity and ecology within microbial communities. One key step in metagenomics analysis is to assemble reads into longer contigs which are then binned into groups of contigs that belong to different species present in the metagenomic sample. Binning of contigs plays an important role in metagenomics and most available binning algorithms bin contigs using genomic features such as oligonucleotide/k-mer composition and contig coverage. As metagenomic contigs are derived from the assembly process, th

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Nazeer, Irfan, Tabasam Rashid, and Muhammad Tanveer Hussain. "Cyclic connectivity index of fuzzy incidence graphs with applications in the highway system of different cities to minimize road accidents and in a network of different computers." PLOS ONE 16, no. 9 (2021): e0257642. http://dx.doi.org/10.1371/journal.pone.0257642.

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A parameter is a numerical factor whose values help us to identify a system. Connectivity parameters are essential in the analysis of connectivity of various kinds of networks. In graphs, the strength of a cycle is always one. But, in a fuzzy incidence graph (FIG), the strengths of cycles may vary even for a given pair of vertices. Cyclic reachability is an attribute that decides the overall connectedness of any network. In graph the cycle connectivity (CC) from vertex a to vertex b and from vertex b to vertex a is always one. In fuzzy graph (FG) the CC from vertex a to vertex b and from verte

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Zhao, Yong, Yuqi Cheng, Xishan Zhang, et al. "Real-Time Orthophoto Mosaicing on Mobile Devices for Sequential Aerial Images with Low Overlap." Remote Sensing 12, no. 22 (2020): 3739. http://dx.doi.org/10.3390/rs12223739.

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Orthophoto generation is a popular topic in aerial photogrammetry and 3D reconstruction. It is generally computationally expensive with large memory consumption. Inspired by the simultaneous localization and mapping (SLAM) workflow, this paper presents an online sequential orthophoto mosaicing solution for large baseline high-resolution aerial images with high efficiency and novel precision. An appearance and spatial correlation-constrained fast low-overlap neighbor candidate query and matching strategy is used for efficient and robust global matching. Instead of estimating 3D positions of spa

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Sun, Zequn, Chengming Wang, Wei Hu, et al. "Knowledge Graph Alignment Network with Gated Multi-Hop Neighborhood Aggregation." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 01 (2020): 222–29. http://dx.doi.org/10.1609/aaai.v34i01.5354.

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Graph neural networks (GNNs) have emerged as a powerful paradigm for embedding-based entity alignment due to their capability of identifying isomorphic subgraphs. However, in real knowledge graphs (KGs), the counterpart entities usually have non-isomorphic neighborhood structures, which easily causes GNNs to yield different representations for them. To tackle this problem, we propose a new KG alignment network, namely AliNet, aiming at mitigating the non-isomorphism of neighborhood structures in an end-to-end manner. As the direct neighbors of counterpart entities are usually dissimilar due to

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Gauthier, Jérémy, Charlotte Mouden, Tomasz Suchan, et al. "DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics." PeerJ 8 (June 10, 2020): e9291. http://dx.doi.org/10.7717/peerj.9291.

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Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specifi

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Birol, Inanç, Justin Chu, Hamid Mohamadi, et al. "Spaced Seed Data Structures forDe NovoAssembly." International Journal of Genomics 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/196591.

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De novoassembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the

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Brodkorb, Felix, Arjan Kuijper, Gennady Andrienko, Natalia Andrienko, and Tatiana von Landesberger. "Overview with details for exploring geo-located graphs on maps." Information Visualization 15, no. 3 (2015): 214–37. http://dx.doi.org/10.1177/1473871615597077.

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Geo-located graph drawings often suffer from map visualization problems, such as overplotting of nodes as well as edges and location of parts of the graph being outside of the screen. One cause of these problems is often an irregular distribution of nodes on the map. Zooming and panning do not solve the problems, as they either only show the overview of the whole graph or only the details of a part of the graph. We present an interactive graph drawing technique that overcomes these problems without affecting the overall geographical structure of the graph. First, we introduce a method that use

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Pyrkina, Olga E., and Sergey A. Zadadaev. "Application of Graph Analytics for Simulations of Electronic Money Turnover: Solutions, Evaluations, Forecasts." EPJ Web of Conferences 224 (2019): 06006. http://dx.doi.org/10.1051/epjconf/201922406006.

