Correctness by Construction for Pairwise Sequence Alignment Algorithm in Bio-Sequence

Pairwise sequence alignment is a classical problem in bioinformatics, aiming at finding the similarity between two sequences, which is important for discovering functional, structural and evolutionary information in biological sequences. More algorithms have been developed for the sequence alignment problem. There is no formal development process for the existing pairwise sequence algorithms and leads to the low trustworthiness of those algorithms. In addition, the application of formal methods in the field of bioinformatics algorithm development is rarely seen. In this paper, we use a formal method PAR to construct a pairwise sequence algorithm, analyze the essence of the pairwise sequence alignment problem, construct the Apla algorithm program by stepwise refinement, and further verify its correctness. Finally a highly reliable and executable pairwise sequence alignment algorithm program is generated from Apla program via PAR platform. The formal construction process ensures the reliability of algorithm, and also demonstrates the algorithm design idea clearly, which makes the originally difficult algorithm design process easier. The successful practice of this method on the pairwise sequence alignment problem in biological sequence analysis can provide a reference for the construction of highly reliable algorithms in complex bioinformatics from both methodological and practical aspects

Pattern matching : a sheaf-theoretic approach

A general theory of pattern matching is presented by adopting an extensional, geometric view of patterns. The extension of the matching relation consists of the occurrences of all possible patterns in a particular target. The geometry of the pattern describes the structure of the pattern and the spatial relationships among parts of the pattern. The extension and the geometry, when combined, produce a structure called a sheaf. Sheaf theory is a well developed branch of mathematics which studies the global consequences of locally defined properties. For pattern matching, an occurrence of a pattern, a global property of the pattern, is obtained by gluing together occurrences of parts of the pattern, which are locally defined properties.A sheaf-theoretic view of pattern rnatching provides a uniforrn treatrnent of pattern matching on any kind of data structure-strings, trees, graphs, hypergraphs, and so on. Such a parametric description is achieved by using the language of category theory, a highly abstract description of commonly occurring structures and relationships in mathematics.A generalized version of the Knuth-Morris-Pratt pattern matching algorithm is derived by gradually converting the extensional description of pattern rnatching as a sheaf into an intensional description. The algorithm results from a synergy of four very general program synthesis/transformation techniques: (1) Divide and conquer: exploit the sheaf condition; assemble a full match by gluing together partial matches; (2) Finite differencing: collect and update partial matches incrementally while traversing the target; (3) Backtracking: instead of saving all partial matches, save just one; when this partial match cannot be extended, fail back to another; (4) Partial evaluation: precompute pattern-based (and therefore constant) computations.The derivation is carried out in a general frarnework using Grothendieck topologies. By appropriately instantiating the underlying data structures and topologies, the sarne scheme results in matching algorithms for patterns with variables and with multiple patterns. Slight variations of the derivation result in Earley's algorithm for context-free parsing, and Waltz filtering, a relaxation algorithm for providing 3-D interpretations to 2-D irnages.Other applications of a geometric view of patterns are briefly considered: rewrites, parallel algorithms, induction and computability

Seventh Annual Workshop on Space Operations Applications and Research (SOAR 1993), volume 1

This document contains papers presented at the Space Operations, Applications and Research Symposium (SOAR) Symposium hosted by NASA/Johnson Space Center (JSC) on August 3-5, 1993, and held at JSC Gilruth Recreation Center. SOAR included NASA and USAF programmatic overview, plenary session, panel discussions, panel sessions, and exhibits. It invited technical papers in support of U.S. Army, U.S. Navy, Department of Energy, NASA, and USAF programs in the following areas: robotics and telepresence, automation and intelligent systems, human factors, life support, and space maintenance and servicing. SOAR was concerned with Government-sponsored research and development relevant to aerospace operations. More than 100 technical papers, 17 exhibits, a plenary session, several panel discussions, and several keynote speeches were included in SOAR '93

Forecasting monthly airline passenger numbers with small datasets using feature engineering and a modified principal component analysis

In this study, a machine learning approach based on time series models, different feature engineering, feature extraction, and feature derivation is proposed to improve air passenger forecasting. Different types of datasets were created to extract new features from the core data. An experiment was undertaken with artificial neural networks to test the performance of neurons in the hidden layer, to optimise the dimensions of all layers and to obtain an optimal choice of connection weights – thus the nonlinear optimisation problem could be solved directly. A method of tuning deep learning models using H2O (which is a feature-rich, open source machine learning platform known for its R and Spark integration and its ease of use) is also proposed, where the trained network model is built from samples of selected features from the dataset in order to ensure diversity of the samples and to improve training. A successful application of deep learning requires setting numerous parameters in order to achieve greater model accuracy. The number of hidden layers and the number of neurons, are key parameters in each layer of such a network. Hyper-parameter, grid search, and random hyper-parameter approaches aid in setting these important parameters. Moreover, a new ensemble strategy is suggested that shows potential to optimise parameter settings and hence save more computational resources throughout the tuning process of the models. The main objective, besides improving the performance metric, is to obtain a distribution on some hold-out datasets that resemble the original distribution of the training data. Particular attention is focused on creating a modified version of Principal Component Analysis (PCA) using a different correlation matrix – obtained by a different correlation coefficient based on kinetic energy to derive new features. The data were collected from several airline datasets to build a deep prediction model for forecasting airline passenger numbers. Preliminary experiments show that fine-tuning provides an efficient approach for tuning the ultimate number of hidden layers and the number of neurons in each layer when compared with the grid search method. Similarly, the results show that the modified version of PCA is more effective in data dimension reduction, classes reparability, and classification accuracy than using traditional PCA.</div

