Code Generation = A* + BURS

A system called BURS that is based on term rewrite systems and a search algorithm A* are combined to produce a code generator that generates optimal code. The theory underlying BURS is re-developed, formalised and explained in this work. The search algorithm uses a cost heuristic that is derived from the termrewrite system to direct the search. The advantage of using a search algorithm is that we need to compute only those costs that may be part of an optimal rewrite sequence

IMPROVING BWA-MEM WITH GPU PARALLEL COMPUTING

Due to the many advances made in designing algorithms, especially the ones used in bioinformatics, it is becoming harder and harder to improve their efficiencies. Therefore, hardware acceleration using General-Purpose computing on Graphics Processing Unit has become a popular choice. BWA-MEM is an important part of the BWA software package for sequence mapping. Because of its high speed and accuracy, we choose to parallelize the popular short DNA sequence mapper. BWA has been a prevalent single node tool in genome alignment, and it has been widely studied for acceleration for a long time since the first version of the BWA package came out. This thesis presents the Big Data GPGPU distributed BWA-MEM, a tool that combines GPGPU acceleration and distributed computing. The four hardware parallelization techniques used are CPU multi-threading, GPU paralleled, CPU distributed, and GPU distributed. The GPGPU distributed software typically outperforms other parallelization versions. The alignment is performed on a distributed network, and each node in the network executes a separate GPGPU paralleled version of the software. We parallelize the chain2aln function in three levels. In Level 1, the function ksw\_extend2, an algorithm based on Smith-Waterman, is parallelized to handle extension on one side of the seed. In Level 2, the function chain2aln is parallelized to handle chain extension, where all seeds within the same chain are extended. In Level 3, part of the function mem\_align1\_core is parallelized for extending multiple chains. Due to the program's complexity, the parallelization work was limited at the GPU version of ksw\_extend2 parallelization Level 3. However, we have successfully combined Spark with BWA-MEM and ksw\_extend2 at parallelization Level 1, which has shown that the proposed framework is possible. The paralleled Level 3 GPU version of ksw\_extend2 demonstrated noticeable speed improvement with the test data set

Sensitivity of Nonrenormalizable Trajectories to the Bare Scale

Working in scalar field theory, we consider RG trajectories which correspond to nonrenormalizable theories, in the Wilsonian sense. An interesting question to ask of such trajectories is, given some fixed starting point in parameter space, how the effective action at the effective scale, Lambda, changes as the bare scale (and hence the duration of the flow down to Lambda) is changed. When the effective action satisfies Polchinski's version of the Exact Renormalization Group equation, we prove, directly from the path integral, that the dependence of the effective action on the bare scale, keeping the interaction part of the bare action fixed, is given by an equation of the same form as the Polchinski equation but with a kernel of the opposite sign. We then investigate whether similar equations exist for various generalizations of the Polchinski equation. Using nonperturbative, diagrammatic arguments we find that an action can always be constructed which satisfies the Polchinski-like equation under variation of the bare scale. For the family of flow equations in which the field is renormalized, but the blocking functional is the simplest allowed, this action is essentially identified with the effective action at Lambda = 0. This does not seem to hold for more elaborate generalizations.Comment: v1: 23 pages, 5 figures, v2: intro extended, refs added, published in jphy

Combinatorics on Words. New Aspects on Avoidability, Defect Effect, Equations and Palindromes