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The graph model for electronic money turnover developed in this paper considers the system of electronic money turnover as a technological complex network. This network includes systems of electronic money payments, communications between bank and its clients, and interbank communications. The application of the graph models is based on its essential advantages such as an opportunity to expand this system to arbitrary size and visualization of the system links. While graph plotting provides us with the opportunity of carrying out qualitative (visual) system analysis, e computations of the grap

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PALAMARA, GIAN MARCO, VINKO ZLATIĆ, ANTONIO SCALA, and GUIDO CALDARELLI. "POPULATION DYNAMICS ON COMPLEX FOOD WEBS." Advances in Complex Systems 14, no. 04 (2011): 635–47. http://dx.doi.org/10.1142/s0219525911003116.

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In this work we analyze the topological and dynamical properties of a simple model of complex food webs, namely the niche model. In order to underline competition among species, we introduce "prey" and "predators" weighted overlap graphs derived from the niche model and compare synthetic food webs with real data. Doing so, we find new tests for the goodness of synthetic food web models and indicate a possible direction of improvement for existing ones. We then exploit the weighted overlap graphs to define a competition kernel for Lotka–Volterra population dynamics and find that for such a mode

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Liu, Xiaotong, Han-Wei Shen, and Yifan Hu. "Supporting multifaceted viewing of word clouds with focus+context display." Information Visualization 14, no. 2 (2014): 168–80. http://dx.doi.org/10.1177/1473871614534095.

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Word clouds provide an effective way to visually summarize important keywords from a large collection of text. Despite their increasing popularity, relatively less attention has been paid on developing interactive techniques for flexible word cloud navigation and manipulation. In this article, we present a focus + context display technique to support multifaceted viewing of word clouds. In our algorithm, the sizes of words in a word cloud are first changed to reflect the current importance metric selected by the user and then scaled to balance space utilization and word readability. To remove

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Boutsi, A. M., C. Ioannidis, and S. Soile. "HYBRID MOBILE AUGMENTED REALITY: WEB-LIKE CONCEPTS APPLIED TO HIGH RESOLUTION 3D OVERLAYS." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-2/W17 (November 29, 2019): 85–92. http://dx.doi.org/10.5194/isprs-archives-xlii-2-w17-85-2019.

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Abstract. Mobile Augmented Reality (MAR) aligns toward current technological advances with more intuitive interfaces, realistic graphic content and flexible development processes. The case of overlaying precise 3D representations exploits their high penetration to induct users to a world where data are perceived as real counterparts. The work presented in this paper integrates web-like concepts with hybrid mobile tools to visualize high-quality and complex 3D geometry on the real environment. The implementation involves two different operational mechanisms: anchors and location-sensitive track

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Shan, Xin, Jingyi Qiu, Bo Wang, Yongcheng Dang, Tingxiang LU, and Yiming Zheng. "Place Retrieval in Knowledge Graph." Scientific Programming 2020 (July 1, 2020): 1–10. http://dx.doi.org/10.1155/2020/5060635.

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With the rapid development of Internet and big data, place retrieval has become an indispensable part of daily life. However, traditional retrieval technology cannot meet the semantic needs of users. Knowledge graph has been introduced into the new-generation retrieval systems to improve retrieval performance. Knowledge graph abstracts things into entities and establishes relationships among entities, which are expressed in the form of triples. However, with the expansion of knowledge graph and the rapid increase of data volume, traditional place retrieval methods on knowledge graph have low p

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Krich, Christopher, Jakob Runge, Diego G. Miralles, et al. "Estimating causal networks in biosphere–atmosphere interaction with the PCMCI approach." Biogeosciences 17, no. 4 (2020): 1033–61. http://dx.doi.org/10.5194/bg-17-1033-2020.

