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Genome dedoubling by DCJ and reversal

BMC BIOINFORMATICS 2011年第s9期12卷 1-9页

作者： Thomas, Antoine Varre, Jean-Stephane Ouangraoua, Aida Univ Lille 1 INRIA Lille Nord Europe UMR CNRS 8022 LIFL F-59655 Villeneuve Dascq France

Background: Segmental duplications in genomes have been studied for many years. Recently, several studies have highlighted a biological phenomenon called breakpoint-duplication that apparently associates a significant proportion of segmental duplications in Mammals, and the Drosophila species group, to breakpoints in rearrangement events. Results: In this paper, we introduce and study a combinatorial problem, inspired from the breakpoint-duplication phenomenon, called the Genome Dedoubling Problem. It consists of finding a minimum length rearrangement scenario required to transform a genome with duplicated segments into a non-duplicated genome such that duplications are caused by rearrangement breakpoints. We show that the problem, in the Double-Cut-and-Join (DCJ) and the reversal rearrangement models, can be reduced to an APX-complete problem, and we provide algorithms for the Genome Dedoubling Problem with 2-approximable parts. We apply the methods for the reconstruction of a non-duplicated ancestor of Drosophila yakuba. Conclusions: We present the Genome Dedoubling Problem, and describe two algorithms solving the problem in the DCJ model, and the reversal model. The usefulness of the problems and the methods are showed through an application to real Drosophila data.

关键词： Segmental Duplication Ancestral Genome Duplicate Segment Rearrangement Event linear time complexity

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linear time manageable edge-aware filtering on complementary tree structures

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COMPUTERS & GRAPHICS-UK 2024年 118卷 133-145页

作者： Bu, Penghui Wang, Hang Yang, Tao Zhao, Hong Xian Shiyou Univ Sch Mech Engn 18Elect Second Rd Xian 710065 Shaanxi Peoples R China Xian Chishine Optoelect Technol Co 69 Jin Ye Rd Xian 710076 Shaanxi Peoples R China Xi An Jiao Tong Univ State Key Lab Mfg Syst Engn 28 Xianning West Rd Xian 710049 Shaanxi Peoples R China

Typical non-local edge-aware filtering methods build long-range connections by deriving a minimum spanning tree (MST) from the input image. Each pixel on the MST only connects to a sub-set of pixels in the 8-connected neighborhood, resulting in piece-wise constant output with fake edges among sub-trees for the unbalanced information propagation along eight directions. In this paper, we propose two complementary spatial trees to incorporate information from the entire image. The structure of each tree depends on the spatial relationships of neighboring pixels. The distances between any two pixels in both spatial space and intensity space are the shortest distances on each tree. We introduce an efficient algorithm to recursively compute the output and the normalization constant on each tree with linear time complexity. For each pixel, we first calculate the outputs from eight subtrees and then fuse them to obtain the result on each tree structure. The final filtering output of our method is the weighted average of the results from two complementary spatial trees. Moreover, we present a distance mapping scheme to adjust the intensity distance between neighboring pixels, enabling our method to filter out a manageable degree of low-amplitude structures while sharpening major edges. Extensive experiments in graphic applications, such as image denoising, JPEG artifact removal, tone mapping, detail enhancement, and colorization, demonstrate the effectiveness and versatility of our method.

关键词： Non-local edge-aware filtering Complementary trees linear time complexity Distance mapping Spatial relationship Manageable smoothing

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An efficient algorithm for the computation of the metric average of two intersecting convex polygons, with application to morphing

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ADVANCES IN COMPUTATIONAL MATHEMATICS 2007年第1-3期26卷 269-282页

作者： Lipovetsky, Evgeny Dyn, Nira Tel Aviv Univ Sch Math Sci IL-69978 Tel Aviv Israel

Motivated by the method for the reconstruction of 3D objects from a set of parallel cross sections, based on the binary operation between 2D sets termed "metric average", we developed an algorithm for the computation of the metric average between two intersecting convex polygons in 2D. For two 1D sets there is an algorithm for the computation of the metric average, with linear time in the number of intervals in the two 1D sets. The proposed algorithm has linear computation time in the number of vertices of the two polygons. As an application of this algorithm, a new technique for morphing between two convex polygons is developed. The new algorithm performs morphing in a non-intuitive way.

