### Optimal Algorithms for Stabbing Polygons by Monotone Chains

"... In this paper we present optimal algorithms to compute monotone stabbers for convex polygons. More precisely, given a set of m convex polygons with n vertices in total we want to stab the polygons with an x-monotone polygonal chain such that each polygon is entered at its leftmost point and departed ..."

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In this paper we present optimal algorithms to compute monotone stabbers for convex polygons. More precisely, given a set of m convex polygons with n vertices in total we want to stab the polygons with an x-monotone polygonal chain such that each polygon is entered at its leftmost point and departed at its rightmost point. Since such a stabber does not exist in general, we study two related problems. In the first problem we want to compute a monotone stabber that stabs as many convex polygons as possible. The second problem is to compute the minimal number of x-monotone stabbers that are necessary to stab all given convex polygons. We present optimal O(m log m + n) algorithms for both problems. TOPICS: Computational Geometry, Algorithms and Data Structures. 1 Introduction Given a set of m objects, an object that intersects each of them is said to be a stabber or a traversal of the set. There have been many variations to the problem depending on the types of objects, as well as on the...

### Empirical Analysis of Algorithms is Easy (or is it?)

, 2001

"... In this paper I argue that empirical analysis is generally considered to be easy and thus not worth teaching or explaining but that it is in fact difficult and requires a place in our curricula. I then discuss how I planned to include coverage of this topic through lectures, discussions and practi ..."

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In this paper I argue that empirical analysis is generally considered to be easy and thus not worth teaching or explaining but that it is in fact difficult and requires a place in our curricula. I then discuss how I planned to include coverage of this topic through lectures, discussions and practical work and the approach that I took in the Honours Analysis of Algorithms topic at the University of the Witwatersrand in 2001. I report on what I feel are the successes and failures of the approach taken; discuss the results of a survey conducted on the Honours class; and suggest some improvements for 2002. 1

### The DSOL simulation suite/

"... The DSOL simulation suite Enabling multi-formalism simulation in a distributed context The DSOL simulation suite Enabling multi-formalism simulation in a distributed context PROEFSCHRIFT ter verkrijging van de graad van doctor ..."

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The DSOL simulation suite Enabling multi-formalism simulation in a distributed context The DSOL simulation suite Enabling multi-formalism simulation in a distributed context PROEFSCHRIFT ter verkrijging van de graad van doctor

### Budapest Preface

"... The purpose of our research is to enhance the efficiency of AI problem solvers by automating representation changes. We have developed a system that improves the description of input problems and selects an appropriate search algorithm for each given problem. Motivation. Researchers have accumulated ..."

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The purpose of our research is to enhance the efficiency of AI problem solvers by automating representation changes. We have developed a system that improves the description of input problems and selects an appropriate search algorithm for each given problem. Motivation. Researchers have accumulated much evidence on the importance of appropriate representations for the efficiency of AI systems. The same problem may be easy or difficult, depending on the way we describe it and on the search algorithm we use. Previous work on the automatic improvement of problem descriptions has mostly been limited to the design of individual learning algorithms. The user has traditionally been responsible for the choice of algorithms appropriate for a given problem. We present a system that integrates multiple description-changing and problem-solving algorithms. The purpose of the reported work is to formalize the concept of representation and to confirm the following hypothesis: An effective representation-changing system can be built from three parts:

### Implementing Deletion in B-Trees

"... This paper describes algorithms for key deletion in B-trees. There are published algorithms and pseu-docode for searching and inserting keys, but deletion, due to its greater complexity and perceived lesser im-portance, is glossed over completely or left as an ex-ercise to the reader. To remedy this ..."

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This paper describes algorithms for key deletion in B-trees. There are published algorithms and pseu-docode for searching and inserting keys, but deletion, due to its greater complexity and perceived lesser im-portance, is glossed over completely or left as an ex-ercise to the reader. To remedy this situation, we provide a well documented
owchart, algorithm, and pseudo-code for deletion, their relation to search and insertion algorithms, and a reference to a freely avail-able, complete B-tree library written in the C pro-gramming language. 1

### Data Structures and Algorithms

- IN ENCYLOPEDIA OF ELECTRICAL AND ELECTRONIC ENGINEERING, JOHN WILEY AND SONS.

"... In this article we provide an introduction to data structures and algorithms. We consider some basic data structures and deal with implementations of a dictionary and a priority queue. Algorithms for such basic problems as matrix multiplication, binary search, sorting, and selection are given. The c ..."