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Abstract. The dynamics of biochemical processes in terrestrial ecosystems are tightly coupled to local meteorological conditions. Understanding these interactions is an essential prerequisite for predicting, e.g. the response of the terrestrial carbon cycle to climate change. However, many empirical studies in this field rely on correlative approaches and only very few studies apply causal discovery methods. Here we explore the potential for a recently proposed causal graph discovery algorithm to reconstruct the causal dependency structure underlying biosphere–atmosphere interactions. Using ar

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Kontogiannis, Spyros, Andreas Paraskevopoulos, and Christos Zaroliagis. "Time-Dependent Alternative Route Planning: Theory and Practice." Algorithms 14, no. 8 (2021): 220. http://dx.doi.org/10.3390/a14080220.

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We consider the problem of computing a set of meaningful alternative origin-to-destination routes, in real-world road network instances whose arcs are accompanied by travel-time functions rather than fixed costs. In this time-dependent alternative route scenario, we present a novel query algorithm, called Time-Dependent Alternative Graph (TDAG), that exploits the outcome of a time-consuming preprocessing phase to create a manageable amount of travel-time metadata, in order to provide answers for arbitrary alternative-routes queries, in only a few milliseconds for continental-size instances. Th

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Sun, Yange, Zhihai Wang, Yang Bai, Honghua Dai, and Saeid Nahavandi. "A Classifier Graph Based Recurring Concept Detection and Prediction Approach." Computational Intelligence and Neuroscience 2018 (June 7, 2018): 1–13. http://dx.doi.org/10.1155/2018/4276291.

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It is common in real-world data streams that previously seen concepts will reappear, which suggests a unique kind of concept drift, known as recurring concepts. Unfortunately, most of existing algorithms do not take full account of this case. Motivated by this challenge, a novel paradigm was proposed for capturing and exploiting recurring concepts in data streams. It not only incorporates a distribution-based change detector for handling concept drift but also captures recurring concept by storing recurring concepts in a classifier graph. The possibility of detecting recurring drifts allows re

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McBrearty, Ian W., Joan Gomberg, Andrew A. Delorey, and Paul A. Johnson. "Earthquake Arrival Association with Backprojection and Graph Theory." Bulletin of the Seismological Society of America 109, no. 6 (2019): 2510–31. http://dx.doi.org/10.1785/0120190081.

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Abstract The association of seismic‐wave arrivals with causative earthquakes becomes progressively more challenging as arrival detection methods become more sensitive, and particularly when earthquake rates are high. For instance, seismic waves arriving across a monitoring network from several sources may overlap in time, false arrivals may be detected, and some arrivals may be of unknown phase (e.g., P or S waves). We propose an automated method to associate arrivals with earthquake sources and obtain source locations applicable to such situations. To do so, we use a pattern detection metric

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Gong, Xiaolong, Linpeng Huang, and Fuwei Wang. "Feature Sampling Based Unsupervised Semantic Clustering for Real Web Multi-View Content." Proceedings of the AAAI Conference on Artificial Intelligence 33 (July 17, 2019): 102–9. http://dx.doi.org/10.1609/aaai.v33i01.3301102.

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Real web datasets are often associated with multiple views such as long and short commentaries, users preference and so on. However, with the rapid growth of user generated texts, each view of the dataset has a large feature space and leads to the computational challenge during matrix decomposition process. In this paper, we propose a novel multi-view clustering algorithm based on the non-negative matrix factorization that attempts to use feature sampling strategy in order to reduce the complexity during the iteration process. In particular, our method exploits unsupervised semantic informatio

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Jalgaonkar, Kirti, Manoj Kumar Mahawar, Sakharam Kale, et al. "Response surface optimization for development of Dragon fruit based ready to serve drink." Journal of Applied and Natural Science 10, no. 1 (2018): 272–78. http://dx.doi.org/10.31018/jans.v10i1.1617.

