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2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011

作者： Salem, Saeed Alroobi, Rami Banitaan, Shadi Seridi, Loqmane Brewer, James Aljarah, Ibrahim Department of Computer Science North Dakota State University Fargo ND 58102 United States Math. and Comp. Sci. and Eng. Division KAUST 23955-6900 Saudi Arabia

ISBN: (纸本)9781450307963

Functional module discovery aims to find well-connected subnetworks which can serve as candidate protein complexes. Advances in High-throughput proteomic technologies have enabled the collection of large amount of interaction data as well as gene expression data. We propose, CLARM, a clustering algorithm that integrates gene expression profiles and protein protein interaction network for biological modules discovery. The main premise is that by enriching the interaction network by adding interactions between genes which are highly co-expressed over a wide range of biological and environmental conditions, we can improve the quality of the discovered modules. Protein protein interactions, known protein complexes, and gene expression profiles for diverse environmental conditions from the yeast Saccharomyces cerevisiae were used for evaluate the biological significance of the reported modules. Our experiments show that the CLARM approach is competitive to wellestablished module discovery methods. Copyright © 2011 ACM.

关键词： Clustering algorithms

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Administration and academic staff performance management system using content management system (CMS) technologies

Administration and academic staff performance management sys...

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International Conference on Electronics, computer and Computation (ICECCO)

作者： Moussa Mahamat Boukar Isa Muslu Department of Computer Science Nigerian Turkish Nile University Abuja Nigeria Department of Applied Math. International Ataturk Alatoo University Bishkek Kyrgyzstan

Content management systems (CMS) provide an optimal solution by organizing information and, mostly, creating and managing an enterprises knowledge. This paper aims to construct an interactive dynamic system base on CMS technologies, on which a range of problems concerning the administration and academic aspects of a university management system can be analyzed and certain policies for overcoming these problems can be tested and improved. This pilot was developed to explore the versatility of content management system (CMS) and to use the technology of CMS as precursor to handle content of a full blown automation of administration and academic performance management system.

关键词： Content management Educational institutions Instruments Information management Automation Companies

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A promising approach to morphological endocardial signal discriminations: Adapted multiresolution signal decompositions

Applied Signal Processing

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applied Signal Processing 1999年第4期6卷 182-193页

作者： Strauss, D. Sinnwell, T. Rieder, A. Manoli, Y. Jung, J. Applied Math. and Computer Science University of Mannheim Building D7 27 Room 201 D-68131 Mannheim Germany

A major challenge for currently used algorithms in dual-chamber implantable cardioverter-defibrillators is the discrimination of ventricular tachycardias with 1:1 retrograde conduction from sinus tachycardia. Here the morphology of endocardial electrograms can be used to discriminate the physiological from the pathological state of the heart. Recently, wavelet-type multiresolution decompositions have been proposed for the detection of cardiac arrhythmias. However, the choice of appropriate wavelets used for electrogram decompositions still remains an issue. The aim of the presented paper is to assess adapted multiresolution signal decompositions of atrial endocardial electrograms as a new morphological analysis tool for a rate-independent identification of tachyarrhythmias. For the adaptation we used a library of discrete-time wavelets generated by a completely parameterised lattice structure. The results presented show that the proposed discrimination scheme is effective and promising for a morphological discrimination of endocardial electrograms.

关键词： Signal filtering and prediction

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A software system for stent planning, stent simulation and follow-up examinations in the vascular domain

A software system for stent planning, stent simulation and f...

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2009 22nd IEEE International Symposium on computer-Based Medical Systems, CBMS 2009

作者： Egger, Jan Großkopf, Stefan O'Donnell, Thomas Freisleben, Bernd Dept. of Math. and Computer Science University of Marburg Germany Siemens Healthcare Dept. of Computed Tomography Forchheim Germany Imaging and Visualization Department Siemens Corporate Research Princeton United States

ISBN: (纸本)9781424448784

In this paper, a software system for supporting stenting in the vascular domain is presented. The system covers all treatment phases from diagnosis to follow-up examinations. During the preoperative phase, the system supports the physician by suggesting the date and the kind (open surgery, minimally invasive) of intervention based on segmenting the patient's CT data. Therapy planning is additionally supported by a computer-aided stent simulation. Using virtual stenting, it is possible to simulate stents of different manufacturers in the preoperative CT data of the patient. As a result, it can be decided whether a chosen stent has proper dimensions and should be used during the following intervention. The intraoperative phase is supported by visualizing the selected stent from the planning phase at the requested position. After stenting, regular follow-up examinations are necessary to detect stent migration and endoleaks. These time-consuming procedures are also supported by the developed system. ©2009 IEEE.