关键词： convex polygons metric average morphing linear time complexity

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A note on the linearity of Ratliff and Rosenthal's algorithm for optimal picker routing

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OPERATIONS RESEARCH LETTERS 2022年第2期50卷 155-159页

作者： Hessler, Katrin Irnich, Stefan Johannes Gutenberg Univ Mainz Gutenberg Sch Management & Econ Chair Logist Management Jakob Welder Weg 9 D-55128 Mainz Germany

Ratliff and Rosenthal state that their dynamic programming algorithm for optimal picker routing has linear complexity in the number of aisles. Indeed, solving the dynamic program is linear, but computing the cost coefficients of the dynamic program certainly requires the consideration of all picking positions, whose number is independent of the number of aisles. For a given unsorted sequence of picking positions, our algorithm is linear in the sum of the number of aisles and number of picking positions. (C) 2022 Elsevier B.V. All rights reserved.

关键词： Picker routing problem Dynamic programming linear time complexity Maximum gap problem

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Hybrid Stochastic Computing of linear time O(N) and Its In-Memory Computing for High Performances

Hybrid Stochastic Computing of Linear Time O(N) and Its In-M...

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IEEE-Computer-Society Annual Symposium on VLSI (ISVLSI)

作者： Chen, Yuhao Li, Hongge Song, Yinjie Zhu, Xinyu Beihang Univ Coll Elect Informat Engn Beijing Peoples R China

ISBN: (纸本)9798350354119

Stochastic computing (SC) reduces the complexity of arithmetic circuits but brings extra conversion cost and time complexity of O(2(N)), which leads to a much lower efficiency than binary. This paper proposes a linear-time, O(N), and conversionfree hybrid stochastic computing (HSC). Moreover, a hybrid stochastic computing in-memory method is proposed, mapping addition and multiplication of HSC into memory's enable and addressing circuits. Thus, the basic memory having enable and addressing circuits can realize HSC operation without additional circuits. The experiment shows that HSC in block memory (BRAM) based on FPGA for matrix multiplication reaches 2.304 TOPS (operation per second) and 17.2 TOPS/***. Each 18K-BRAM provides 18 GOPS (INT8) with 8.34 mW at 600 MHz.

关键词： Hybrid stochastic computing linear time complexity Computing in memory High performance

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A NEW APPROXIMATE REASONING BASED ON SPMF

A NEW APPROXIMATE REASONING BASED ON SPMF

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10th International Conference on Enterprise Information Systems

作者： Choi, Dae-Young YUHAN Coll Dept MIS Puchon Kyungki Do South Korea

A new approximate reasoning based on standardized parametric membership functions (SPMF) is proposed. It provides an efficient mechanism for approximate reasoning within linear time complexity.

ISBN: (纸本)9789898111371

A new approximate reasoning based on standardized parametric membership functions (SPMF) is proposed. It provides an efficient mechanism for approximate reasoning within linear time complexity.

关键词： Approximate reasoning linear time complexity

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An efficient hierarchical clustering algorithm via root searching 17

An efficient hierarchical clustering algorithm via root sear...

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IEEE 17th International Conference on Computational Science and Engineering (CSE)

作者： Xie, Wenbo Liu, Zhen Univ Elect Sci & Technol China Sch Comp Sci & Engn Web Sci Ctr Chengdu Peoples R China

ISBN: (纸本)9781479979813

As an important branch of machine learning, clustering is wildly used for data analysis in various domains. Hierarchical clustering algorithm, one of the traditional clustering algorithms, has excellent stability yet relatively poor time complexity. In this paper, we proposed an efficient hierarchical clustering algorithm by searching given nodes' nearest neighbors iteratively, which depends on an assumption: the representative node (root) may exist in the densest data area. The experiments results preformed on 14 UCI datasets show that our algorithm exhibits the best accuracies on most datasets. Moreover, our method has a linear time complexity which is significantly better than other traditional clustering methods like UPGMA and K-Means.

