A General Illumination Model for Molecular Visualization

Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom‐based representations are the Space‐filling, the Solvent Excluded Surface, the Balls‐and‐Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large‐scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom‐based molecular representations. The proposed model can be further evaluated in real‐time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.     

Attributed linear intermediate representations for retargetable code generators

This paper illustrates the usefulness of an attributed prefix linear intermediate representation for compiler code generation. In separating the machine-independent and machine-dependent aspects of a compiler, we discuss the advantages and disadvantages of an attributed linear intermediate representation with respect to tree-structured intermediate representations. Some of these issues are relevant to fundamental questions of compiler structure with particular emphasis on retargetability. We discuss our implementation experience using this linear intermediate representation with a table-driven code generation scheme for a variety of target architectures.     

Static generation of UML sequence diagrams

UML sequence diagrams are visual representations of object interactions in a system and can provide valuable information for program comprehension, debugging, maintenance, and software archeology. Sequence diagrams generated from legacy code are independent of existing documentation that may have eroded. We present a framework for static generation of UML sequence diagrams from object-oriented source code. The framework provides a query refinement system to guide the user to interesting interactions in the source code. Our technique involves constructing a hypergraph representation of the source code, traversing the hypergraph with respect to a user-defined query, and generating the corresponding set of sequence diagrams. We implemented our framework as a tool, StaticGen (supporting software: StaticGen), analyzing a corpus of 30 Android applications. We provide experimental results demonstrating the efficacy of our technique (originally appeared in the Proceedings of Fundamental Approaches to Software Engineering—20th International Conference, FASE 2017, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2017, Uppsala, Sweden, April 22–29, 2017).

     

Software visualization

The field of software visualization (SV) investigates approaches and techniques for static and dynamic graphical representations of algorithms, programs (code), and processed data. SV is concerned primarily with the analysis of programs and their development. The goal is to improve our understanding of inherently invisible and intangible software, particularly when dealing with large information spaces that characterize domains like software maintenance, reverse engineering, and collaborative development. The main challenge is to find effective mappings from different software aspects to graphical representations using visual metaphors. This paper provides an overview of the SV research, describes current research directions, and includes an extensive list of recommended readings.     

基于多模态对比学习的代码表征增强预训练方法

代码表征旨在融合源代码的特征,以获取其语义向量,在基于深度学习的代码智能中扮演着重要角色.传统基于手工的代码表征依赖领域专家的标注,繁重耗时,且无法灵活地复用于特定下游任务,这与绿色低碳的发展理念极不相符.因此,近年来,许多自监督学习的编程语言大规模预训练模型(如CodeBERT)应运而生,为获取通用代码表征提供了有效途径.这些模型通过预训练获得通用的代码表征,然后在具体任务上进行微调,取得了显著成果.但是,要准确表示代码的语义信息,需要融合所有抽象层次的特征(文本级、语义级、功能级和结构级).然而,现有模型将编程语言仅视为类似于自然语言的普通文本序列,忽略了它的功能级和结构级特征.因此,旨在进一步提高代码表征的准确性,提出了基于多模态对比学习的代码表征增强的预训练模型(representation enhanced contrastive multimodal pretraining, REcomp). REcomp设计了新的语义级-结构级特征融合算法,将它用于序列化抽象语法树,并通过多模态对比学习的方法将该复合特征与编程语言的文本级和功能级特征相融合,以实现更精准的语义建模.最后,...     

Are Edges Incomplete?

We address the problem of computing a general-purpose early visual representation that satisfies two criteria. 1) Explicitness: To be more useful than the original pixel array, the representation must take a significant step toward making important image structure explicit. 2) Completeness: To support a diverse set of high-level tasks, the representation must not discard information of potential perceptual relevance. The most prevalent representation in image processing and computer vision that satisfies the completeness criterion is the wavelet code. In this paper, we propose a very different code which represents the location of each edge and the magnitude and blur scale of the underlying intensity change. By making edge structure explicit, we argue that this representation better satisfies the first criterion than do wavelet codes. To address the second criterion, we study the question of how much visual information is lost in the representation. We report a novel method for inverting the edge code to reconstruct a perceptually accurate estimate of the original image, and thus demonstrate that the proposed representation embodies virtually all of the perceptually relevant information contained in a natural image. This result bears on recent claims that edge representations do not contain all of the information needed for higher level tasks.     

