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TMAinspiration: Decode Interdependencies in Multifactorial Tissue Microarray Data

CANCER INFORMATICS 2016年第15期15卷 143-149页

作者： Boecker, Florian Buerger, Horst Mallela, Nikhil V. Korsching, Eberhard Univ Munster Inst Bioinformat Munster Germany Univ Bonn INRES Crop Bioinformat Bonn Germany Inst Pathol Paderborn Germany Breast Canc Ctr Paderborn Germany Univ Utrecht Inst Pathol Utrecht Netherlands

There are no satisfying tools in tissue microarray (TMA) data analysis up to now to analyze the cooperative behavior of all measured markers in a multifactorial TMA approach. The developed tool TMAinspiration is not only offering an analysis option to close this gap but also offering an ecosystem consisting of quality control concepts and supporting scripts to make this approach a platform for informed practice and further research. The TMAinspiration method is specifically focusing on the demands of the TMA analysis by controlling errors and noise by a generalized regression scheme while at the same time avoiding to introduce a priori too many constraints into the analysis of the data. So, we are testing partitions of a proximity table to find an optimal support for a ranking scheme of molecular dependencies. The idea of combining several partitions to one ensemble, which is balancing the optimization process, is based on the main assumption that all these perspectives on the cellular network need to be self-consistent. Several application examples in breast cancer and one in squamous cell carcinoma demonstrate that this procedure is nicely confirming a priori knowledge on the expression characteristics of protein markers, while also integrating many new results discovered in the treasury of a bigger TMA experiment. The code and software are now freely available at: http://***/tma_***.

关键词： tissue microarray protein expression combinatorial algorithm systems biology pathology cancer

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An Efficient algorithm for Haplotype Inference on Pedigrees with a Small Number of Recombinants

An Efficient Algorithm for Haplotype Inference on Pedigrees ...

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17th Annual European Symposium on algorithms

作者： Xiao, Jing Lou, Tiancheng Jiang, Tao IBM China Res Lab Beijing Peoples R China Tsinghua Univ Dept Comp Sci & Technol Beijing Peoples R China Univ Calif Riverside Dept Comp Sci & Engn Riverside CA 92521 USA

ISBN: (纸本)9783642041273

combinatorial (or rule-based) methods for inferring haplotypes from genotypes on a pedigree have been studied extensively in the recent literature. These methods generally try to reconstruct the haplotypes of each individual so that the total number of recombinants is minimized in the pedigree. The problem is NP-hard, although it is known that the number of recombinants in a practical dataset is usually very small. In this paper, we consider the question of how to efficiently infer haplotypes on a large pedigree when the number of recombinants is bounded by a small constant, i.e. the so called k-recombinant haplotype configuration (k-RHC) problem. We introduce a simple probabilistic model for k-RHC where the prior haplotype probability of a founder and the haplotype transmission probability from a parent to a child are all assumed to follow the uniform distribution and k random recombinants are assumed to have taken place uniformly and independently in the pedigree. We present an O(mn log(k+1) n) time algorithm for k-RHC on tree pedigrees without mating loops, where in is the number of loci and n is the size of the input pedigree, and prove that when 90 log n < m < n(3), the algorithm can correctly find a feasible haplotype configuration that obeys the Mendelian law of inheritance and requires no more than k recombinants with probability 1 - O(k(2)log(2)n/mn + 1/(n2)). The algorithm is efficient when k is of a moderate value and could thus be used to infer haplotypes from genotypes on large tree pedigrees efficiently in practice. We have implemented the algorithm as a C++ program named TREE-k-RHC. The implementation incorporates several ideas for dealing with missing data and data with a large number of recombinants effectively. Our experimental results on both simulated and real datasets show that TREE-k-RHC can reconstruct haplotypes with a high accuracy and is much faster than the best combinatorial method in the literature.

