Kai Salomaa

Bio: Kai Salomaa is an academic researcher from Queen's University. The author has contributed to research in topics: Regular language & Nondeterministic finite automaton. The author has an hindex of 28, co-authored 280 publications receiving 3379 citations. Previous affiliations of Kai Salomaa include University of Western Ontario & Natural Sciences and Engineering Research Council.

A sharpening of the Parikh mapping

Abstract: In this paper we introduce a sharpening of the Parikh map- ping and investigate its basic properties. The new mapping is based on square matrices of a certain form. The classical Parikh vector appears in such a matrix as the second diagonal. However, the matrix prod- uct gives more information about a word than the Parikh vector. We characterize the matrix products and establish also an interesting in- terconnection between mirror images of words and inverses of matrices. Mathematics Subject Classification. 68Q45, 68Q70.

State complexity of basic operations on finite languages

Abstract: The state complexity of basic operations on regular languages has been studied in [9,10,11]. Here we focus on finite languages. We show that the catenation of two finite languages accepted by an restate and an n-state DFA, respectively, with m > n is accepted by a DFA of (m - n + 3)2 n-2 - 1 states in the two-letter alphabet case, and this bound is shown to be reachable. We also show that the tight upper-bounds for the number of states of a DFA that accepts the star of an n-state finite language is 2-3 + 2 n-4 in the two-letter alphabet case. The same bound for reversal is 3.2 p-1 - 1 when n is even and 2 p - 1 when n is odd. Results for alphabets of an arbitrary size are also obtained. These upper-bounds for finite languages are strictly lower than the corresponding ones for general regular languages.

A formal study of practical regular expressions

Abstract: Regular expressions are used in many practical applications. Practical regular expressions are commonly called "regex". It is known that regex are different from regular expressions. In this paper, we give regex a formal treatment. We make a distinction between regex and extended regex; while regex represent regular languages, extended regex represent a family of languages larger than regular languages. We prove a pumping lemma for the languages expressed by extended regex. We show that the languages represented by extended regex are incomparable with context-free languages and a proper subset of context-sensitive languages. Other properties of the languages represented by extended regex are also studied.

Coverage control for mobile sensing networks

Abstract: This paper presents control and coordination algorithms for groups of vehicles. The focus is on autonomous vehicle networks performing distributed sensing tasks where each vehicle plays the role of a mobile tunable sensor. The paper proposes gradient descent algorithms for a class of utility functions which encode optimal coverage and sensing policies. The resulting closed-loop behavior is adaptive, distributed, asynchronous, and verifiably correct.

Tree Automata Techniques and Applications

Abstract: CONTENTS 7 Acknowledgments Many people gave substantial suggestions to improve the contents of this book. These are, in alphabetic order, Introduction During the past few years, several of us have been asked many times about references on finite tree automata. On one hand, this is the witness of the liveness of this field. On the other hand, it was difficult to answer. Besides several excellent survey chapters on more specific topics, there is only one monograph devoted to tree automata by Gécseg and Steinby. Unfortunately, it is now impossible to find a copy of it and a lot of work has been done on tree automata since the publication of this book. Actually using tree automata has proved to be a powerful approach to simplify and extend previously known results, and also to find new results. For instance recent works use tree automata for application in abstract interpretation using set constraints, rewriting, automated theorem proving and program verification, databases and XML schema languages. Tree automata have been designed a long time ago in the context of circuit verification. Many famous researchers contributed to this school which was headed by A. Church in the late 50's and the early 60's: B. Trakhtenbrot, Many new ideas came out of this program. For instance the connections between automata and logic. Tree automata also appeared first in this framework, following the work of Doner, Thatcher and Wright. In the 70's many new results were established concerning tree automata, which lose a bit their connections with the applications and were studied for their own. In particular, a problem was the very high complexity of decision procedures for the monadic second order logic. Applications of tree automata to program verification revived in the 80's, after the relative failure of automated deduction in this field. It is possible to verify temporal logic formulas (which are particular Monadic Second Order Formulas) on simpler (small) programs. Automata, and in particular tree automata, also appeared as an approximation of programs on which fully automated tools can be used. New results were obtained connecting properties of programs or type systems or rewrite systems with automata. Our goal is to fill in the existing gap and to provide a textbook which presents the basics of tree automata and several variants of tree automata which have been devised for applications in the aforementioned domains. We shall discuss only finite tree automata, and the …

Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings (Lecture Notes in Computer Science / Lecture Notes in Bioinformatics)

Abstract: Expression.- Spectral Clustering Gene Ontology Terms to Group Genes by Function.- Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.- Clustering Gene Expression Series with Prior Knowledge.- A Linear Time Biclustering Algorithm for Time Series Gene Expression Data.- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds.- Phylogeny.- A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem.- Computing the Quartet Distance Between Trees of Arbitrary Degree.- Using Semi-definite Programming to Enhance Supertree Resolvability.- An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree.- Pattern Identification in Biogeography.- On the Complexity of Several Haplotyping Problems.- A Hidden Markov Technique for Haplotype Reconstruction.- Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event.- Networks.- A Faster Algorithm for Detecting Network Motifs.- Reaction Motifs in Metabolic Networks.- Reconstructing Metabolic Networks Using Interval Analysis.- Genome Rearrangements.- A 1.375-Approximation Algorithm for Sorting by Transpositions.- A New Tight Upper Bound on the Transposition Distance.- Perfect Sorting by Reversals Is Not Always Difficult.- Minimum Recombination Histories by Branch and Bound.- Sequences.- A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds.- Generalized Planted (l,d)-Motif Problem with Negative Set.- Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).- The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity.- Multiple Structural RNA Alignment with Lagrangian Relaxation.- Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons.- Ortholog Clustering on a Multipartite Graph.- Linear Time Algorithm for Parsing RNA Secondary Structure.- A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance.- Structure.- Optimal Protein Threading by Cost-Splitting.- Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.- Rotamer-Pair Energy Calculations Using a Trie Data Structure.- Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity.- The Main Structural Regularities of the Sandwich Proteins.- Discovery of Protein Substructures in EM Maps.

Components of software development risk: how to address them? A project manager survey

Abstract: Software risk management can be defined as an attempt to formalize risk oriented correlates of development success into a readily applicable set of principles and practices. By using a survey instrument we investigate this claim further. The investigation addresses the following questions: 1) What are the components of software development risk? 2) how does risk management mitigate risk components, and 3) what environmental factors if any influence them? Using principal component analysis we identify six software risk components: 1) scheduling and timing risks, 2) functionality risks, 3) subcontracting risks, 4) requirements management, 5) resource usage and performance risks, and 6) personnel management risks. By using one-way ANOVA with multiple comparisons we examine how risk management (or the lack of it) and environmental factors (such as development methods, manager's experience) influence each risk component. The analysis shows that awareness of the importance of risk management and systematic practices to manage risks have an effect on scheduling risks, requirements management risks, and personnel management risks. Environmental contingencies were observed to affect all risk components. This suggests that software risks can be best managed by combining specific risk management considerations with a detailed understanding of the environmental context and with sound managerial practices, such as relying on experienced and well-educated project managers and launching correctly sized projects.