An Exploratory Study of Data Sketching for Visual Representation

Hand‐drawn sketching on napkins or whiteboards is a common, accessible method for generating visual representations. This practice is shared by experts and non‐experts and is probably one of the faster and more expressive ways to draft a visual representation of data. In order to better understand the types of and variations in what people produce when sketching data, we conducted a qualitative study. We asked people with varying degrees of visualization expertise, from novices to experts, to manually sketch representations of a small, easily understandable dataset using pencils and paper and to report on what they learned or found interesting about the data. From this study, we extract a data sketching representation continuum from numeracy to abstraction; a data report spectrum from individual data items to speculative data hypothesis; and show the correspondence between the representation types and the data reports from our results set. From these observations we discuss the participants’ representations in relation to their data reports, indicating implications for design and potentially fruitful directions for research.     

Converting legacy code into Ada: a cognitive approach

Describes a code conversion tool that helps programmers visualize and understand system design. The author first reviews current software reengineering tools and then describe a new cognitive approach to system (re)engineering based on code comprehension tools that provide a visual representation of code containing less cognitive noise. This better enables programmers to understand system design. The approach integrates code comprehension tools with current reengineering methodologies to create an integrated reengineering workbench for converting legacy code into newer languages such as Ada or C/C++     

代码知识图谱构建及智能化软件开发方法研究

智能化软件开发正在经历从简单的代码检索到语义赋能的代码自动生成的转变,传统的语义表达方式无法有效地支撑人、机器和代码之间的语义交互,探索机器可理解的语义表达机制迫在眉睫.首先指出了代码知识图谱是实现智能化软件开发的基础,进而分析了大数据时代智能化软件开发的新特点以及基于代码知识图谱进行智能化软件开发的新挑战;随后回顾了智能化软件开发和代码知识图谱的研究现状,指出了现有智能化软件开发的研究仍然处于较低水平,而现有知识图谱的研究主要面向开放领域知识图谱,无法直接应用于代码领域知识图谱.因此,从代码知识图谱的建模与表示、构建与精化、存储与演化管理、查询语义理解以及智能化应用这5个方面详细探讨了研究新趋势,以更好地满足基于代码知识图谱进行智能化软件开发的需要.     

Software requirements as an application domain for natural language processing

Mapping functional requirements first to specifications and then to code is one of the most challenging tasks in software development. Since requirements are commonly written in natural language, they can be prone to ambiguity, incompleteness and inconsistency. Structured semantic representations allow requirements to be translated to formal models, which can be used to detect problems at an early stage of the development process through validation. Storing and querying such models can also facilitate software reuse. Several approaches constrain the input format of requirements to produce specifications, however they usually require considerable human effort in order to adopt domain-specific heuristics and/or controlled languages. We propose a mechanism that automates the mapping of requirements to formal representations using semantic role labeling. We describe the first publicly available dataset for this task, employ a hierarchical framework that allows requirements concepts to be annotated, and discuss how semantic role labeling can be adapted for parsing software requirements.     

Efficient representation and transformation of image data on the connection machine system

We discuss the transformation of image data from one level of representation to another using the data parallel programming model of the Connection Machine System.¹ Emphasis is placed on maintaining locality of reference in order to take advantage of fast, local communications. Image pyramids illustrate the transformation of image-based representations. We review pointer jumping as a transformation from the image to a sequence-based representation, the primary representation of data outside of the image plane. Using communication primitives, especially segmented scans, we review utilities for representing and manipulating such sequences. We then compare several algorithms for matching and evidence accumulation. The techniques emphasize the use of sorting and sparse representations of space, in order to limit the computational requirements of high level vision. Connection Machine is a registered trademark of Thinking Machines Corporation. Address reprint requests to: Library, Thinking Machines Corporation, 245 First St., Cambridge, MA 02142, USA     