关键词： hierarchical clustering root searching nearest neighbor densest data area linear time complexity

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SOCEN-CLUSTER : A New Rapid Clustering Technique

SOCEN-CLUSTER : A New Rapid Clustering Technique

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1st International Conference on Electrical Engineering and Software Applications (ICEESA)

作者： Baccari, Farouk Sayadi, Mounir Univ Tunis ESSTT SICISI Unit Tunis 1008 Tunisia

ISBN: (纸本)9781467363020;9781467363006

In this paper, we present a novel clustering technique for unindexed, randomized, multidimensional, datasets. The main advantage of the proposed technique is the time and space complexity that were reduced to linear cardinality dependency. The algorithmic implementation shown in this paper uses some heuristics to enhance the overall execution time and space required making them fully scalable. This particularity makes it easier for ASICS / FPGA architects to implement such a technique in a constrained environment.

关键词： component clustering classification linear time complexity herarchical clustering incremental clustering algorithmic hurisitcs scalable clustering technique

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BaW 1.0-A Problem Specific SAT Solver for Effective Strong Connectivity Testing in Sparse Directed Graphs 18

BaW 1.0-A Problem Specific SAT Solver for Effective Strong C...

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18th IEEE International Symposium on Computational Intelligence and Informatics (CINTI)

作者： Biro, Csaba Kusper, Gabor Eszterhazy Karoly Univ Inst Math & Informat Eger Hungary

ISBN: (纸本)9781728111179

In our previous works, we proved that if a directed graph is strongly connected, then the generated 2-SAT problem is a black-and-white 2-SAT problem, which has two solutions: where each variable is true (the white assignment), and where each variable is false (the black one). We proved also theoretically that these problems could be solved in linear time. In this article we present a DPLL-based problem specific SAT solver called BaW 1.0. Problem specific, because the BaW 1.0 is not a complete SAT solver, it is only validated for our special black-and-white 2-SAT problem based benchmarks. First, we show how to solve the black-and-white 2-SAT problems in linear time and how to use this solver for effective strong connectivity testing in large and sparse directed graphs. After that we present our results on these benchmarks which show that remarkable improvements have taken place in the number of solved instances as well as in the computation time compared to existing modern State-of-the-art SAT solvers (CSFLOC 8, Glucose 3.0).

关键词： BaW 1.0-a problem specific SAT solver black-and-white 2-SAT problem directed graph 2-SAT problem strong connectivity linear time complexity

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Novel contour vectorization using holistic feature of object

Novel contour vectorization using holistic feature of object

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Chinese Conference on Pattern Recognition

作者： Lu, Qichao Yang, Guang Gao, Feng School of Computer Science and Engineering BeiHang University Beijing 100193 China

ISBN: (纸本)9781424472109

In this paper, a novel contour vectorization approach based on holistic feature of object is proposed, which aims at avoiding segmenting an entire contour of target into some discrete sets of curves. This method consists of two steps:(1) Digitize pixel-based contour into vectors or arcs referring to holistic feature of object, and the contour trend used in the implementation of vectorization is defined here;(2)Approximate vectors and arcs to regular figures, including various postprocessing treatments. Innovative and significant features of this approach includes: preservation of original contour shape;low-loss of performance in noisy environments;linear time complexity and neglectable space complexity. The experimental results obtained confirm the validity of the proposed approach. ©2010 IEEE.

关键词： computational complexity computer vision contour vectorization discrete set feature extraction holistic object feature linear time complexity noisy environment object detection pixel based contour postprocessing treatment regular figure space complexity

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