In this thesis we examine four well-known and traditional concepts of combinatorics on words. However the contexts in which these topics are treated are not the traditional ones. More precisely, the question of avoidability is asked, for example, in terms of k-abelian squares. Two words are said to be k-abelian equivalent if they have the same number of occurrences of each factor up to length k. Consequently, k-abelian equivalence can be seen as a sharpening of abelian equivalence. This fairly new concept is discussed broader than the other topics of this thesis. The second main subject concerns the defect property. The defect theorem is a well-known result for words. We will analyze the property, for example, among the sets of 2-dimensional words, i.e., polyominoes composed of labelled unit squares. From the defect effect we move to equations. We will use a special way to define a product operation for words and then solve a few basic equations over constructed partial semigroup. We will also consider the satisfiability question and the compactness property with respect to this kind of equations. The final topic of the thesis deals with palindromes. Some finite words, including all binary words, are uniquely determined up to word isomorphism by the position and length of some of its palindromic factors. The famous Thue-Morse word has the property that for each positive integer n, there exists a factor which cannot be generated by fewer than n palindromes. We prove that in general, every non ultimately periodic word contains a factor which cannot be generated by fewer than 3 palindromes, and we obtain a classification of those binary words each of whose factors are generated by at most 3 palindromes. Surprisingly these words are related to another much studied set of words, Sturmian words.Siirretty Doriast

Determining The Word Processing Software to Meet the Needs of The Business User

Computerized word processing with computer software packages is common throughout industry today. However, selection of the appropriate software is a complicated procedure and requires a careful examination and comparison of the complexity of the software (features available) with the ease of learning to use the software. With the wide variety of products that run on IBM PC\u27s and the IBM compatibles, it is possible that the business manager can find one that adequately fills both needs. When selecting an appropriate word processing software package, one must first determine how the product will be used so that the purchaser can weigh the advantages and disadvantages of easy versus powerful packages and come up with an adequate compromise. Some of the easier-to-use programs can make great learning tools, especially for computer novices. They also work nicely if the major word processing application is the production of short letters and memos. However, if the user is expected to do a great deal of tabular typing or produce hundreds of form letters or many long reports, the business might be better off sacrificing some of those user-friendly features in favor of powerful capabilities that will make these tasks easier. On long reports, for example, production goes faster with software that automatically writes tables of contents and indexes, and numbers, chapters and lists. The decisions involved in selecting an appropriate word processing software package often revolve around how long a learning curve the business can_ afford and which sophisticated features are needed. Some of the more powerful packages require extensive training and practice before users can use then competently and with efficiency. The friendlier packages save learning time, but in the long run might cost time because they do not automate many production tasks. Another ease-of-use feature is the quality and organization of the software instruction manuals. Some manuals explain in detail how to use the program; others just list the features of the program. Most of the documentation included with software packages could use improvement. For many buyers, availability of features ranks higher than ease-of-use. In this study the word processing g software packages were evaluated, and a comparison was done to determine which features were available from a list of more than three hundred features, reporting and foreign language ability. including scientific No word processing software package does everything, and those. that do many things often have a variety of weaknesses. Since packages with more features are more complicated to use, the purchaser is wise to buy software which contains only the features the users will needs. In addition, it is always wise to insist on a demonstration of the needed features before purchasing. Balancing ease-of-use and power of word processing software packages is a continuing process. This study\u27 s goal is to make the selection of computer programs for individuals and business firms more efficient because they can now see an evaluation and comparison. Of the different programs available

Tropical polar cones, hypergraph transversals, and mean payoff games

We discuss the tropical analogues of several basic questions of convex duality. In particular, the polar of a tropical polyhedral cone represents the set of linear inequalities that its elements satisfy. We characterize the extreme rays of the polar in terms of certain minimal set covers which may be thought of as weighted generalizations of minimal transversals in hypergraphs. We also give a tropical analogue of Farkas lemma, which allows one to check whether a linear inequality is implied by a finite family of linear inequalities. Here, the certificate is a strategy of a mean payoff game. We discuss examples, showing that the number of extreme rays of the polar of the tropical cyclic polyhedral cone is polynomially bounded, and that there is no unique minimal system of inequalities defining a given tropical polyhedral cone.Comment: 27 pages, 6 figures, revised versio

A Tutorial on Algol 68

This paper is an introduction to the main features of ALGOL 68, emphasizing the novel features not found in many other programming languages. The topics, data types (modes), type conversion (coercion), generalized expressions (units), procedures, operators, the standard prelude, and input/output, form the basis of the paper. Th