Effective approaches to combining lexical and syntactical information for code summarization

Natural language summaries of source codes are important during software development and maintenance. Recently, deep learning based models have achieved good performance on the task of automatic code summarization, which encode token sequence or abstract syntax tree (AST) of code with neural networks. However, there has been little work on the efficient combination of lexical and syntactical information of code for better summarization quality. In this paper, we propose two general and effective approaches to leveraging both types of information: a convolutional neural network that aims to better extract vector representation of AST node for downstream models; and a Switch Network that learns an adaptive weight vector to combine different code representations for summary generation. We integrate these approaches into a comprehensive code summarization model, which includes a sequential encoder for token sequence of code and a tree based encoder for its AST. We evaluate our model on a large Java dataset. The experimental results show that our model outperforms several state-of-the-art models on various metrics, and the proposed approaches contribute a lot to the improvements.     

Agentsheets: a medium for creating domain-oriented visual languages

Customized visual representations enable end users to achieve their programming goals. Here, designers work with users to tailor visual programming languages to specific problem domains. We describe a design methodology and a tool for creating domain oriented, end user programming languages that effectively use visualization. We first describe a collaborative design methodology involving end users and designers. We then present Agentsheets, a tool for creating domain oriented visual programming languages, and illustrate how it supports collaborative design by examining experiences from a real language design project. Finally, we summarize the contributions of our approach and discuss its viability in industrial design projects     

An Overview of 3D Software Visualization

Software visualization studies techniques and methods for graphically representing different aspects of software. Its main goal is to enhance, simplify and clarify the mental representation a software engineer has of a computer system. During many years, visualization in 2D space has been actively studied, but in the last decade, researchers have begun to explore new 3D representations for visualizing software. In this article, we present an overview of current research in the area, describing several major aspects like: visual representations, interaction issues, evaluation methods and development tools. We also perform a survey of some representative tools to support different tasks, i.e., software maintenance and comprehension, requirements validation and algorithm animation for educational purposes, among others. Finally, we conclude identifying future research directions.     

Genotype representations in grammatical evolution

Grammatical evolution (GE) is a form of grammar-based genetic programming. A particular feature of GE is that it adopts a distinction between the genotype and phenotype similar to that which exists in nature by using a grammar to map between the genotype and phenotype. Two variants of genotype representation are found in the literature, namely, binary and integer forms. For the first time we analyse and compare these two representations to determine if one has a performance advantage over the other. As such this study seeks to extend our understanding of GE by examining the impact of different genotypic representations in order to determine whether certain representations, and associated diversity-generation operators, improve GE’s efficiency and effectiveness. Four mutation operators using two different representations, binary and gray code representation, are investigated. The differing combinations of representation and mutation operator are tested on three benchmark problems. The results provide support for the use of an integer-based genotypic representation as the alternative representations do not exhibit better performance, and the integer representation provides a statistically significant advantage on one of the three benchmarks. In addition, a novel wrapping operator for the binary and gray code representations is examined, and it is found that across the three problems examined there is no general trend to recommend the adoption of an alternative wrapping operator. The results also back up earlier findings which support the adoption of wrapping.     

Discovering joint audio–visual codewords for video event detection

Detecting complex events in videos is intrinsically a multimodal problem since both audio and visual channels provide important clues. While conventional methods fuse both modalities at a superficial level, in this paper we propose a new representation—called bi-modal words—to explore representative joint audio–visual patterns. We first build a bipartite graph to model relation across the quantized words extracted from the visual and audio modalities. Partitioning over the bipartite graph is then applied to produce the bi-modal words that reveal the joint patterns across modalities. Different pooling strategies are then employed to re-quantize the visual and audio words into the bi-modal words and form bi-modal Bag-of-Words representations. Since it is difficult to predict the suitable number of bi-modal words, we generate bi-modal words at different levels (i.e., codebooks with different sizes), and use multiple kernel learning to combine the resulting multiple representations during event classifier learning. Experimental results on three popular datasets show that the proposed method achieves statistically significant performance gains over methods using individual visual and audio feature alone and existing popular multi-modal fusion methods. We also find that average pooling is particularly suitable for bi-modal representation, and using multiple kernel learning to combine multi-modal representations at various granularities is helpful.     