关键词： Stents

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Natural Image Denoising: Optimality and Inherent Bounds

Natural Image Denoising: Optimality and Inherent Bounds

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IEEE Conference on computer Vision and Pattern Recognition

作者： Anat Levin Boaz Nadler Department of Computer Science and Applied Math The Weizmann Institute of Science

ISBN: (纸本)9781457703942

The goal of natural image denoising is to estimate a clean version of a given noisy image, utilizing prior knowledge on the statistics of natural images. The problem has been studied intensively with considerable progress made in recent years. However, it seems that image denoising algorithms are starting to converge and recent algorithms improve over previous ones by only fractional dB values. It is thus important to understand how much more can we still improve natural image denoising algorithms and what are the inherent limits imposed by the actual statistics of the data. The challenge in evaluating such limits is that constructing proper models of natural image statistics is a long standing and yet unsolved problem. To overcome the absence of accurate image priors, this paper takes a non parametric approach and represents the distribution of natural images using a huge set of 10~(10) patches. We then derive a simple statistical measure which provides a lower bound on the optimal Bayesian minimum mean square error (MMSE). This imposes a limit on the best possible results of denoising algorithms which utilize a fixed support around a denoised pixel and a generic natural image prior. Our findings suggest that for small windows, state of the art denoising algorithms are approaching optimality and cannot be further improved beyond ～ 0.1dB values.

关键词： image denoising Noisy Image fixed pivot DATA(STATISTICS) images optimality Mean square error Converge Prior Learning Noise reduction

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Adjacency Sketches in Adversarial Environments

arXiv

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arXiv 2023年

作者： Naor, Moni Pekel, Eugene Department of Computer Science and Applied Math Weizmann Institute of Science

An adjacency sketching or implicit labeling scheme for a family F of graphs is a method that defines for any n vertex G ∈ F an assignment of labels to each vertex in G, so that the labels of two vertices tell you whether or not they are adjacent. The goal is to come up with labeling schemes that use as few bits as possible to represent the labels. By using randomness when assigning labels, it is sometimes possible to produce adjacency sketches with much smaller label sizes, but this comes at the cost of introducing some probability of error. Both deterministic and randomized labeling schemes have been extensively studied, as they have applications for distributed data structures and deeper connections to universal graphs and communication complexity. The main question of interest is which graph families have schemes using short labels, usually O(log n) in the deterministic case or constant for randomized sketches. In this work we consider the resilience of probabilistic adjacency sketches against an adversary making adaptive queries to the labels. This differs from the previously analyzed probabilistic setting which is "one shot". We show that in the adaptive adversarial case the size of the labels is tightly related to the maximal degree of the graphs in F . This results in a stronger characterization compared to what is known in the non-adversarial setting. In more detail, we construct sketches that fail with probability Ε for graphs with maximal degree d using 2d log(1/Ε) bit labels and show that this is roughly the best that can be done for any specific graph of maximal degree d, e.g. a d-ary *** Codes 68W20, 68W40, 68Q87 Copyright © 2023, The Authors. All rights reserved.

