Leveraging Software Clones for Software Comprehension: Techniques and Practice

RÉSUMÉ Le corps de cette thèse est centré sur deux aspects de la détection de clones logiciels: la détection et l’application. En détection, la contribution principale de cette thèse est un nouveau détecteur de clones conçu avec la librairie mtreelib, elle-même développée expressément pour ce travail. Cette librairie implémente un arbre de métrique général, une structure de donnée spécialisée dans la division des espaces de métriques dans le but d’accélérer certaines requêtes communes, comme les requêtes par intervalles ou les requêtes de plus proche voisin. Cette structure est utilisée pour construire un détecteur de clones qui approxime la distance de Levenshtein avec une forte précision. Une brève évaluation est présentée pour soutenir cette précision. D’autres résultats pertinents sur les métriques et la détection incrémentale de clones sont également présentés. Plusieurs applications du nouveau détecteur de clones sont présentés. Tout d’abord, un algorithme original pour la reconstruction d’informations perdus dans les systèmes de versionnement est proposé et testé sur plusieurs grands systèmes. Puis, une évaluation qualitative et quantitative de Firefox est faite sur la base d’une analyse du plus proche voisin; les courbes obtenues sont utilisées pour mettre en lumière les difficultés d’effectuer une transition entre un cycle de développement lent et rapide. Ensuite, deux expériences industrielles d’utilisation et de déploiement d’une technologie de détection de clonage sont présentés. Ces deux expériences concernent les langages C/C++, Java et TTCN-3. La grande différence de population de clones entre C/C++ et Java et TTCN-3 est présentée. Finalement, un résultat obtenu grâce au croisement d’une analyse de clones et d’une analyse de flux de sécurité met en lumière l’utilité des clones dans l’identification des failles de sécurité. Le travail se termine par une conclusion et quelques perspectives futures.----------ABSTRACT This thesis explores two topics in clone analysis: detection and application. The main contribution in clone detection is a new clone detector based on a library called mtreelib. This library is a package developed for clone detection that implements the metric data structure. This structure is used to build a clone detector that approximates the Levenshtein distance with high accuracy. A small benchmark is produced to assess the accuracy. Other results from these regarding metrics and incremental clone detection are also presented. Many applications of the clone detector are introduced. An original algorithm to reconstruct missing information in the structure of software repositories is described and tested with data sourced from large existing software. An insight into Firefox is exposed showing the quantity of change between versions and the link between different release cycle types and the number of bugs. Also, an analysis crossing the results from pattern traversal, flow analysis and clone detection is presented. Two industrial experiments using a different clone detector, CLAN, are also presented with some developers’ perspectives. One of the experiments is done on a language never explored in clone detection, TTCN-3, and the results show that the clone population in that language differs greatly from other well-known languages, like C/C++ and Java. The thesis concludes with a summary of the findings and some perspectives for future research

Scalable Automated Incrementalization for Real-Time Static Analyses

This thesis proposes a framework for easy development of static analyses, whose results are incrementalized to provide instantaneous feedback in an integrated development environment (IDE). Today, IDEs feature many tools that have static analyses as their foundation to assess software quality and catch correctness problems. Yet, these tools often fail to provide instantaneous feedback and are thus restricted to nightly build processes. This precludes developers from fixing issues at their inception time, i.e., when the problem and the developed solution are both still fresh in mind. In order to provide instantaneous feedback, incrementalization is a well-known technique that utilizes the fact that developers make only small changes to the code and, hence, analysis results can be re-computed fast based on these changes. Yet, incrementalization requires carefully crafted static analyses. Thus, a manual approach to incrementalization is unattractive. Automated incrementalization can alleviate these problems and allows analyses writers to formulate their analyses as queries with the full data set in mind, without worrying over the semantics of incremental changes. Existing approaches to automated incrementalization utilize standard technologies, such as deductive databases, that provide declarative query languages, yet also require to materialize the full dataset in main-memory, i.e., the memory is permanently blocked by the data required for the analyses. Other standard technologies such as relational databases offer better scalability due to persistence, yet require large transaction times for data. Both technologies are not a perfect match for integrating static analyses into an IDE, since the underlying data, i.e., the code base, is already persisted and managed by the IDE. Hence, transitioning the data into a database is redundant work. In this thesis a novel approach is proposed that provides a declarative query language and automated incrementalization, yet retains in memory only a necessary minimum of data, i.e., only the data that is required for the incrementalization. The approach allows to declare static analyses as incrementally maintained views, where the underlying formalism for incrementalization is the relational algebra with extensions for object-orientation and recursion. The algebra allows to deduce which data is the necessary minimum for incremental maintenance and indeed shows that many views are self-maintainable, i.e., do not require to materialize memory at all. In addition an optimization for the algebra is proposed that allows to widen the range of self-maintainable views, based on domain knowledge of the underlying data. The optimization works similar to declaring primary keys for databases, i.e., the optimization is declared on the schema of the data, and defines which data is incrementally maintained in the same scope. The scope makes all analyses (views) that correlate only data within the boundaries of the scope self-maintainable. The approach is implemented as an embedded domain specific language in a general-purpose programming language. The implementation can be understood as a database-like engine with an SQL-style query language and the execution semantics of the relational algebra. As such the system is a general purpose database-like query engine and can be used to incrementalize other domains than static analyses. To evaluate the approach a large variety of static analyses were sampled from real-world tools and formulated as incrementally maintained views in the implemented engine