关键词： computational biology haplotype inference pedigree recombination combinatorial algorithm probabilistic model

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Evaluating performance of image segmentation criteria and techniques

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EURO JOURNAL ON COMPUTATIONAL OPTIMIZATION 2013年第1-2期1卷 155-180页

作者： Hochbaum, Dorit S. Lyu, Cheng Bertelli, Erik Univ Calif Berkeley Dept Ind Engn & Operat Res Berkeley CA 94720 USA

The image segmentation problem is to delineate, or segment, a salient feature in an image. As such, this is a bipartition problem with the goal of separating the foreground from the background. An NP-hard optimization problem, the Normalized Cut problem, is often used as a model for image segmentation. The common approach for solving the normalized cut problem is the spectralmethod which generates heuristic solutions based upon finding the Fiedler eigenvector. Recently, Hochbaum (IEEE Trans Pattern Anal Mach Intell 32(5): 889-898, 2010) presented a new relaxation of the normalized cut problem, called normalized cut' problem, which is solvable in polynomial time by a combinatorial algorithm. We compare this new algorithm with the spectral method and present experimental evidence that the combinatorial algorithm provides solutions which better approximate the optimal normalized cut solution. In addition, the subjective visual quality of the segmentations provided by the combinatorial algorithm greatly improves upon those provided by the spectral method. Our study establishes an interesting observation about the normalized cut criterion that the segmentation which provides the subjectively best visual bipartition rarely corresponds to the segmentation which minimizes the objective function value of the normalized cut problem. We conclude that modeling the image segmentation problem as normalized cut criterion might not be appropriate. Instead, normalized cut not only provides better visual segmentations but is also solvable in polynomial time. Therefore, normalized cut' should be the preferred segmentation criterion for both complexity and good segmentation quality reasons.

关键词： Image segmentation Normalized cut Network flow combinatorial algorithm Spectral method

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Dynamic Fair Division of Multiple Resources with Satiable Agents in Cloud Computing Systems 5

Dynamic Fair Division of Multiple Resources with Satiable Ag...

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IEEE 5th International Conference on Big Data and Cloud Computing (BDCloud)

作者： Liu, Xi Zhang, Xiaolu Zhang, Xuejie Li, Weidong Yunnan Univ Kunming Peoples R China

ISBN: (纸本)9781467371834

Dynamic multi-resource fair allocation became an important topic for cloud resource management. We consider a generalized version of the dynamic multi-resource fair allocation problem, where an agent is satisfied when all tasks it submitted can be processed. We design a generalized dynamic dominant resource fairness mechanism, and develop a combinatorial algorithm to find a fair allocation. Experimental results show that the solution produced by the proposed mechanism is close to the optimal solution.

关键词： Cloud computing dominant resource fairness dynamic multi-resource fair allocation combinatorial algorithm

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Recurrent-and-Parallel Computing in the Problem of Vector Autoregressive Modelling 12

Recurrent-and-Parallel Computing in the Problem of Vector Au...

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12th International Scientific and Technical Conference on Computer Sciences and Information Technologies (CSIT)

作者： Yefimenko, Serhiy Int Res & Training Ctr Informat Technol & Syst Dept Informat Technol Induct Modelling Kiev Ukraine

ISBN: (纸本)9781538616390

The paper presents theoretical grounds of recurrent-and-parallel computing applying in combinatorial GMDH algorithm for modeling and prediction of complex multidimensional interrelated processes in the class of vector autoregressive models. The effectiveness of the constructed algorithm is demonstrated by modeling of interrelated processes in the field of Ukraine energy sphere with the purpose of effective managerial decision making.

关键词： VAR inductive modelling GMDH combinatorial algorithm recurrent-and-parallel computing

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Three-strand pretzel knots, knot Floer homology and concordance invariants

Three-strand pretzel knots, knot Floer homology and concorda...

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作者： Waite, Daniel University of Glasgow

