Data structures and dynamic programming background for editing highly structured texts

The interactive editing and formatting of texts structured by a hierarchy of non-standard layout features requires a thorough study of the data structures and algorithms used. It is well known that many text processing systems in this field suffer either from bad performance or reduced quality of outputs and screen representation. The aim of this note is to demonstrate how to overcome these difficulties using dynamic programming algorithms and suitably designed data structures controlling the layout of structured texts.     

XGobi: Interactive Dynamic Data Visualization in the X Window System

Abstract

XGobi is a data visualization system with state-of-the-art interactive and dynamic methods for the manipulation of views of data. It implements 2-D displays of projections of points and lines in high-dimensional spaces, as well as parallel coordinate displays and textual views thereof. Projection tools include dotplots of single variables, plots of pairs of variables, 3-D data rotations, various grand tours, and interactive projection pursuit. Views of the data can be reshaped. Points can be labeled and brushed with glyphs and colors. Lines can be edited and colored. Several XGobi processes can be run simultaneously and linked for labeling, brushing, and sharing of projections. Missing data are accommodated and their patterns can be examined; multiple imputations can be given to XGobi for rapid visual diagnostics. XGobi includes an extensive online help facility. XGobi can be integrated in other software systems, as has been done for the data analysis language S, the geographic information system (GIS) Arc View?, and the interactive multidimensional scaling program XGvis. XGobi is implemented in the X Window System? for portability as well as the ability to run across a network.     

MCQ4Structures to compute similarity of molecule structures

Comparison of molecular structures in order to identify their similarity is an important step in solving various problems derived from computational biology, like structure alignment and modelling, motif search or clustering. Thus, there is a constant need for the development of good measures to determine distances between the structures and tools to display these distances in an easily interpretable form. In the paper we present MCQ4Structures, a new method and tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. We discuss its unique features as compared with the other measures, including RMSD and LGA, and we show its experimental use in comparison of a number of 3D structures as well as evaluation of models predicted within RNA-Puzzles contest. MCQ4Structures software is available as a free Java WebStart application at: http://www.cs.put.poznan.pl/tzok/mcq/. The source code licensed under BSD can be downloaded from the same website.     

Model development and optimization in interactive computing environments

Integrated computing systems—such as Maple, Mathematica, and MATLAB—enable the development of “live” electronic documents that include explanatory text, calculations, custom programming (code development), visualization, and other features. As a result, teachers and students, researchers and practitioners can develop applications in a completely interactive format. Such e-documents can be put to good use in developing textbooks, lecture notes, assignments and presentations, as well as in the context of research and development (R&D) projects. The interactive approach accelerates and enhances the process of learning and research. To illustrate this approach, we discuss a nonlinear (global and local) optimization software product and a topical electronic book that support interactive model development and optimization in Maple. We highlight the key features of the e-book and the software, present illustrative examples, and point towards a range of scientific and engineering applications.      

Graphically Displaying Text

Abstract

There are many examples of text data bases, including literary corpora and computer source code, in which statistics are associated with each line. A visualization technique for this class of data represents the text lines as thin colored rows within columns. The position, length, and indentation of each row corresponds to that of the text. The color of each row is determined by a statistic associated with each line. The display looks like a miniature picture of the text with the color showing the spatial distribution of the statistic within the text. Using this technique, SeeSoft?, a dynamic graphics software tool, can easily display 50,000 lines of text simultaneously on a high-resolution monitor.     

Recent Publications in JSS

The following papers were recently accepted to the Journal of Statistical Software (JSS). JSS is free; code and papers may be downloaded at no cost. Code means source code, not binaries, so that algorithms may be easily customized or extended. The journal has cross-referencing and a search engine to allow for easy browsing. It can be accessed at www.jstatsoft.org.     