Metric Selection and Metric Learning for Matching Tasks

A quarter of a century after the world-wide web was born, we have grown accustomed to having easy access to a wealth of data sets and open-source software. The value of these resources is restricted if they are not properly integrated and maintained. A lot of this work boils down to matching; finding existing records about entities and enriching them with information from a new data source. In the realm of code this means integrating new code snippets into a code base while avoiding duplication. In this thesis, we address two different such matching problems. First, we leverage the diverse and mature set of string similarity measures in an iterative semisupervised learning approach to string matching. It is designed to query a user to make a sequence of decisions on specific cases of string matching. We show that we can find almost optimal solutions after only a small amount of such input. The low labelling complexity of our algorithm is due to addressing the cold start problem that is inherent to Active Learning; by ranking queries by variance before the arrival of enough supervision information, and by a self-regulating mechanism that counteracts initial biases. Second, we address the matching of code fragments for deduplication. Programming code is not only a tool, but also a resource that itself demands maintenance. Code duplication is a frequent problem arising especially from modern development practice. There are many reasons to detect and address code duplicates, for example to keep a clean and maintainable codebase. In such more complex data structures, string similarity measures are inadequate. In their stead, we study a modern supervised Metric Learning approach to model code similarity with Neural Networks. We find that in such a model representing the elementary tokens with a pretrained word embedding is the most important ingredient. Our results show both qualitatively (by visualization) that relatedness is modelled well by the embeddings and quantitatively (by ablation) that the encoded information is useful for the downstream matching task. As a non-technical contribution, we unify the common challenges arising in supervised learning approaches to Record Matching, Code Clone Detection and generic Metric Learning tasks. We give a novel account to string similarity measures from a psychological standpoint and point out and document one longstanding naming conflict in string similarity measures. Finally, we point out the overlap of latest research in Code Clone Detection with the field of Natural Language Processing

Broadening the Scope of Multi-Objective Optimizations in Physical Synthesis of Integrated Circuits.

In modern VLSI design, physical synthesis tools are primarily responsible for satisfying chip-performance constraints by invoking a broad range of circuit optimizations, such as buffer insertion, logic restructuring, gate sizing and relocation. This process is known as timing closure. Our research seeks more powerful and efficient optimizations to improve the state of the art in modern chip design. In particular, we integrate timing-driven relocation, retiming, logic cloning, buffer insertion and gate sizing in novel ways to create powerful circuit transformations that help satisfy setup-time constraints. State-of-the-art physical synthesis optimizations are typically applied at two scales: i) global algorithms that affect the entire netlist and ii) local transformations that focus on a handful of gates or interconnections. The scale of modern chip designs dictates that only near-linear-time optimization algorithms can be applied at the global scope — typically limited to wirelength-driven placement and legalization. Localized transformations can rely on more time-consuming optimizations with accurate delay models. Few techniques bridge the gap between fully-global and localized optimizations. This dissertation broadens the scope of physical synthesis optimization to include accurate transformations operating between the global and local scales. In particular, we integrate groups of related transformations to break circular dependencies and increase the number of circuit elements that can be jointly optimized to escape local minima. Integrated transformations in this dissertation are developed by identifying and removing obstacles to successful optimizations. Integration is achieved through mapping multiple operations to rigorous mathematical optimization problems that can be solved simultaneously. We achieve computational scalability in our techniques by leveraging analytical delay models and focusing optimization efforts on carefully selected regions of the chip. In this regard, we make extensive use of a linear interconnect-delay model that accounts for the impact of subsequent repeated insertion. Our integrated transformations are evaluated on high-performance circuits with over 100,000 gates. Integrated optimization techniques described in this dissertation ensure graceful timing-closure process and impact nearly every aspect of a typical physical synthesis flow. They have been validated in EDA tools used at IBM for physical synthesis of high-performance CPU and ASIC designs, where they significantly improved chip performance.Ph.D.Computer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/78744/1/iamyou_1.pd

