Dotplot: A Program for Exploring Self-Similarity in Millions of Lines of Text and Code

Abstract

An interactive program, dotplot, has been developed for browsing millions of lines of text and source code, using an approach borrowed from biology for studying homology (self-similarity) in DNA sequences. With conventional browsing tools such as a screen editor, it is difficult to identify structures that are too big to fit on the screen. In contrast, with dotplots we find that many of these structures show up as diagonals, squares, textures, and other visually recognizable features, as will be illustrated in examples selected from biology and two new application domains, text (AP news, Canadian Hansards) and source code (5ESS®). In an attempt to isolate the mechanisms that produce these features, we have synthesized similar features in dotplots of artificial sequences. We also introduce an approximation that makes the calculation of dotplots practical for use in an interactive browser.     

Approximations of solutions to neutral functional differential equations with nonlocal history conditions

This work is concerned with a class of neutral functional differential equations with nonlocal history conditions in a Hilbert space. The approximation of solution to a class of such problems is studied. Moreover, the convergence of Faedo-Galerkin approximation of solution is shown. For illustration, an example is worked out.     

图论在网络出版传播中的应用

利用图论理论研究了网络连通度与广播时间的关系问题 ,获得了网络单信息广播时间的一个界和最少时间广播网的几个充分条件 ,并建立了一个有效的广播方案 .     

Teiji Takagi, Founder of the Japanese School of Modern Mathematics

This article is a brief historical report on Teiji Takagi which was prepared at the commencement of ‘Takagi Lectures’ of The Mathematical Society of Japan. The first of its two purposes is to give some informations on the circumstances of education and research of mathematics in Japan surrounding Takagi who could finally established himself as the founder of the Japanese school of modern mathematics. The other is a brief overview on Takagi’s works of mathematics some of which are still attractive to and influential on especially ambitious students of mathematics. The author hopes that careful readers may find some hints for the questions how and why Takagi was able to establish his class field theory. At the end of this article the readers will find an English translation of the preface of his book Algebraic theory of numbers (in Japanese) which is the only thing that he left for us to see his total view over class field theory after the establishment of Artin’s reciprocity law.     

Fast detection of common sequence structure patterns in RNAs

We developed a dynamic programming approach for computing common exact sequential and structural patterns between two RNAs, given their sequences and their secondary structures. An RNA consists of a sequence of nucleotides and a secondary structure defined via bonds linking together complementary nucleotides. It is known that secondary structures are more preserved than sequences in the evolution of RNAs.We are able to compute all patterns between two RNAs in time O(nm) and space O(nm), where n and m are the lengths of the RNAs. Our method is useful for describing and detecting local motifs. It is especially suitable for finding similar regions of large RNAs that do not share global similarities. An implementation is available in C++ and can be obtained by contacting one of the authors.     

一类二分图的k-匹配数

设G是一个具有二分类(X_1,X_2)的简单偶图,|X_1|=|X_2|=n,如果对于给定的c>0,|M(S)|≥(1+c)|S|对任意满足|S|≤n/2的S(?)X_i(i=1,2)都成立,其中N(S)是S的邻集,则称G是(n,c)-扩张图.给出了(n,c)-扩张图的k-匹配数与完美匹配数之比的顺从界.     

一类新图的匹配唯一性

利用图的匹配多项式及其最大实数根的性质证明了树T(1,1,n,2,1)及补图匹配唯一的充要条件是n≠1,2,5,8.     

Calculating distances for dissimilar strings: The shortest path formulation revisited

Fast detection of string differences is a prerequisite for string clustering problems. An example of such a problem is the identification of duplicate information in the data cleansing stage of the data mining process. The relevant algorithms allow the application of large-scale clustering techniques in order to create clusters of similar strings. The vast majority of comparisons, in such cases, is between very dissimilar strings, therefore methods that perform better at detecting large differences are preferable. This paper presents approaches which comply with this requirement, based on reformulation of the underlying shortest path problem. It is believed that such methods can lead to a family of new algorithms. An upper bound algorithm is presented, as an example, which produces promising results.     

Rejection of the Light Quantum: The Dark Side of Niels Bohr

Evidence is recalled of the strong opposition of Niels Bohr, at the time of the Old Quantum Theory 1913–1925, to the Lichtquanten hypothesis of Einstein. Some episodes with H. A. Kramers, J. C. Slater, and W. Heisenberg are recollected; Bohr's changing point of view is traced back to some philosophical antecedents and to his endeavor to deduce quantum results from the Correspondence Principle. Some consequences for the future interpretation of Quantum Mechanics, specially to the Complementarity Principle, are considered.