Recent Publications in JSS

The following papers were recently accepted to the Journal of Statistical Software (JSS). JSS is free; code and papers may be downloaded at no cost. Code means source code, not binaries, so that algorithms may be easily customized or extended. The journal has cross-referencing and a search engine to allow for easy browsing. It can be accessed at www.jstatsoft.org.     

Mathematics instruction and the tablet PC

The use of tablet PCs in teaching is a relatively new phenomenon. A cross between a notebook computer and a personal digital assistant (PDA), the tablet PC has all of the features of a notebook with the additional capability that the screen can also be used for input. Tablet PCs are usually equipped with a stylus that allows the user to write on the screen. Handwriting recognition software converts this input into text for use with software such as internet browsers and email programs. As an educational tool, two of the most important features of the tablet PC are annotation and wireless communication. The annotation feature allows the user to write on almost any document much as one would annotate a printout of the same document. The wireless communication feature allows tablet PCs to share information with one another. The advantages of these features and their impact on the Murray State University (MSU) classroom will be discussed in the evaluation section.     

On the classification of perfect codes: side class structures

The side class structure of a perfect 1-error correcting binary code (hereafter referred to as a perfect code) C describes the linear relations between the coset representatives of the kernel of C. Two perfect codes C and C′ are linearly equivalent if there exists a non-singular matrix A such that AC = C′ where C and C′ are matrices with the code words of C and C′ as columns. Hessler proved that the perfect codes C and C′ are linearly equivalent if and only if they have isomorphic side class structures. The aim of this paper is to describe all side class structures. It is shown that the transpose of any side class structure is the dual of a subspace of the kernel of some perfect code and vice versa; any dual of a subspace of a kernel of some perfect code is the transpose of the side class structure of some perfect code. The conclusion is that for classification purposes of perfect codes it is sufficient to find the family of all kernels of perfect codes.     

Lehmer code transforms and Mahonian statistics on permutations

In 2000 Babson and Steingrímsson introduced the notion of vincular patterns in permutations. They show that essentially all well-known Mahonian permutation statistics can be written as combinations of such patterns. Also, they proved and conjectured that other combinations of vincular patterns are still Mahonian. These conjectures were proved later: by Foata and Zeilberger in 2001, and by Foata and Randrianarivony in 2006.In this paper we give an alternative proof of some of these results. Our approach is based on permutation codes which, like the Lehmer code, map bijectively permutations onto subexcedant sequences. More precisely, we give several code transforms (i.e., bijections between subexcedant sequences) which when applied to the Lehmer code yield new permutation codes which count occurrences of some vincular patterns. These code transforms can be seen as a pre-compression step of the Lehmer code because they map some redundancies into runs of 0s. Also, our proofs, unlike the previous ones, provide explicit bijections between permutations having a given value for two different Mahonian pattern-based statistics.     

Distance Geometry Optimization for Protein Structures

We study the performance of the dgsol code for the solution of distance geometry problems with lower and upper bounds on distance constraints. The dgsol code uses only a sparse set of distance constraints, while other algorithms tend to work with a dense set of constraints either by imposing additional bounds or by deducing bounds from the given bounds. Our computational results show that protein structures can be determined by solving a distance geometry problem with dgsol and that the approach based on dgsol is significantly more reliable and efficient than multi-starts with an optimization code.     

On the predictive ability of narrative disclosures in annual reports

We investigate whether narrative disclosures in 10-K and 10K-405 filings contain value-relevant information for predicting market performance. We apply text classification techniques from computer science to machine code text disclosures in a sample of 4280 filings by 1236 firms over five years. Our methodology develops a model using documents and actual performance for a training sample. This model, when applied to documents from a test set, leads to performance prediction. We find that a portfolio based on model predictions earns significantly positive size-adjusted returns, indicating that narrative disclosures contain value-relevant information. Supplementary analyses show that the text classification model captures information not contained in document-level features of clarity, tone and risk sentiment considered in prior research. However, we find that the narrative score is not providing information incremental to traditional predictors such as size, market-to-book and momentum, but rather affects investors’ use of price momentum as a factor that predicts excess returns.     