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Dragon fruit based ready to serve drink (RTS) was formulated using dragon fruit (60-80% v/v), grape juice (0-10% v/v) and sugar syrup (2-6% v/v). The juice concentrations were optimized using response surface methodology (RSM) following box-behnken design (BBD) for obtaining blended RTS drink with higher functional and nutritional characteristics like total soluble solid (TSS), titratable acidity, ascorbic acid content, total phenol content, colour and sensory evaluation. Results showed that there was significant (P<0.01) effect of incorporating grape juice and sugar syrup which further imp

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Börner, Katy, Adam Maltese, Russell Nelson Balliet, and Joe Heimlich. "Investigating aspects of data visualization literacy using 20 information visualizations and 273 science museum visitors." Information Visualization 15, no. 3 (2015): 198–213. http://dx.doi.org/10.1177/1473871615594652.

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In the information age, a person’s ability to read and make data visualizations is nearly as important as being able to read and write text. This article reports the results of a multi-phase study conducted in informal learning environments in three US science museums. The goal of the study was to determine the familiarity of youth and adult museum visitors with different visualization types. To address this, a total of 273 visitors were shown 5 out of 20 different visualizations that included two charts, five maps, eight graphs, and five network layouts. They were asked to judge the familiari

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Cariou, Claude, Steven Le Moan, and Kacem Chehdi. "Improving K-Nearest Neighbor Approaches for Density-Based Pixel Clustering in Hyperspectral Remote Sensing Images." Remote Sensing 12, no. 22 (2020): 3745. http://dx.doi.org/10.3390/rs12223745.

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We investigated nearest-neighbor density-based clustering for hyperspectral image analysis. Four existing techniques were considered that rely on a K-nearest neighbor (KNN) graph to estimate local density and to propagate labels through algorithm-specific labeling decisions. We first improved two of these techniques, a KNN variant of the density peaks clustering method dpc, and a weighted-mode variant of knnclust, so the four methods use the same input KNN graph and only differ by their labeling rules. We propose two regularization schemes for hyperspectral image analysis: (i) a graph regulari

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He, Ziping, Kewen Xia, Tiejun Li, Baokai Zu, Zhixian Yin, and Jiangnan Zhang. "A Constrained Graph-Based Semi-Supervised Algorithm Combined with Particle Cooperation and Competition for Hyperspectral Image Classification." Remote Sensing 13, no. 2 (2021): 193. http://dx.doi.org/10.3390/rs13020193.

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Semi-supervised learning (SSL) focuses on the way to improve learning efficiency through the use of labeled and unlabeled samples concurrently. However, recent research indicates that the classification performance might be deteriorated by the unlabeled samples. Here, we proposed a novel graph-based semi-supervised algorithm combined with particle cooperation and competition, which can improve the model performance effectively by using unlabeled samples. First, for the purpose of reducing the generation of label noise, we used an efficient constrained graph construction approach to calculate t

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He, Ziping, Kewen Xia, Tiejun Li, Baokai Zu, Zhixian Yin, and Jiangnan Zhang. "A Constrained Graph-Based Semi-Supervised Algorithm Combined with Particle Cooperation and Competition for Hyperspectral Image Classification." Remote Sensing 13, no. 2 (2021): 193. http://dx.doi.org/10.3390/rs13020193.

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Semi-supervised learning (SSL) focuses on the way to improve learning efficiency through the use of labeled and unlabeled samples concurrently. However, recent research indicates that the classification performance might be deteriorated by the unlabeled samples. Here, we proposed a novel graph-based semi-supervised algorithm combined with particle cooperation and competition, which can improve the model performance effectively by using unlabeled samples. First, for the purpose of reducing the generation of label noise, we used an efficient constrained graph construction approach to calculate t

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Tran, Cong, Won-Yong Shin, and Andreas Spitz. "Community Detection in Partially Observable Social Networks." ACM Transactions on Knowledge Discovery from Data 16, no. 2 (2021): 1–24. http://dx.doi.org/10.1145/3461339.

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The discovery of community structures in social networks has gained significant attention since it is a fundamental problem in understanding the networks’ topology and functions. However, most social network data are collected from partially observable networks with both missing nodes and edges . In this article, we address a new problem of detecting overlapping community structures in the context of such an incomplete network, where communities in the network are allowed to overlap since nodes belong to multiple communities at once. To solve this problem, we introduce KroMFac , a new framewor

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Deng, Xutao, Samia N. Naccache, Terry Ng, et al. "An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data." Nucleic Acids Research 43, no. 7 (2015): e46-e46. http://dx.doi.org/10.1093/nar/gkv002.

