The Java system dependence graph

The Program Dependence Graph was introduced by Ottenstein and Ottenstein in 1984 [14]. It was suggested to be a suitable internal program representation for monolithic programs, for the purpose of carrying out certain software engineering operations such as slicing and the computation of program metrics. Since then, Horwitz et al. have introduced the multi-procedural equivalent System Dependence Graph [9]. Many authors have proposed object-oriented dependence graph construction approaches [11, 10, 20, 12]. Every approach provides its own benefits, some of which are language specific. This paper is based on Java and combines the most important benefits from a range of approaches. The result is a Java System Dependence Graph, which summarises the key benefits offered by different approaches and adapts them (if necessary) to the Java language

Understanding object-oriented source code from the behavioural perspective

Comprehension is a key activity that underpins a variety of software maintenance and engineering tasks. The task of understanding object-oriented systems is hampered by the fact that the code segments that are related to a user-level function tend to be distributed across the system. We introduce a tool-supported code extraction technique that addresses this issue. Given a minimal amount of information about a behavioural element of the system that is of interest (such as a use-case), it extracts a trail of the methods (and method invocations) through the system that are needed in order to achieve an understanding of the implementation of the element of interest. We demonstrate the feasibility of our approach by implementing it as part of a code extraction tool, presenting a case study and evaluating the approach and tool against a set of established criteria for program comprehension tools

Crystallization of a Mos1 transposase-inverted-repeat DNA complex: biochemical and preliminary crystallographic analyses

A complex formed between Mos1 transposase and its inverted-repeat DNA has been crystallized. The crystals diffract to 3.25 Å resolution and exhibit monoclinic (P2(1)) symmetry, with unit-cell parameters a = 120.8, b = 85.1, c = 131.6 Å, β = 99.3°. The X-ray diffraction data display noncrystallographic twofold symmetry and characteristic dsDNA diffraction at ∼3.3 Å. Biochemical analyses confirmed the presence of DNA and full-length protein in the crystals. The relationship between the axis of noncrystallographic symmetry, the unit-cell axes and the DNA diffraction pattern are discussed. The data are consistent with the previously proposed model of the paired-ends complex containing a dimer of the transposase

Data and analysis code for GP EFSM inference

This artifact captures the workflow that we adopted for our experimental evaluation in our ICSME paper on inferring state transition functions during EFSM inference. To summarise, the paper uses Genetic Programming to infer data transformations, to enable the inference of fully 'computational' extended finite state machine models. This submission shows how we generated, transformed, analysed, and visualised our raw data. It includes everything needed to generate raw results and provides the relevant R code in the form of a re-usable Jupyter Notebook (accompanied by a descriptive narrative)

Inferring Computational State Machine Models from Program Executions

The challenge of inferring state machines from log data or execution traces is well-established, and has led to the development of several powerful techniques. Current approaches tend to focus on the inference of conventional finite state machines or, in few cases, state machines with guards. However, these machines are ultimately only partial, because they fail to model how any underlying variables are computed during the course of an execution, they are not computational. In this paper we introduce a technique based upon Genetic Programming to infer these data transformation functions, which in turn render inferred automata fully computational. Instead of merely determining whether or not a sequence is possible, they can be simulated, and be used to compute the variable values throughout the course of an execution. We demonstrate the approach by using a Cross-Validation study to reverse-engineer complete (computational) EFSMs from traces of established implementations

Effectively incorporating expert knowledge in automated software remodularisation

Remodularising the components of a software system is challenging: sound design principles (e.g., coupling and cohesion) need to be balanced against developer intuition of which entities conceptually belong together. Despite this, automated approaches to remodularisation tend to ignore domain knowledge, leading to results that can be nonsensical to developers. Nevertheless, suppling such knowledge is a potentially burdensome task to perform manually. A lot information may need to be specified, particularly for large systems. Addressing these concerns, we propose the SUMO (SUpervised reMOdularisation) approach. SUMO is a technique that aims to leverage a small subset of domain knowledge about a system to produce a remodularisation that will be acceptable to a developer. With SUMO, developers refine a modularisation by iteratively supplying corrections. These corrections constrain the type of remodularisation eventually required, enabling SUMO to dramatically reduce the solution space. This in turn reduces the amount of feedback the developer needs to supply. We perform a comprehensive systematic evaluation using 100 real world subject systems. Our results show that SUMO guarantees convergence on a target remodularisation with a tractable amount of user interaction

SEPIA: Search for Proofs Using Inferred Automata

This paper describes SEPIA, a tool for automated proof generation in Coq. SEPIA combines model inference with interactive theorem proving. Existing proof corpora are modelled using state-based models inferred from tactic sequences. These can then be traversed automatically to identify proofs. The SEPIA system is described and its performance evaluated on three Coq datasets. Our results show that SEPIA provides a useful complement to existing automated tactics in Coq.Comment: To appear at 25th International Conference on Automated Deductio

Mining State-Based Models from Proof Corpora

Interactive theorem provers have been used extensively to reason about various software/hardware systems and mathematical theorems. The key challenge when using an interactive prover is finding a suitable sequence of proof steps that will lead to a successful proof requires a significant amount of human intervention. This paper presents an automated technique that takes as input examples of successful proofs and infers an Extended Finite State Machine as output. This can in turn be used to generate proofs of new conjectures. Our preliminary experiments show that the inferred models are generally accurate (contain few false-positive sequences) and that representing existing proofs in such a way can be very useful when guiding new ones.Comment: To Appear at Conferences on Intelligent Computer Mathematics 201

Reasoning about uncertainty in empirical results

Conclusions that are drawn from experiments are subject to varying degrees of uncertainty. For example, they might rely on small data sets, employ statistical techniques that make assumptions that are hard to verify, or there may be unknown confounding factors. In this paper we propose an alternative but complementary mechanism to explicitly incorporate these various sources of uncertainty into reasoning about empirical findings, by applying Subjective Logic. To do this we show how typical traditional results can be encoded as "subjective opinions" -- the building blocks of Subjective Logic. We demonstrate the value of the approach by using Subjective Logic to aggregate empirical results from two large published studies that explore the relationship between programming languages and defects or failures

Reverse-engineering EFSMs with data dependencies

EFSMs provide a way to model systems with internal data variables. In situations where they do not already exist, we need to infer them from system behaviour. A key challenge here is inferring the functions which relate inputs, outputs, and internal variables. Existing approaches either work with white-box traces, which expose variable values, or rely upon the user to provide heuristics to recognise and generalise particular data-usage patterns. This paper presents a preprocessing technique for the inference process which generalises the concrete values from the traces into symbolic functions which calculate output from input, even when this depends on values not present in the original traces. Our results show that our technique leads to more accurate models than are produced by the current state-of-the-art and that somewhat accurate models can still be inferred even when the output of particular transitions depends on values not present in the original traces