A Generalized Erdös-Rényi Law for Sequence Analysis Problems

We consider a class of random variables that includes scoring functions arising in computational molecular biology, such as sequence alignment and folding. We characterize the class by a set of properties, and show that, under certain conditions, such random variables follow an Erdös-Rényi law of large numbers. That is,

Linking ArcView™ and XGobi: Insight behind the Front End

Abstract

This article presents aspects of the implementation of a bidirectional link between the Geographic Information System (GIS) ArcView? and the interactive dynamic statistical graphics program XGobi. We describe the main functionality of the link, the underlying remote procedure call (RPC) mechanism, and internal data structures, and discuss topics such as security, concurrency, and linked brushing. We think that these topics are of particular interest to software authors intending to link similar software packages, and software users learning about strengths (and weaknesses) of the implementation of our link.     

Visual software analytics for the build optimization of large-scale software systems

Visual analytics is the science of analytical reasoning facilitated by interactive visual interfaces. In this paper, we present an adaptation of the visual analytics framework to the context of software understanding for maintenance. We discuss the similarities and differences of the general visual analytics context with the software maintenance context, and present in detail an instance of a visual software analytics application for the build optimization of large-scale code bases. Our application combines and adapts several data mining and information visualization techniques in answering several questions that help developers in assessing and reducing the build cost of such code bases by means of user-driven, interactive analysis techniques.     

Analysis using natural language processing of feedback data from two mathematics support centres

ABSTRACT

This paper explores analysis of feedback data collected from student consultations at two mathematics support centres at universities in Australia and Ireland. Unstructured text data was collected over six years and includes qualitative data on student queries collected during the consultations from mathematics and statistics related subjects. Topic modelling and clustering algorithms are used to uncover key themes in the data across stages. Common areas of difficulty experienced by undergraduate students at both universities are investigated and a comparison between them is shown. The results suggest that, despite institutional differences, there is considerable overlap in the types of mathematical and statistical difficulties experienced by students in their first and second year of university at these institutions. We discuss how the ability to uncover such common mathematical and statistical themes with the aid of text mining techniques can be used to improve the support provided by mathematics support centres in terms of providing an efficient and effective service. The code for analyses at both institutions is provided in a GitHub repository so other academic support centres may use it. Outcomes of this analysis have implications for mainstream mathematics and statistics instructors who wish to gain further insights into their students' learning.     

New designs of frequency hopping sequences with low hit zone

Frequency hopping sequences have been found wide applications in various modern frequency hopping spread spectrum communications and radar systems. With potential applications to these areas such as ultra wide bandwidth time hopping code division multiple access radio systems, multi-user and sonar systems, the design of quasi-synchronous time/frequency hopping code division multiple access systems by employing low hit zone hopping sequences has attracted wide attentions. In this paper, we present three construction methods for the low Hamming correlation zone frequency hopping sequences. The parameters of these sets of frequency hopping sequences with low hit zone are new and flexible. The constructed sequences are almost optimal and optimal respectively with respect to the Peng?CFan?CLee bounds. The simplicity of this technique makes it attractive for practical use.     

Translation grammars for compilation and decompilation

A notation is presented for specifying the compilation and decompilation of high-level language programs. Given the decompilation grammar of a programming language, it is possible to study certain properties of that language, such as the redundancy of source language constructs that yield identical object code sequences and the ambiguity of object code generated by procedure calls.     

Weighted Hamming metric structures

It is known that the binary generalized Goppa codes are perfect codes for the weighted Hamming metrics. In this paper, we present the existence of a weighted Hamming metric that admits a binary Hamming code (resp. an extended binary Hamming code) to be perfect code. For a special weighted Hamming metric, we also give some structures of a 2-perfect code, show how to construct a 2-perfect linear code and obtain the weight distribution of a 2-perfect code from the partial information of the code.