学位级别：博士

This thesis is concerned with determining the knot Floer homology and concordance invariants of pretzel knots, in particular three-strand pretzel knots. Knot Floer homology is a package of knot invariants developed by Ozsvath and Szabo, and despite the invariants being known for simple classes of knots --- for example quasi-alternating, two-bridge and L-space knots --- there are still many simple families for which knot Floer homology and the associated concordance invariants are not known. Recent work by Ozsvath-Szabo developed a construction of an algebraic invariant C(D), conjectured by them to be equal to a variant of knot Floer homology. This complex is a bigraded, bifiltered chain complex whose filtered chain homotopy type is an invariant of a knot. Their construction --- which has also been implemented in a C++ program -- is a divide and conquer method which decomposes knot diagrams in a certain form into smaller pieces, to which algebraic objects are then associated. These algebraic objects are themselves invariants (up to appropriate equivalence) of partial knot diagrams, and are pieced together to form the full invariant. As with classical knot Floer homology, one can study the homology of this complex C(D), or the homology of subcomplexes and quotient complexes, which are also invariants of a knot. Even more recent work of Ozsvath and Szabo confirms that this conjectured equivalence between the theories holds. Hence, like the well-known grid homology of a knot, this algebraic method provides a combinatorial construction of knot Floer homology --- or in this case some slightly modified version of classical knot Floer homology, like that presented by Dai-Hom-Stroffregen-Truong. The benefit of such combinatorial constructions is that they do not rely on computation of the counts of pseudo-holomorphic representatives of Whitney disks in some high-dimensional space, unlike classical knot Floer homology. The grid homology developed by Manolescu-Ozsvath-Sarkar h

关键词： Knot Floer Homology Pretzel knots Algebraic invariant Bordered invariants combinatorial algorithm Divide and conquer Heegaard diagrams

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A Note on the Stable Marriage Problem

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SN Computer Science 2020年第2期1卷 1-4页

作者： Zivkovic, Dejan Faculty of Informatics and Computing Singidunum University Belgrade Serbia

Since the pioneering work of Gale and Shapley, the stable marriage problem has received wide treatment by researchers due to its elegance and applicability. The original problem has been generalized and well studied from different angles, and many algorithms have been proposed for the solution of many variants of the traditional formulation. This short note tries to shed some more light on the original algorithm by providing a more direct proof of its correctness. © 2020, Springer Nature Singapore Pte Ltd.

关键词： combinatorial algorithm Gale–Shapley algorithm Matching problem Stable marriage problem

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Quantifying Blocks World State Space

Quantifying Blocks World State Space

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2020 International Conference on INnovations in Intelligent SysTems and Applications, INISTA 2020

作者： Badicc, Amelia Bcdicc, Costin Buligiu, Ion Ciora, Liviu Ion Petcusin, Felix University of Craiova Dept. of Statistics and Business Informatics Craiova Romania

ISBN: (纸本)9781728167992

Blocks World is a prototype artificial intelligence problem used to exemplify problem solving using searching and planning algorithms. In this paper we present and experimentally evaluate combinatorial algorithms for measuring the size of the search graph associated to this problem. We focus on evaluating exactly a few metrics on the Blocks World state space graph, including the number of states, the average number of stacks per state, the number of transitions, and the average branching factor. © 2020 IEEE.

关键词： blocks world combinatorial algorithm state space graph

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A simple MAX-CUT algorithm for planar graphs 8

A simple MAX-CUT algorithm for planar graphs

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8th Cologne-Twente Workshop on Graphs and combinatorial Optimization, CTW 2009

作者： Liers, F. Pardella, G. Institut für Informatik Universität zu Köln Pohligstraße 1 KölnD-50969 Germany

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On Asymptotic Properties of the GMDH Criteria 14

On Asymptotic Properties of the GMDH Criteria

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14th IEEE International Scientific and Technical Conference on Computer Sciences and Information Technologies, CSIT 2019

作者： Stepashko, Volodymyr International Research and Training Center for Information Technologies and Systems Department for Information Technologies of Inductive Modelling Kyiv Ukraine

ISBN: (纸本)9781728108063

The paper analyses the problem of the convergence investigation for typical GMDH criteria based on the data sample division into two subsamples. This study is significant for additional justification of applying the GMDH-based inductive modeling in case of large samples. The inductive modeling problem is defined and main external criteria are presented. An approach to the asymptotic investigations is explained based on assumptions of strong regularity of regressors. The study results demonstrate the convergence of any external criterion to some finite values in probability. Moreover, the minimal value of an accuracy criterion at infinity corresponds to the true model. This means that such criteria are consistent. © 2019 IEEE.

关键词： combinatorial algorithm GMDH inductive modeling multistage algorithm recurrent computations successive search

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