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RECASTING algorithmS TO ENCOURAGE REUSE (VOL 11, PG 80, 1994)

IEEE SOFTWARE 1994年第6期11卷 4-4页

作者： WEIDE, BW OGDEN, WF Ohio State Uinversity USA

Instead of viewing algorithms as single large operations, the authors use a machine-oriented view to show how they can be viewed as collections of smaller objects and operations. Their approach promises more flexibility especially in making performance trade-offs, and encourages black-box reuse. They recommend black-box reuse because the real value of reused code lies in its properties, such as correctness with respect to an abstract specification. If you make even small structural or environmental changes, the confidence in these properties tends to evaporate, and with it most of the component\'s value. They show how to design an entire category of more flexible black-box reusable software components by applying a general design technique that recasts algorithms as objects. To illustrate the technique, they recast a sorting algorithm and a spanning-forest algorithm into objects.

关键词： accuracy class confidence algorithms recasting editing sorting algorithm

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Stochastic analysis of shell sort

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algorithmICA 2001年第3期31卷 442-457页

作者： Smythe, RT Wellner, J Oregon State Univ Dept Stat Corvallis OR 97331 USA Univ Washington Dept Stat Seattle WA 98195 USA

We analyze the Shell Sort algorithm under the usual random permutation model. Using empirical distribution functions, we recover Louchard's result that the running time of the 1-stage of (2, 1)-Shell Sort has a limiting distribution given by the area under the absolute Brownian bridge. The analysis extends to (h, 1)Shell Sort where we find a limiting distribution given by the sum of areas under correlated absolute Brownian bridges. A variation of (h, 1)-Shell Sort which is slightly more efficient is presented and its asymptotic behavior analyzed.

关键词： empirical distribution functions Brownian bridge sorting algorithm random permutation model asymptotic distribution

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Engineering faster sorters for small sets of items

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SOFTWARE-PRACTICE & EXPERIENCE 2021年第5期51卷 965-1004页

作者： Bingmann, Timo Marianczuk, Jasper Sanders, Peter Karlsruhe Inst Technol Inst Theoret Informat Fasanengarten 5 D-76131 Karlsruhe Germany

sorting a set of items is a task that can be useful by itself or as a building block for more complex operations. That is why a lot of effort has been put into finding sorting algorithms that sort large sets as efficiently as possible. But the more sophisticated and complex the algorithms become, the less efficient they are for small sets of items due to large constant factors. A relatively simple sorting algorithm that is often used as a base case sorter is insertion sort, because it has small code size and small constant factors influencing its execution time. We aim to determine if there is a faster way to sort small sets of items to provide an efficient base case sorter. We looked at sorting networks, at how they can improve the speed of sorting few elements, and how to implement them in an efficient manner using conditional moves. Since sorting networks need to be implemented explicitly for each set size, providing networks for larger sizes becomes less efficient due to increased code sizes. To also enable the sorting of slightly larger base cases, we adapted sample sort to Register Sample Sort, to break down those larger sets into sizes that can in turn be sorted by sorting networks. From our experiments we found that when sorting only small sets of integers, the sorting networks outperform insertion sort by a factor of at least 1.76 for any array size between six and 16, and by a factor of 2.72 on average across all machines and array sizes. When integrating sorting networks as a base case sorter into Quicksort, we achieved far less performance improvements over using insertion sort, which is probably due to the networks having a larger code size and cluttering the L1 instruction cache. The same effect occurs when including Register Sample Sort as a base case sorter for IPS4o. But for x86 machines that have a larger L1 instruction cache of 64 KiB or more, we obtained speedups of 12.7% when using sorting networks as a base case sorter in std::sort, and of 5%-6

关键词： base case sorting sample sort sorter sorting sorting algorithm sorting networks

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LiCABEDS II. Modeling of Ligand Selectivity for G-Protein-Coupled Cannabinoid Receptors

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JOURNAL OF CHEMICAL INFORMATION AND MODELING 2013年第1期53卷 11-26页

作者： Ma, Chao Wang, Lirong Yang, Peng Myint, Kyaw Z. Xie, Xiang-Qun Univ Pittsburgh Sch Pharm Dept Pharmaceut Sci Computat Chem Genom Screening Ctr Pittsburgh PA 15260 USA Univ Pittsburgh Dept Computat & Syst Biol Pittsburgh PA 15260 USA Univ Pittsburgh Ctr Chem Methodol & Lib Dev UPCMLD Pittsburgh PA 15260 USA Univ Pittsburgh Drug Discovery Inst Pittsburgh PA 15260 USA