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Abstract Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (d

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Abeywickrama, Tenindra, Victor Liang, and Kian-Lee Tan. "Optimizing bipartite matching in real-world applications by incremental cost computation." Proceedings of the VLDB Endowment 14, no. 7 (2021): 1150–58. http://dx.doi.org/10.14778/3450980.3450983.

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The Kuhn-Munkres (KM) algorithm is a classical combinatorial optimization algorithm that is widely used for minimum cost bipartite matching in many real-world applications, such as transportation. For example, a ride-hailing service may use it to find the optimal assignment of drivers to passengers to minimize the overall wait time. Typically, given two bipartite sets, this process involves computing the edge costs between all bipartite pairs and finding an optimal matching. However, existing works overlook the impact of edge cost computation on the overall running time. In reality, edge compu

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Ficara, Annamaria, Lucia Cavallaro, Francesco Curreri, et al. "Criminal networks analysis in missing data scenarios through graph distances." PLOS ONE 16, no. 8 (2021): e0255067. http://dx.doi.org/10.1371/journal.pone.0255067.

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Data collected in criminal investigations may suffer from issues like: (i) incompleteness, due to the covert nature of criminal organizations; (ii) incorrectness, caused by either unintentional data collection errors or intentional deception by criminals; (iii) inconsistency, when the same information is collected into law enforcement databases multiple times, or in different formats. In this paper we analyze nine real criminal networks of different nature (i.e., Mafia networks, criminal street gangs and terrorist organizations) in order to quantify the impact of incomplete data, and to determ

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Huzsvár, Tamás, Richárd Wéber, and Csaba János Hős. "Analysis of the Segment Graph of Water Distribution Networks." Periodica Polytechnica Mechanical Engineering 63, no. 4 (2019): 295–300. http://dx.doi.org/10.3311/ppme.13739.

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One of the basic infrastructures of every settlement is the water distribution system, which provides clean and potable water for both private houses, industrial consumers and institution establishments. The operational robustness and vulnerabilities of these networks is an essential issue, both for the quality of life and for the preservation of the environment. Even with frequent and careful maintenance, unintentional pipe bursts might occur, and during the reparation time, the damaged section must be isolated hydraulically from the main body of the water distribution network. Due to the siz

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Patil, Shubham, Debopriyo Banerjee, and Shamik Sural. "A Graph Theoretic Approach for Multi-Objective Budget Constrained Capsule Wardrobe Recommendation." ACM Transactions on Information Systems 40, no. 1 (2022): 1–33. http://dx.doi.org/10.1145/3457182.

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Traditionally, capsule wardrobes are manually designed by expert fashionistas through their creativity and technical prowess. The goal is to curate minimal fashion items that can be assembled into several compatible and versatile outfits. It is usually a cost and time intensive process, and hence lacks scalability. Although there are a few approaches that attempt to automate the process, they tend to ignore the price of items or shopping budget. In this article, we formulate this task as a multi-objective budget constrained capsule wardrobe recommendation ( MOBCCWR ) problem. It is modeled as

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Bosilca, George, Aurelien Bouteiller, Amina Guermouche, et al. "A failure detector for HPC platforms." International Journal of High Performance Computing Applications 32, no. 1 (2017): 139–58. http://dx.doi.org/10.1177/1094342017711505.

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Building an infrastructure for exascale applications requires, in addition to many other key components, a stable and efficient failure detector. This article describes the design and evaluation of a robust failure detector that can maintain and distribute the correct list of alive resources within proven and scalable bounds. The detection and distribution of the fault information follow different overlay topologies that together guarantee minimal disturbance to the applications. A virtual observation ring minimizes the overhead by allowing each node to be observed by another single node, prov

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Liu, Hongying, Derong Xu, Tianwen Zhu, et al. "Graph Convolutional Networks by Architecture Search for PolSAR Image Classification." Remote Sensing 13, no. 7 (2021): 1404. http://dx.doi.org/10.3390/rs13071404.

