BACKGROUND: DNA methylation is essential in various biological processes, including imprinting, development, inflammation, and numerous disorders, such as cancer. Bisulfite sequencing (BS) serves as the gold standard for measuring DNA methylation at single-base resolution by converting unmethylated cytosines to thymines while leaving methylated cytosines intact. However, this C-to-T conversion presents a well-known challenge in conventional short-read aligners, which treat these conversions as substitutions. Many aligners that require seed sequences fail when frequent C-to-T conversions occur over short distances, resulting in reduced alignment accuracy. To address this challenge, two alignment methods have been well established: three-letter alignment and wildcard alignment. Three-letter alignment faces the significant issue of data loss by converting all thymines to cytosines, which obscures meaningful information. On the other hand, wildcard alignment introduces a biased alignment, failing to treat reads from unmethylated and methylated regions equally, leading to artifacts in methylation level estimation and inaccuracies in quantifying DNA methylation. This work introduces ARYANA-BS, a novel BS aligner that diverges from conventional DNA aligners by directly integrating BS-specific base alterations within its alignment engine. Leveraging known DNA methylation patterns across different genomic contexts, ARYANA-BS constructs five indexes from the reference genome, aligns each read to all indexes, and selects the alignment with the minimum penalty. To further refine alignment accuracy, an optional Expectation-Maximization (EM) step is incorporated, which integrates methylation probability information into the decision-making process for choosing the optimal index for each read. This approach aims to enhance BS read alignment accuracy by accommodating the complexities of DNA methylation patterns across diverse genomic contexts. RESULTS: Experimental evaluations on both simulated and real data reveal that ARYANA-BS achieves state-of-the-art accuracy, maintaining competitive speed and memory efficiency. CONCLUSIONS: ARYANA-BS significantly improves alignment accuracy for bisulfite sequencing data by effectively integrating DNA methylation-specific alterations and genomic context. It outperforms existing methods, such as BSMAP, bwa-meth, Bismark, BSBolt, and abismal, particularly in robustness against genomic biases and alignment of longer, higher-error reads, demonstrating suitability for cancer research and cell-free DNA studies. While the Expectation-Maximization (EM) algorithm provides only modest initial improvements, it establishes a valuable framework for future refinement and potential enhancements in sensitive applications.

Testing plays an essential role in ensuring the safety and quality of cyberphysical systems (CPSs). One of the main challenges in automated and software-in-the-loop simulation testing of CPSs is defining effective oracles that can check that a given system conforms to expectations of desired behavior. Manually specifying such oracles can be tedious, complex, and error-prone, and so techniques for automatically learning oracles are attractive. Characteristics of CPSs, such as limited or no access to source code, behavior that is non-deterministic and sensitive to noise, and that the system may respond differently to input based on its context introduce considerable challenges for automated oracle learning. We present Mithra, a novel, unsupervised oracle learning technique for CPSs that operates on existing telemetry data. It uses a three-step multivariate time series clustering to discover the set of unique, correct behaviors for a CPS, which it uses to construct robust oracles. We instantiate our proposed technique for ArduPilot, a popular, open-source autopilot software. On a set of 24 bugs, we show that Mithra effectively identifies buggy executions with few false positives and outperforms AR-SI, a state-of-the-art CPS oracle learning technique. We demonstrate Mithra’s wider applicability by applying it to an autonomous racer built for the Robot Operating System.

Robotics simulation plays an important role in the design, development, and verification and validation of robotics systems. Simulation represents a potentially cheaper, safer, and more reliable alternative to the widely used practice of manual field testing, and introduces valuable opportunities for extensive test automation. The goal of this paper is to develop a principled understanding of the ways robotics developers use simulation in their testing processes and the challenges they face in doing so. This understanding can guide the improvement of simulators and testing techniques for modern robotics development.To that end, we conduct a survey of 82 robotics developers from a diversity of backgrounds, addressing the current capabilities and limits of simulation in practice. We find that simulation is used by 84% of our participants for testing, and that many participants want to use simulation as part of their test automation. Using qualitative and quantitative research methods, we identify 10 high-level challenges that impede developers from using simulation for manual and automated testing and in general. These challenges include the gap between simulation and reality, a lack of reproducibility, and considerable resource costs associated with simulation. Finally, we outline ways in which simulators can be improved for use as a means of verification and validation and ways that the software engineering community can contribute to these improvements.