Well-Formed and Scalable Invasive Software Composition

Software components provide essential means to structure and organize software effectively. However, frequently, required component abstractions are not available in a programming language or system, or are not adequately combinable with each other. Invasive software composition (ISC) is a general approach to software composition that unifies component-like abstractions such as templates, aspects and macros. ISC is based on fragment composition, and composes programs and other software artifacts at the level of syntax trees. Therefore, a unifying fragment component model is related to the context-free grammar of a language to identify extension and variation points in syntax trees as well as valid component types. By doing so, fragment components can be composed by transformations at respective extension and variation points so that always valid composition results regarding the underlying context-free grammar are yielded. However, given a language’s context-free grammar, the composition result may still be incorrect. Context-sensitive constraints such as type constraints may be violated so that the program cannot be compiled and/or interpreted correctly. While a compiler can detect such errors after composition, it is difficult to relate them back to the original transformation step in the composition system, especially in the case of complex compositions with several hundreds of such steps. To tackle this problem, this thesis proposes well-formed ISC—an extension to ISC that uses reference attribute grammars (RAGs) to specify fragment component models and fragment contracts to guard compositions with context-sensitive constraints. Additionally, well-formed ISC provides composition strategies as a means to configure composition algorithms and handle interferences between composition steps. Developing ISC systems for complex languages such as programming languages is a complex undertaking. Composition-system developers need to supply or develop adequate language and parser specifications that can be processed by an ISC composition engine. Moreover, the specifications may need to be extended with rules for the intended composition abstractions. Current approaches to ISC require complete grammars to be able to compose fragments in the respective languages. Hence, the specifications need to be developed exhaustively before any component model can be supplied. To tackle this problem, this thesis introduces scalable ISC—a variant of ISC that uses island component models as a means to define component models for partially specified languages while still the whole language is supported. Additionally, a scalable workflow for agile composition-system development is proposed which supports a development of ISC systems in small increments using modular extensions. All theoretical concepts introduced in this thesis are implemented in the Skeletons and Application Templates framework SkAT. It supports “classic”, well-formed and scalable ISC by leveraging RAGs as its main specification and implementation language. Moreover, several composition systems based on SkAT are discussed, e.g., a well-formed composition system for Java and a C preprocessor-like macro language. In turn, those composition systems are used as composers in several example applications such as a library of parallel algorithmic skeletons

Trusted product lines

This thesis describes research undertaken into the application of software product line approaches to the development of high-integrity, embedded real-time software systems that are subject to regulatory approval/certification. The motivation for the research arose from a real business need to reduce cost and lead time of aerospace software development projects. The thesis hypothesis can be summarised as follows: It is feasible to construct product line models that allow the specification of required behaviour within a reference architecture that can be transformed into an effective product implementation, whilst enabling suitable supporting evidence for certification to be produced. The research concentrates on the following four main areas: 1. Construction of an argument framework in which the application of product line techniques to high-integrity software development can be assessed and critically reviewed. 2. Definition of a product-line reference architecture that can host components containing variation. 3. Design of model transformations that can automatically instantiate products from a set of components hosted within the reference architecture. 4. Identification of verification approaches that may provide evidence that the transformations designed in step 3 above preserve properties of interest from the product line model into the product instantiations. Together, these areas form the basis of an approach we term “Trusted Product Lines”. The approach has been evaluated and validated by deployment on a real aerospace project; the approach has been used to produce DO-178B/ED-12B Level A applications of over 300 KSLOC in size. The effect of this approach on the software development process has been critically evaluated in this thesis, both quantitatively (in terms of cost and relative size of process phases) and qualitatively (in terms of software quality). The “Trusted Product Lines” approach, as described within the thesis, shows how product line approaches can be applied to high-integrity software development, and how certification evidence created and arguments constructed for products instantiated from the product line. To the best of our knowledge, the development and effective application of product line techniques in a certification environment is novel and unique

Algebraic Algorithm Design and Local Search

Formal, mathematically-based techniques promise to play an expanding role in the development and maintenance of the software on which our technological society depends. Algebraic techniques have been applied successfully to algorithm synthesis by the use of algorithm theories and design tactics, an approach pioneered in the Kestrel Interactive Development System (KIDS). An algorithm theory formally characterizes the essential components of a family of algorithms. A design tactic is a specialized procedure for recognizing in a problem specification the structures identified in an algorithm theory and then synthesizing a program. Design tactics are hard to write, however, and much of the knowledge they use is encoded procedurally in idiosyncratic ways. Algebraic methods promise a way to represent algorithm design knowledge declaratively and uniformly. We describe a general method for performing algorithm design that is more purely algebraic than that of KIDS. This method is then applied to local search. Local search is a large and diverse class of algorithms applicable to a wide range of problems; it is both intrinsically important and representative of algorithm design as a whole. A general theory of local search is formalized to describe the basic properties common to all local search algorithms, and applied to several variants of hill climbing and simulated annealing. The general theory is then specialized to describe some more advanced local search techniques, namely tabu search and the Kernighan-Lin heuristic

Syllable-based constraints on properties of English sounds

Also issued as Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1989.Includes bibliographical references (p. 169-174).Work sponsored in part by the Office of Naval Research. N00014-82-K-0727Mark A. Randolph