Using aspects for testing of embedded software: experiences from two industrial case studies

Aspect-oriented software testing is emerging as an important alternative to conventional procedural and object-oriented testing techniques. This paper reports experiences from two case studies where aspects were used for the testing of embedded software in the context of an industrial application. In the first study, we used code-level aspects for testing non-functional properties. The methodology we used for deriving test aspect code was based on translating high-level requirements into test objectives, which were then implemented using test aspects in AspectC++. In the second study, we used high-level visual scenario-based models for the test specification, test generation, and aspect-based test execution. To specify scenario-based tests, we used a UML2-compliant variant of live sequence charts. To automatically generate test code from the models, a modified version of the S2A Compiler, outputting AspectC++ code, was used. Finally, to examine the results of the tests, we used the Tracer, a prototype tool for model-based trace visualization and exploration. The results of the two case studies show that aspects offer benefits over conventional techniques in the context of testing embedded software; these benefits are discussed in detail. Finally, towards the end of the paper, we also discuss the lessons learned, including the technological and other barriers to the future successful use of aspects in the testing of embedded software in industry.     

Software trustworthiness 2.0—A semantic web enabled global source code analysis approach

There has been an ongoing trend toward collaborative software development using open and shared source code published in large software repositories on the Internet. While traditional source code analysis techniques perform well in single project contexts, new types of source code analysis techniques are ermerging, which focus on global source code analysis challenges. In this article, we discuss how the Semantic Web, can become an enabling technology to provide a standardized, formal, and semantic rich representations for modeling and analyzing large global source code corpora. Furthermore, inference services and other services provided by Semantic Web technologies can be used to support a variety of core source code analysis techniques, such as semantic code search, call graph construction, and clone detection. In this paper, we introduce SeCold, the first publicly available online linked data source code dataset for software engineering researchers and practitioners. Along with its dataset, SeCold also provides some Semantic Web enabled core services to support the analysis of Internet-scale source code repositories. We illustrated through several examples how this linked data combined with Semantic Web technologies can be harvested for different source code analysis tasks to support software trustworthiness. For the case studies, we combine both our linked-data set and Semantic Web enabled source code analysis services with knowledge extracted from StackOverflow, a crowdsourcing website. These case studies, we demonstrate that our approach is not only capable of crawling, processing, and scaling to traditional types of structured data (e.g., source code), but also supports emerging non-structured data sources, such as crowdsourced information (e.g., StackOverflow.com) to support a global source code analysis context.     

Mining Mid-level Visual Patterns with Deep CNN Activations

The purpose of mid-level visual element discovery is to find clusters of image patches that are representative of, and which discriminate between, the contents of the relevant images. Here we propose a pattern-mining approach to the problem of identifying mid-level elements within images, motivated by the observation that such techniques have been very effective, and efficient, in achieving similar goals when applied to other data types. We show that Convolutional Neural Network (CNN) activations extracted from image patches typical possess two appealing properties that enable seamless integration with pattern mining techniques. The marriage between CNN activations and a pattern mining technique leads to fast and effective discovery of representative and discriminative patterns from a huge number of image patches, from which mid-level elements are retrieved. Given the patterns and retrieved mid-level visual elements, we propose two methods to generate image feature representations. The first encoding method uses the patterns as codewords in a dictionary in a manner similar to the Bag-of-Visual-Words model. We thus label this a Bag-of-Patterns representation. The second relies on mid-level visual elements to construct a Bag-of-Elements representation. We evaluate the two encoding methods on object and scene classification tasks, and demonstrate that our approach outperforms or matches the performance of the state-of-the-arts on these tasks.