On the Combinatorics of Rooted Binary Phylogenetic Trees

We study subtree-prune-and-regraft (SPR) operations on leaf-labelled rooted binary trees, also known as rooted binary phylogenetic trees. This study is motivated by the problem of graphically representing evolutionary histories of biological sequences subject to recombination. We investigate some basic properties of the induced SPR-metric on the space of leaf-labelled rooted binary trees with n leaves. In contrast to the case of unrooted trees, the number |U(T)| of trees in which are one SPR operation away from a given tree depends on the topology of T. In this paper, we construct recursion relations which allow one to determine the unit-neighbourhood size |U(T)| efficiently for any tree topology. In fact, using the recursion relations we are able to derive a simple closed-form formula for the unit-neighbourhood size. As a corollary, we construct sharp upper and lower bounds on the size of unit-neighbourhoods and investigate the diameter of . Lastly, we consider an enumeration problem relevant to population genetics.AMS Subject Classification: 05C05, 92D15.     

On the Semigroup Algebra of Binary Relations

The semigroup of binary relations on {1,…, n} with the relative product is isomorphic to the semigroup B _n of n × n zero-one matrices with the Boolean matrix product. Over any field F, we prove that the semigroup algebra FB _n contains an ideal K _n of dimension (2 ⁿ  ? 1)², and we construct an explicit isomorphism of K _n with the matrix algebra M _{2 ⁿ ?1}(F).     

On Minimal Coalgebras

We define an out-degree for F-coalgebras and show that the coalgebras of outdegree at most κ form a covariety. As a subcategory of all F-coalgebras, this class has a terminal object, which for many problems can stand in for the terminal F-coalgebra, which need not exist in general. As examples, we derive structure theoretic results about minimal coalgebras, showing that, for instance minimization of coalgebras is functorial, that products of finitely many minimal coalgebras exist and are given by their largest common subcoalgebra, that minimal subcoalgebras have no inner endomorphisms and show how minimal subcoalgebras can be constructed from Moore-automata. Since the elements of minimal subcoalgebras must correspond uniquely to the formulae of any logic characterizing observational equivalence, we give in the last section a straightforward and self-contained account of the coalgebraic logic of D. Pattinson and L. Schröder, which we believe is simpler and more direct than the original exposition.     

Classically complete modal relevant logics

A variety of modal logics based on the relevant logic R are presented. Models are given for each of these logics and completeness is shown. It is also shown that each of these logics admits Ackermann's rule γ and as a corollary of this it is proved that each logic is a conservative extension of its counterpart based on classical logic, hence we call them “classically complete”. MSC: 03B45, 03B46.     

符号和数值混合计算

符号计算和数值计算是两种不同的解决科学和技术发展中问题的计算方法.符号计算可以得到问题精确的完备解,但是计算量大且表达形式往往十分庞大;数值计算可以快速地处理很多实际应用中的问题,但是一般只能得到近似的局部解.特别地,数值计算处理病态问题时,收敛往往较慢且容易出错.着重介绍了符号计算和数值计算之间的密切联系,以及如何运用这两大领域的最新研究成果,探索和开发符号和数值混合计算算法和软件,使之兼备符号计算的完备化和数值计算的高效性.     

A simple bijection between a subclass of 2-binary trees and ternary trees

A bijection between binary trees, with nodes labelled black or white, and a black node never having a white right child, and ternary trees is given. It is simpler than another bijection that has recently appeared in this journal.     

Realizations and LP

LP can be seen as a logic of knowledge with justifications. See [S. Artemov, The logic of justification, The Review of Symbolic Logic 1 (4) (2008) 477–513] for a recent comprehensive survey of justification logics generally. Artemov’s Realization Theorem says justifications can be extracted from validities in the more conventional Hintikka-style logic of knowledge S4, in which they are not explicitly present. Justifications, however, are far from unique. There are many ways of realizing each theorem of S4 in the logic LP. If the machinery of justifications is to be applied to artificial intelligence, or better yet, to everyday reasoning, we will need to work with whatever justifications we may have at hand—one version may not be interchangeable with another, even though they realize the same S4 formula. In this paper we begin the process of providing tools for reasoning about justifications directly. The tools are somewhat complex, but in retrospect this should not be surprising. Among other things, we provide machinery for combining two realizations of the same formula, and for replacing subformulas by equivalent subformulas. (The second of these is actually weaker than just stated, but this is not the place for a detailed formulation.) The results are algorithmic in nature—semantics for LP plays no role. We apply our results to provide a new algorithmic proof of Artemov’s Realization Theorem itself. This paper is a much extended version of [M.C. Fitting, Realizations and LP, in: S. Artemov, A. Nerode (Eds.), Logical Foundations of Computer Science—New York ’07, in: Lecture Notes in Computer Science, vol. 4514, Springer-Verlag, 2007, pp. 212–223].     

On the allocation of binary trees to secondary storage

Two paging techniques proposed by Muntz and Uzgalis to store a binary tree in secondary storage are considered. The first method (sequential allocation) is the basic allocation technique and here an exact formula is given, to be considered as a touchstone for every other method. Then a modification to the second method (grouped allocation) is proposed which gains control on storage utilization. This allows the structure to maintain both a high loading factor and a low retrieving time.     