关键词： Graphic methods

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Computing inverse ST in linear complexity

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19th Annual Symposium on Combinatorial Pattern Matching

作者： Nong, Ge Zhang, Sen Chan, Wai Hong Computer Science Department Sun Yat-Sen University China Dept. of Math. Comp. Sci. and Stat. SUNY College Oneonta United States Department of Mathematics Hong Kong Baptist University Hong Kong Hong Kong

ISBN: (纸本)9783540690665

The Sort Transform (ST) can significantly speed up the block sorting phase of the Burrows-Wheeler transform (BWT) by sorting only limited order contexts. However, the best result obtained so far for the inverse ST has a time complexity O(N log k) and a space complexity O(N), where N and k are the text size and the context order of the transform, respectively. In this paper, we present a novel algorithm that can compute the inverse ST in an O(N) time/space complexity, a linear result independent of k. The main idea behind the design of the linear algorithm is a set of cycle properties of k-order contexts we explored for this work. These newly discovered cycle properties allow us to quickly compute the longest common prefix (LCP) between any pair of adjacent k-order contexts that may belong to two different cycles, leading to the proposed linear inverse ST algorithm.

关键词： math.matical transformations

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Unexpected universality results for three classes of P systems with symport/antiport

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Natural Computing 2003年第4期2卷 337-348页

作者： Ionescu, Mihai Martín-Vide, Carlos Pǎun, Andrei Pǎun, Gheorghe Faculty of Mathematics University of Bucharest 70109 Bucharest Str. Academiei 14 Romania Research Group on Math. Linguistics Rovira i Virgili University 43005 Tarragona Pl. Imperial Tárraco 1 Spain Department of Computer Science University of Western Ontario London Ont. N6A 5B7 Canada Research Group on Math. Linguistics Inst. of Math. of the Romanian Acad. 70700 Bucharest PO Box 1-764 Romania

Symport and antiport are biological ways of transporting molecules through membranes in "collaborating" pairs;in the case of symport the two molecules pass in the same direction, in the case of antiport the two molecules pass in opposite directions. Here we first survey the results about the computing power of membrane systems (P systems) using only symport/antiport rules (hence these systems compute by communication only), then we consider a recently introduced, way of defining the result of a computation in a membrane system: looking for the trace of certain objects in their movement through membranes. Rather unexpected, in this way we get characterizations of recursively enumerable languages by means of membrane systems with symport/antiport which work with multisets of objects (note the qualitative difference between the data structure used by computations - multisets: no ordering - and the data structure of the output - strings: linear ordering). A similar remark holds true for the case of analysing P systems, which work in an automata-like manner: the sequence of certain distinguished objects taken from the environment during a computation is the string recognized by the computation. We also survey universality results from this area, with sketched proofs. Some open problems are also formulated. © 2003 Kluwer Academic Publishers.

关键词： Chomsky hierarchy Membrane computing P system Turing computability

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The Grad of a Graph and Classes with Bounded Expansion

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Electronic Notes in Discrete math.matics 2005年 22卷 101-106页

作者： Nešetřil, Jaroslav Ossona de Mendez, Patrice Department of Applied Mathematics Institute of Theoretical Computer Science Charles University Praha Czech Republic Centre d'Analyse Mathématiques Sociales - CNRS UMR 8557 Paris France

We introduce classes of graphs with bounded expansion as a generalization of both proper minor closed classes and degree bounded classes. Such classes are based on a new invariant, the greatest reduced average density (grad) of G with rank r, ∇_r (G). We generalize to these classes some results proved for proper minor closed classes and bounded degree graphs, such as the existence of low tree-width colorings and homomorphism dualities. © 2005 Elsevier B.V. All rights reserved.

关键词： Bounded expansion Coloring Constrained orientation Homomorphism Restricted duality Transitive fraternal augmentation Tree-depth

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Fraternal Augmentations of graphs, Coloration and Minors

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Electronic Notes in Discrete math.matics 2007年 28卷 223-230页

We introduce classes of graphs with bounded expansion as a generalization of both proper minor closed classes and degree bounded classes. Such classes are based on a new invariant, the greatest reduced average density (grad) of G with rank r, ∇_r (G). We generalize to these classes some results proved for proper minor closed classes and bounded degree graphs, such as the existence of low tree-width colorings, a linear time algorithm to check subgraph isomorphism for a fixed pattern and homomorphism dualities. © 2007 Elsevier B.V. All rights reserved.

关键词： Bounded expansion Coloring Graph Algorithm Homomorphism Ramsey number Restricted duality Subgraph Isomorphism Transitive fraternal augmentation Tree-depth

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