The cannabinoid receptor subtype 2 (CB2) is a promising therapeutic target for blood cancer, pain relief, osteoporosis, and immune system disease. The recent withdrawal of Rimonabant, which targets another closely related cannabinoid receptor (CB1), accentuates the importance of selectivity for the development of CB2 ligands in order to minimize their effects on the CB1 receptor. In our previous study, LiCABEDS (Ligand Classifier of Adaptively Roosting Ensemble Decision Stumps) was reported as a generic ligand classification algorithm for the prediction of categorical molecular properties. Here, we report extension of the application of LiCABEDS to the modeling of cannabinoid ligand selectivity with molecular fingerprints as descriptors. The performance of LiCABEDS was systematically compared with another popular classification algorithm, support vector machine (SVM), according to prediction precision and recall rate. In addition, the examination of LiCABEDS models revealed the difference in structure diversity of CB1 and CB2 selective ligands. The structure determination from data mining could be useful for the design of novel cannabinoid lead compounds. More importantly, the potential of LiCABEDS was demonstrated through successful identification of newly synthesized CB2 selective compounds.

关键词： selectivity Modeling Receptors, Cannabinoid Retrieval recall Cannabinoids cannabinoid 1 receptor CNR1 gene ligands CNR2 gene rimonabant sorting algorithm

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A framework for Kernel-based multi-category classification

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JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH 2007年第0期30卷 525-564页

作者： Hill, Simon I. Doucet, Arnaud Univ Cambridge Dept Engn Cambridge CB2 1PZ England Univ British Columbia Dept Stat Vancouver BC V6T 1W5 Canada Univ British Columbia Dept Comp Sci Vancouver BC V6T 1W5 Canada

A geometric framework for understanding multi-category classification is introduced, through which many existing 'all-together' algorithms can be understood. The structure enables parsimonious optimisation, through a direct extension of the binary methodology. The focus is on Support Vector Classification, with parallels drawn to related methods. The ability of the framework to compare algorithms is illustrated by a brief discussion of Fisher consistency. Its utility in improving understanding of multi-category analysis is demonstrated through a derivation of improved generalisation bounds. It is also described how this architecture provides insights regarding how to further improve on the speed of existing multi-category classification algorithms. An initial example of how this might be achieved is developed in the formulation of a straightforward multi-category Sequential Minimal Optimisation algorithm. Proof-of-concept experimental results have shown that this, combined with the mapping of pairwise results, is comparable with benchmark optimisation speeds.

关键词： ARCHITECTURE sorting algorithm derivation Building construction Cohort Analysis Frameworks algorithms Optimization algorithms

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A BENCHMARK PARALLEL SORT FOR SHARED MEMORY MULTIPROCESSORS

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IEEE TRANSACTIONS ON COMPUTERS 1988年第12期37卷 1619-1626页

作者： FRANCIS, RS MATHIESON, ID Dept. of Comput. Sci. La Trobe Univ. Bundoora Vic. Australia

The first parallel sort algorithm for shared memory MIMD (multiple-instruction-multiple-data-stream) multiprocessors that has a theoretical and measured speedup near linear is exhibited. It is based on a novel asynchronous parallel merge that evenly partitions data to be merged among any number of processors. A benchmark sorting algorithm is proposed that uses this merge to remove the linear time bottleneck inherent in previous multiprocessors sorts. This sort, when applied to data set on p processors, has a time complexity of O((n log n)/p)+O((n log p)/p) and a space complexity of 2n, where n is the number of keys being sorted. Evaluations of the merge and benchmark sort algorithms on a 12-processor Sequent Balance 21000 System demonstrate near-linear speedup when compared to sequential Quicksort.

关键词： shared memory sorting algorithm Multiprocessor BENCHMARKS Keys complexity classes Parallel Lines space complexities Speeding merger sorting programs

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Development of a semi-implicit solver for detailed chemistry in internal combustion engine simulations

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JOURNAL OF ENGINEERING FOR GAS TURBINES AND POWER-TRANSACTIONS OF THE ASME 2007年第1期129卷 271-278页

作者： Liang, Long Kong, Song-Charng Jung, Chulhwa Reitz, Rolf D. Univ Wisconsin Engine Res Ctr Madison WI 53706 USA

An efficient semi-implicit numerical method is developed for solving the detailed chemical kinetic source terms in internal combustion (IC) engine simulations. The detailed chemistry system forms a group of coupled staff ordinary differential equations (ODEs), which presents a very stringent time-step limitation when solved by standard explicit methods, and is computationally expensive when solved by iterative implicit methods. The present numerical solver uses a stiffly stable noniterative semi-implicit method. The formulation of numerical integration exploits the physical requirement that the species density and specific internal energy in the computational cells must be non-negative, so that the Lipschitz time-step constraint is not present and the computation time step can be orders of magnitude larger than that possible in standard explicit methods. The solver exploits the characteristics of the stiffness of the ODEs by using a sequential sort algorithm that ranks an approximation to the dominant eigenvalues of the system to achieve maximum accuracy. Subcycling within the chemistry solver routine is applied for each computational cell in engine simulations, where the subcycle time step is dynamically determined by monitoring the rate of change of concentration of key species, which have short characteristic time scales and are also important to the chemical heat release. The chemistry solver is applied in the KIVA-3V code to diesel engine simulations. Results are compared to those using the CHEMKIN package, which uses the VODE implicit solver Good agreement was achieved for a wide range of engine operating conditions, and 40-70% CPU time savings were achieved by the present solver compared to the standard CHEMKIN.

