As software systems evolve to meet the changing needs of users, understanding the source code becomes a critical step in the process. Clustering techniques, also known as modularization techniques, offer a solution to breaking down complex source code into smaller, more manageable parts. This facilitates improved analysis and understanding of the software’s structure. However, the effectiveness of clustering algorithms in code understanding heavily relies on the chosen criteria. While existing methods typically consider cohesion, coupling, and balance between clusters, we argue that these criteria alone may not fully satisfy one of the primary objectives of clustering, which is to enhance understanding. This is because spaghetti-like structures can be created even when these criteria are satisfied. To address this issue, we introduce two new criteria incorporating program control flow to regulate cluster dependencies. By controlling the uniformity of input and output directions, as well as the distribution of inputs and outputs, clustering algorithms can generate clusters that are more developer-friendly and easier to comprehend. We provide intuitive explanations and real-world projects to demonstrate the effectiveness of our approach and also incorporate feedback from academics and expert programmers. This article reveals that integrating these new criteria into existing clustering algorithms enables developers to gain deeper insights into the structure of software systems. This, in turn, leads to better design decisions and improved developer understanding of the source code.

Drug repurposing is an exciting field of research toward recognizing a new FDA-approved drug target for the treatment of a specific disease. It has received extensive attention regarding the tedious, time-consuming, and highly expensive procedure with a high risk of failure of new drug discovery. Data-driven approaches are an important class of methods that have been introduced for identifying a candidate drug against a target disease. In the present study, a model is proposed illustrating the integration of drug-disease association data for drug repurposing using a deep neural network. The model, so-called IDDI-DNN, primarily constructs similarity matrices for drug-related properties (three matrices), disease-related properties (two matrices), and drug-disease associations (one matrix). Then, these matrices are integrated into a unique matrix through a two-step procedure benefiting from the similarity network fusion method. The model uses a constructed matrix for the prediction of novel and unknown drug-disease associations through a convolutional neural network. The proposed model was evaluated comparatively using two different datasets including the gold standard dataset and DNdataset. Comparing the results of evaluations indicates that IDDI-DNN outperforms other state-of-the-art methods concerning prediction accuracy.

Abstract Users of cloud computing technology can lease resources instead of spending an excessive charge for their ownership. For service delivery in the infrastructure-as-a-service model of the cloud computing paradigm, virtual machines (VMs) are created by the hypervisor. This software is installed on a bare-metal server, called the host, and acted as a broker between the hardware of the host and its VMs. The host is responsible for the allocation of required resources, such as CPU, RAM and network bandwidth, for VMs. Therefore, allocating resources to a VM is equivalent to finding the location of the VM on the hosts. In this paper, we propose a model for resource allocation of a datacenter that includes clusters of hosts. This model is based on the birth–death process of queueing systems and continuous-time Markov chains. We will focus on RAM-intensive VMs and consider the allocation of RAM for a VM as a job in the queueing systems. The purpose of this modeling is to keep the number of running hosts minimum while guaranteeing the quality of service in terms of response. When the utilization of active hosts reaches a predefined threshold value, a new host is added to prevent response time violation, and when host utilization is reduced to a certain threshold, one of the hosts can be deactivated. The experimental results show that, in the long run, the odds of working with more jobs are increased.

A software system evolves over time in order to meet the needs of users. Understanding a program is the most important step to apply new requirements. Clustering techniques through dividing a program into small and meaningful parts make it possible to understand the program. In general, clustering algorithms are classified into two categories: hierarchical and non-hierarchical algorithms (such as search-based approaches). While clustering problems generally tend to be NP-hard, search-based algorithms produce acceptable clustering and have time and space constraints and hence they are inefficient in large-scale software systems. Most algorithms which currently used in software clustering fields do not scale well when applied to large and very large applications. In this paper, we present a new and fast clustering algorithm, FCA, that can overcome space and time constraints of existing algorithms by performing operations on the dependency matrix and extracting other matrices based on a set of features. The experimental results on ten small-sized applications, ten folders with different functionalities from Mozilla Firefox, a large-sized application (namely ITK), and a very large-sized application (namely Chromium) demonstrate that the proposed algorithm achieves higher quality modularization compared with hierarchical algorithms. It can also compete with search-based algorithms and a clustering algorithm based on subsystem patterns. But the running time of the proposed algorithm is much shorter than that of the hierarchical and non-hierarchical algorithms. The source code of the proposed algorithm can be accessed athttps://github.com/SoftwareMaintenanceLab.

Abstract Security is a growing concern in developing software systems. It is important to face unknown threats in order to make the system continue operating properly. Threats are vague and attack methods change frequently. Coping with such changes is a major feature of an adaptive software. Therefore, designing an adaptive secure software is an appropriate solution to address software security challenges. Through estimation of maximum amount of system assets security, one can determine whether the system is protecting the assets or not; if not, reconfiguration can be employed. This paper proposes a new requirement model for secure adaptive systems using fuzzy, goal modeling and Description Logic concepts. The model contains three phases of modeling security aspects of the system, identifying formalizations and relations between the requirements and monitoring and adapting, when needed. To illustrate the relations between the requirements, goal modeling is used in the first phase and fuzzy Description Logic in the second phase. For the third phase, four algorithms are proposed to monitor and determine whether reconfiguration is needed or not. Theorems are given to prove concept satisfaction of the requirements. Furthermore, examples and case studies are discussed to evaluate and show applicability of the proposed model.

Clustering (modularisation) techniques are often employed for the meaningful decomposition of a program aiming to understand it. In the software clustering context, several external metrics are presented to evaluate and validate the resultant clustering obtained by an algorithm. These metrics use a ground‐truth decomposition to evaluate a resultant clustering. When there exists no ground‐truth decomposition for a software system, internal metrics are utilised to validate clustering algorithms. Due to the comparison with a reference decomposition, external metrics are preferred to internal metrics. Available internal metrics used to measure the clustering quality are not appropriate for evaluating because they do not consider the purpose of software clustering, which is to understand a software system. In this study, the authors present six criteria that influence the understanding of a program. Then the authors design an internal metric for estimating the software clustering quality considering those criteria. They selected ten folders of Mozilla Firefox with different sizes and functionalities to assess the reliability of the proposed metric. The experimental results confirm that the proposed internal metric is more accurate than the existing internal metrics in terms of proximity to expert decomposition. The proposed internal metric can be a substitute for external metrics.

One way to speed up the execution of sequential programs is to divide them into concurrent segments and execute such segments in a parallel manner over a distributed computing environment. We argue that the execution speedup primarily depends on the concurrency degree between the identified segments as well as communication overhead between the segments. To guarantee the best speedup, we have to obtain the maximum possible concurrency degree between the identified segments, taking communication overhead into consideration. Existing code distributor and multi-threading approaches do not fulfill such requirements; hence, they cannot provide expected distributability gains in advance. To overcome such limitations, we propose a novel approach for verifying the distributability of sequential object-oriented programs. The proposed approach enables users to see the maximum speedup gains before the actual distributability implementations, as it computes an objective function which is used to measure different distribution values from the same program, taking into consideration both remote and sequential calls. Experimental results showed that the proposed approach successfully determines the distributability of different real-life software applications compared with their real-life sequential and distributed implementations.