Identifying developers’ habits and expectations in copy and paste programming practice

Máster Universitario en Investigación e Innovación en Inteligencia Computacional y Sistemas InteractivosBoth novice and experienced developers rely more and more in external sources of code to include into their programs by copy and paste code snippets. This behavior differs from the traditional software design approach where cohesion was achieved via a conscious design effort. Due to this fact, it is essential to know how copy and paste programming practices are actually carried out, so that IDEs (Integrated Development Environments) and code recommenders can be designed to fit with developer expectations and habit

A Survey on Compiler Autotuning using Machine Learning

Since the mid-1990s, researchers have been trying to use machine-learning based approaches to solve a number of different compiler optimization problems. These techniques primarily enhance the quality of the obtained results and, more importantly, make it feasible to tackle two main compiler optimization problems: optimization selection (choosing which optimizations to apply) and phase-ordering (choosing the order of applying optimizations). The compiler optimization space continues to grow due to the advancement of applications, increasing number of compiler optimizations, and new target architectures. Generic optimization passes in compilers cannot fully leverage newly introduced optimizations and, therefore, cannot keep up with the pace of increasing options. This survey summarizes and classifies the recent advances in using machine learning for the compiler optimization field, particularly on the two major problems of (1) selecting the best optimizations and (2) the phase-ordering of optimizations. The survey highlights the approaches taken so far, the obtained results, the fine-grain classification among different approaches and finally, the influential papers of the field.Comment: version 5.0 (updated on September 2018)- Preprint Version For our Accepted Journal @ ACM CSUR 2018 (42 pages) - This survey will be updated quarterly here (Send me your new published papers to be added in the subsequent version) History: Received November 2016; Revised August 2017; Revised February 2018; Accepted March 2018

Assessing the effect of source code characteristics on changeability

Maintenance is the phase of the software lifecycle that comprises any modification after the delivery of an application. Modifications during this phase include correcting faults, improving internal attributes, as well as adapting the application to different environments. As application knowledge and architectural integrity degrade over time, so does the facility with which changes to the application are introduced. Thus, eliminating source code that presents characteristics that hamper maintenance becomes necessary if the application is to evolve. We group these characteristics under the term Source Code Issues. Even though there is support for detecting Source Code Issues, the extent of their harmfulness for maintenance remains unknown. One of the most studied Source Code Issue is cloning. Clones are duplicated code, usually created as programmers copy, paste, and customize existing source code. However, there is no agreement on the harmfulness of clones. This thesis proposes and follows a novel methodology to assess the effect of clones on the changeability of methods. Changeability is the ease with which a source code entity is modified. It is assessed through metrics calculated from the history of changes of the methods. The impact of clones on the changeability of methods is measured by comparing the metrics of methods that contain clones to those that do not. Source code characteristics are then tested to establish whether they are endemic of methods whose changeability decay increase when cloned. In addition to findings on the harmfulness of cloning, this thesis contributes a methodology that can be applied to assess the harmfulness of other Source Code Issues. The contributions of this thesis are twofold. First, the findings answer the question about the harmfulness of clones on changeability by showing that cloned methods are more likely to change, and that some cloned methods have significantly higher changeability decay when cloned. Furthermore, it offers a characterization of such harmful clones. Second, the methodology provides a guide to analyze the effect of Source Code Characteristics in changeability; and therefore, can be adapted for other Source Code Issues