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Classification of polarimetric synthetic aperture radar (PolSAR) images has achieved good results due to the excellent fitting ability of neural networks with a large number of training samples. However, the performance of most convolutional neural networks (CNNs) degrades dramatically when only a few labeled training samples are available. As one well-known class of semi-supervised learning methods, graph convolutional networks (GCNs) have gained much attention recently to address the classification problem with only a few labeled samples. As the number of layers grows in the network, the par

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Deb, K. "A Quick Computation of Factor of Safety for Biaxial Stress States." Journal of Mechanical Design 120, no. 4 (1998): 721–26. http://dx.doi.org/10.1115/1.2829337.

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Determination of overall factor of safety of a design involves repeated calculation of factor of safety at critical points in the design. For a given stress state at a point, the factor of safety is calculated by first finding the principal stresses and then comparing them with the maximum safe stress that can be applied without causing failure of the material according to an appropriate failure theory. In this paper, we suggest quick and ready-to-use expressions and graphs for calculating factor of safety for biaxial stress states for a number of commonly-used failure theories. These graphs c

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Mendez, Gonzalo, Xavier Ochoa, Katherine Chiluiza, and Bram De Wever. "Curricular Design Analysis: A Data-Driven Perspective." Journal of Learning Analytics 1, no. 3 (2014): 84–119. http://dx.doi.org/10.18608/jla.2014.13.6.

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Learning analytics has been as used a tool to improve the learning process mainly at the micro-level (courses and activities). However, another of the key promises of Learning Analytics research is to create tools that could help educational institutions at the meso- and macro-level to gain a better insight of the inner workings of their programs, in order to tune or correct them. This work presents a set of simple techniques that applied to readily available historical academic data could provide such insights. The techniques described are real course difficulty estimation, course impact on t

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Sarkar, Saswati, and Anirban Kundu. "An Eco-Friendly Efficient Cloud-Searching Technique With Delay." International Journal of Green Computing 9, no. 1 (2018): 20–34. http://dx.doi.org/10.4018/ijgc.2018010102.

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The authors propose a cloud-based disk-searching technique with delay in this article. Cloud computing is responsible for eco-friendly use of computers and other related resources. The proposed technique exerts less energy to search particular data. The searching technique finds a particular element through parallel channels. The energy efficiency is directly proportional to the number of channels for a specific set of data. The parallel searching technique is implemented to reduce time complexity and complexity of delay. The article exhibits a complexity of delay in a real-time scenario. The

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Pruski, Cédric, Nicolas Guelfi, and Chantal Reynaud. "Adaptive Ontology-Based Web Information Retrieval." International Journal of Web Portals 3, no. 3 (2011): 41–58. http://dx.doi.org/10.4018/ijwp.2011070104.

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Finding relevant information on the Web is difficult for most users. Although Web search applications are improving, they must be more “intelligent” to adapt to the search domains targeted by queries, the evolution of these domains, and users’ characteristics. In this paper, the authors present the TARGET framework for Web Information Retrieval. The proposed approach relies on the use of ontologies of a particular nature, called adaptive ontologies, for representing both the search domain and a user’s profile. Unlike existing approaches on ontologies, the authors make adaptive ontologies adapt

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PHAN, VINHTHUY, E. OLUSEGUN GEORGE, QUYNH T. TRAN, SHIRLEAN GOODWIN, SRIDEVI BODREDDIGARI, and THOMAS R. SUTTER. "ANALYZING MICROARRAY DATA WITH TRANSITIVE DIRECTED ACYCLIC GRAPHS." Journal of Bioinformatics and Computational Biology 07, no. 01 (2009): 135–56. http://dx.doi.org/10.1142/s0219720009003972.

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Post hoc assignment of patterns determined by all pairwise comparisons in microarray experiments with multiple treatments has been proven to be useful in assessing treatment effects. We propose the usage of transitive directed acyclic graphs (tDAG) as the representation of these patterns and show that such representation can be useful in clustering treatment effects, annotating existing clustering methods, and analyzing sample sizes. Advantages of this approach include: (1) unique and descriptive meaning of each cluster in terms of how genes respond to all pairs of treatments; (2) insensitivit

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