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In this article we provide an introduction to data structures and algorithms. We consider some basic data structures and deal with implementations of a dictionary and a priority queue. Algorithms for such basic problems as matrix multiplication, binary search, sorting, and selection are given. The concepts of randomized computing and parallel computing are also visited.

### Compression and Computational Gene Finding

"... Gene sequences in DNA are punctuated with regions of “junk ” that are not used during expression of the gene. Identifying these regions is a complex task and many computational techniques have been devised to solve the gene finding problem. DNA can be described as a sequence over an alphabet of four ..."

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Gene sequences in DNA are punctuated with regions of “junk ” that are not used during expression of the gene. Identifying these regions is a complex task and many computational techniques have been devised to solve the gene finding problem. DNA can be described as a sequence over an alphabet of four letters {A, G, C, T} and so a sequence can be considered as a text written in some language. Gene finding methods that use this linguistic approach have been very successful. This research investigated the feasibility of a linguistic approach based on compression. Compression algorithms have been successfully used in the linguistic analysis of human texts, including the differentiation between texts based on language and author. The useful and junk parts of a DNA sequence can be substantially different and can be viewed as two different languages. The research used a compression-based measure of entropy to attempt to differentiate between coding and non-coding regions in DNA sequences. Additionally, the same measure was used to compare genes from different families and parts of different species ’ genomes. The results show that the measure is unable to identify the often subtle variations in genomic data, preventing it from effectively discriminating between different types of DNA sequences. It is reasoned that the measure is not suited to genomic data in general and has limited applications

### Custom Computing for Phylogenetics: Exploring the Solution Space for UPGMA

"... There is great interest in the use of custom computing machines (CCMs) to accelerate the performance of existing, highly optimized software algorithms in Bioinformatics. But, like many applications for CCMs in the sciences, there are many architecture and experimentation “data points ” to be obtaine ..."

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There is great interest in the use of custom computing machines (CCMs) to accelerate the performance of existing, highly optimized software algorithms in Bioinformatics. But, like many applications for CCMs in the sciences, there are many architecture and experimentation “data points ” to be obtained before a solid understanding can be obtained as to the issues of migrating specialized scientific computing software applications to high-performance CCM platforms. This paper presents one such data point, namely, the design and comparative analysis of a custom computing application architecture for the UPGMA algorithm implemented on an FPGA-based platform. We present the UPGMA problem domain and explore design issues encountered in the transition from software algorithm executing on a standard PC platform to a hybrid custom compute “server ” running a VLSI logic-based architecture for the algorithm. Using the low-cost Annapolis WildCard ® platform, we discuss the CCM development method, and present an architecture created that takes into consideration the processing limitations of the platform. Given this implementation, we present results of experiments on system performance, as measured and compared against that of the benchmark UPGMA algorithm written in C, executing on a singleprocessor Pentium ® PC. 1.

### “thesis_main ” — 2005/11/21 — 13:09 — page ii — #2

"... ter verkrijging van de graad van Doctor aan de Universiteit Leiden, op gezag van de Rector Magnificus Dr. D. D. Breimer, hoogleraar in de faculteit der Wiskunde en Natuurwetenschappen en die der Geneeskunde, volgens besluit van het College voor Promoties te verdedigen op woensdag 18 januari 2006 klo ..."

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ter verkrijging van de graad van Doctor aan de Universiteit Leiden, op gezag van de Rector Magnificus Dr. D. D. Breimer, hoogleraar in de faculteit der Wiskunde en Natuurwetenschappen en die der Geneeskunde, volgens besluit van het College voor Promoties te verdedigen op woensdag 18 januari 2006 klokke 15:15 uur door

### door

"... proefschrift ter verkrijging van de graad van Doctor aan de Universiteit Leiden op gezag van de Rector Magnificus Dr. D.D. Breimer, hoogleraar in de faculteit der Wiskunde en Natuurwetenschappen en die der Geneeskunde, volgens besluit van het College voor Promoties te verdedigen op 15 mei 2006 te kl ..."

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proefschrift ter verkrijging van de graad van Doctor aan de Universiteit Leiden op gezag van de Rector Magnificus Dr. D.D. Breimer, hoogleraar in de faculteit der Wiskunde en Natuurwetenschappen en die der Geneeskunde, volgens besluit van het College voor Promoties te verdedigen op 15 mei 2006 te klokke 15.15 uur