On the Computation of Square Roots in Finite Fields

In this paper, two improvements for computing square roots in finite fields are presented. Firstly, we give a simple extension of a method by O. Atkin, which requires two exponentiations in FM _q , when q9 mod 16. Our second method gives a major improvement to the Cipolla–Lehmer algorithm, which is both easier to implement and also much faster. While our method is independent of the power of 2 in q–1, its expected running time is equivalent to 1.33 as many multiplications as exponentiation via square and multiply. Several numerical examples are given that show the speed-up of the proposed methods, compared to the routines employed by Mathematica, Maple, respectively Magma.     

Binary group and Chinese postman polyhedra

A new proof of the characterization of the Chinese postman polyhedra is given. In developing this proof, a theorem of Gomory about homomorphic lifting of facets for group polyhedra is generalized to subproblems. Some results for the Chinese postman problem are generalized to binary group problems. In addition, a connection is made between Fulkerson's blocking polyhedra and a blocking pair of binary group problems. A connection is also developed between minors and lifting of facets for group problems.     

Binary fuzzy goal programming

Goal programming is an important technique for solving many decision/management problems. Fuzzy goal programming involves applying the fuzzy set theory to goal programming, thus allowing the model to take into account the vague aspirations of a decision-maker. Using preference-based membership functions, we can define the fuzzy problem through natural language terms or vague phenomena. In fact, decision-making involves the achievement of fuzzy goals, some of them are met and some not because these goals are subject to the function of environment/resource constraints. Thus, binary fuzzy goal programming is employed where the problem cannot be solved by conventional goal programming approaches. This paper proposes a new idea of how to program the binary fuzzy goal programming model. The binary fuzzy goal programming model can then be solved using the integer programming method. Finally, an illustrative example is included to demonstrate the correctness and usefulness of the proposed model.     

薄壁结构动力计算中若干问题

本文讨论薄板和薄壳之类的薄壁结构受冲击荷载作用时的动力计算问题.主要是求动力因数.在计算中考虑了冲击物和被冲击的薄壁结构系统质量的影响;用相当质量法将薄壁结构的分布质量转化为只有一个集中的相当质量,从而导出薄壁结构系统在冲击力作用下的动力因数,计算比较方便.     

Bisimulations between generalized Veltman models and Veltman models

Interpretability logic is an extension of provability logic. Veltman models and generalized Veltman models are two semantics for interpretability logic. We consider a connection between Veltman semantics and generalized Veltman semantics. We prove that for a complete image‐finite generalized Veltman modelW there is a Veltman model W ′ that is bisimular to W. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

On Finite Model Property for Admissible Rules

Our investigation is concerned with the finite model property (fmp) with respect to admissible rules. We establish general sufficient conditions for absence of fmp w. r. t. admissibility which are applicable to modal logics containing K4: Theorem 3.1 says that no logic λ containing K4 with the co-cover property and of width > 2 has fmp w. r. t. admissibility. Surprisingly many, if not to say all, important modal logics of width > 2 are within the scope of this theorem–K4 itself, S4, GL, K4.1, K4.2, S4.1, S4.2, GL.2, etc. Thus the situation is completely opposite to the case of the ordinary fmp–the absolute majority of important logics have fmp, but not with respect to admissibility. As regards logics of width ≤ 2, there exists a zone for fmp w. r. t. admissibility. It is shown (Theorem 4.3) that all modal logics A of width ≤ 2 extending S4 which are not sub-logics of three special tabular logics (which is equipotent to all these λ extend a certain subframe logic defined over S4 by omission of four special frames) have fmp w.r.t. admissibility.     

An Infinitary Graded Modal Logic (Graded Modalities VI)

We prove a completeness theorem for K, the infinitary extension of the graded version K⁰ of the minimal normal logic K, allowing conjunctions and disjunctions of countable sets of formulas. This goal is achieved using both the usual tools of the normal logics with graded modalities and the machinery of the predicate infinitary logics in a version adapted to modal logic.     

On Optimal Forecasting with Soft Computation for Nonlinear Time Series

In this paper we present a new approach on optimal forecasting by using the fuzzy set theory and soft computing methods for the dynamic data analysis. This research is based on the concepts of fuzzy membership function as well as the natural selection of evolution theory. Some discussions in the sensitivity of the design of fuzzy processing will be provided. Through the design of genetic evolution, the AIC criteria is used as the adjust function, and the fuzzy memberships function of each gene model are calculated. Simulation and empirical examples show that our proposed forecasting technique can give an optimal forecasting in time series analysis.     

Hypersequent calculi for intuitionistic logic with classical atoms

We discuss a propositional logic which combines classical reasoning with constructive reasoning, i.e., intuitionistic logic augmented with a class of propositional variables for which we postulate the decidability property. We call it intuitionistic logic with classical atoms. We introduce two hypersequent calculi for this logic. Our main results presented here are cut-elimination with the subformula property for the calculi. As corollaries, we show decidability, an extended form of the disjunction property, the existence of embedding into an intuitionistic modal logic and a partial form of interpolation.     

A spatial modal logic with a location interpretation

A spatial modal logic (SML) is introduced as an extension of the modal logic S4 with the addition of certain spatial operators. A sound and complete Kripke semantics with a natural space (or location) interpretation is obtained for SML. The finite model property with respect to the semantics for SML and the cut‐elimination theorem for a modified subsystem of SML are also presented. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

二元响应模型的选择

本文在中、小样本试验数据下,研究响应模型的选择问题.文中给出了一个四参数分布族,变化其中两个参数的取值可以得到四种常见的响应分布模型.从而,将四种常见响应分布的选择问题,转化为该分布族的参数检验问题.