关键词： Internal energy Solvers sorting algorithm Nonnegative Population density computational time CPU time Ordinary differential equation simulating gasoline engine Chemistry

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GA(M)E-QSAR: A Novel, Fully Automatic Genetic-algorithm-(Meta)-Ensembles Approach for Binary Classification in Ligand-Based Drug Design

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JOURNAL OF CHEMICAL INFORMATION AND MODELING 2012年第9期52卷 2366-2386页

作者： Perez-Castillo, Yunierkis Lazar, Cosmin Taminau, Jonatan Froeyen, Mathy Angel Cabrera-Perez, Miguel Nowe, Ann Vrije Univ Brussel Fac Sci Dept Comp Sci Computat Modeling Lab CoMo B-1050 Brussels Belgium Univ Cent Marta Abreu Villas Ctr Bioact Quim Mol Simulat & Drug Design Grp Santa Clara Cuba Katholieke Univ Leuven Rega Inst Med Res Med Chem Lab B-3000 Louvain Belgium Univ Miguel Hernandez Fac Pharm Dept Engn Pharm & Pharmaceut Technol Area Alicante 03550 Spain

Computer-aided drug design has become an important component of the drug discovery process. Despite the advances in this field, there is not a unique modeling approach that can be successfully applied to solve the whole range of problems faced during QSAR modeling. Feature selection and ensemble modeling are active areas of research in ligand-based drug design. Here we introduce the GA(M)E-QSAR algorithm that combines the search and optimization capabilities of Genetic algorithms with the simplicity of the Adaboost ensemble-based classification algorithm to solve binary classification problems. We also explore the usefulness of Meta-Ensembles trained with Adaboost and Voting schemes to further improve the accuracy, generalization, and robustness of the optimal Adaboost Single Ensemble derived from the Genetic algorithm optimization. We evaluated the performance of our algorithm using five data sets from the literature and found that it is capable of yielding similar or better classification results to what has been reported for these data sets with a higher enrichment of active compounds relative to the whole actives subset when only the most active chemicals are considered. More important, we compared our methodology with state of the art feature selection and classification approaches and found that it can provide highly accurate, robust, and generalizable models. In the case of the Adaboost Ensembles derived from the Genetic algorithm search, the final models are quite simple since they consist of a weighted sum of the output of single feature classifiers. Furthermore, the Adaboost scores can be used as ranking criterion to prioritize chemicals for synthesis and biological evaluation after virtual screening experiments.

关键词： FULL-SCALE sorting algorithm chemical compounds Searches Binary useful area Drug Design weight sums Feature extraction Genetic algorithm (GA) Robustness

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MODELLING AND OPTIMISATION OF VACUUM COLLECTION SYSTEM FOR CRUISE SHIP KITCHEN GARBAGE

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POLISH MARITIME RESEARCH 2020年第1期27卷 152-161页

作者： Du Jun Li Ruonan Wu Xin Zhao Hang Jiangsu Univ Sci & Technol 2 Mengxi Rd Zhenjiang 212003 Jiangsu Peoples R China

Pollution of the marine environment by ship garbage is an urgent problem to be solved at home and abroad. The ship kitchen garbage vacuum collection system is a new environmental protection scheme for garbage disposal. It has many advantages, such as using a pipeline instead of manual operation, creating high-level sanitary conditions, realising completely closed garbage collection and transportation, eliminating cross-pollution, saving space and so on. In this paper, the system is modelled, and the calculation of pipeline pressure loss, the vacuum degree of the vacuum tank and the energy consumption of the system are briefly introduced. In order to reduce the energy consumption, an algorithm for the emptying and discharging port is presented. In order to solve the problem of optimising relevant parameters, the vacuum transport mechanism of garbage is studied based on an optimisation model of the pipe network, and the experimental platform of a simulation device is set up. In engineering, this is of great significance to the design of cruise ship garbage collection and treatment systems and the development of supporting technology.

关键词： Kitchen waste vacuum collection System modeling sorting algorithm Model experiment

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TRANSITIVE ORIENTATIONS OF GRAPHS: 收藏
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引用; SIAM JOURNAL ON COMPUTING 1988年第6期17卷 1119-1133页; 作者： BOLLOBAS, B BRIGHTWELL, G Univ of Cambridge United Kingdom; Suppose that we have a set X of n objects in some unknown total order << . For G a graph on X, we ask, for each edge <span class="mrow" id="MathJax-Span; Suppose that we have a set X of n objects in some unknown total order $<$ . For G a graph on X, we ask, for each edge $x y$; 来源：评论; 学校读者我要写书评

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