Automated program repair holds the potential to significantly reduce software maintenance effort and cost. However, recent studies have shown that it often produces low-quality patches that repair some but break other functionality. We hypothesize that producing patches by replacing likely faulty regions of code with semantically-similar code fragments, and doing so at a higher level of granularity than prior approaches can better capture abstraction and the intended specification, and can improve repair quality. We create SOSRepair, an automated program repair technique that uses semantic code search to replace candidate buggy code regions with behaviorally-similar (but not identical) code written by humans. SOSRepair is the first such technique to scale to real-world defects in real-world systems. On a subset of the ManyBugs benchmark of such defects, SOSRepair produces patches for 22 (34%) of the 65 defects, including 3, 5, and 6 defects for which previous state-of-the-art techniques Angelix, Prophet, and GenProg do not, respectively. On these 22 defects, SOSRepair produces more patches (9, 41%) that pass all independent tests than the prior techniques. We demonstrate a relationship between patch granularity and the ability to produce patches that pass all independent tests. We then show that fault localization precision is a key factor in SOSRepair's success. Manually improving fault localization allows SOSRepair to patch 23 (35%) defects, of which 16 (70%) pass all independent tests. We conclude that (1) higher-granularity, semantic-based patches can improve patch quality, (2) semantic search is promising for producing high-quality real-world defect repairs, (3) research in fault localization can significantly improve the quality of program repair techniques, and (4) semi-automated approaches in which developers suggest fix locations may produce high-quality patches.

Over the past eleven years, the Robot Operating System (ROS), has grown from a small research project into the most popular framework for robotics development. Composed of packages released on the Rosdistro package manager, ROS aims to simplify development by providing reusable libraries, tools and conventions for building a robot. Still, developing a complete robot is a difficult task that involves bridging many technical disciplines. Experts who create computer vision packages, for instance, may need to rely on software designed by mechanical engineers to implement motor control. As building a robot requires domain expertise in software, mechanical, and electrical engineering, as well as artificial intelligence and robotics, ROS faces knowledge based barriers to collaboration.In this paper, we examine how the necessity of domain specific knowledge impacts the open source collaboration model. We create a comprehensive corpus of package metadata and dependencies over three years in the ROS ecosystem, analyze how collaboration is structured, and study the dependency network evolution. We find that the most widely used ROS packages belong to a small cluster of foundational working groups (FWGs), each organized around a different domain in robotics. We show that the FWGs are growing at a slower rate than the rest of the ecosystem, in terms of their membership and number of packages, yet the number of dependencies on FWGs is increasing at a faster rate. In addition, we mined all ROS packages on GitHub, and showed that 82% rely exclusively on functionality provided by FWGs. Finally, we investigate these highly influential groups and describe the unique model of collaboration they support in ROS.

Robotic systems are increasingly a part of everyday life. Characteristics of robotic systems such as interaction with the physical world, and integration of hardware and software components, differentiate robotic systems from conventional software systems. Although numerous studies have investigated the challenges of software testing in practice, no such study has focused on testing of robotic systems. In this paper, we conduct a qualitative study to better understand the testing practices used by the robotics community, and identify the challenges faced by practitioners when testing their systems. We identify a total of 12 testing practices and 9 testing challenges from our participants' responses. We group these challenges into 3 major themes: Real-world complexities, Community and standards, and Component integration. We believe that further research on addressing challenges described with these three major themes can result in higher adoption of robotics testing practices, more testing automation, and higher-quality robotic systems.

A new wave of collaborative robots designed to work alongside humans is bringing the automation historically seen in large-scale industrial settings to new, diverse contexts. However, the ability to program these machines often requires years of training, making them inaccessible or impractical for many. This paper rethinks what robot programming interfaces could be in order to make them accessible and intuitive for adult novice programmers. We created a block-based interface for programming a one-armed industrial robot and conducted a study with 67 adult novices comparing it to two programming approaches in widespread use in industry. The results show participants using the block-based interface successfully implemented robot programs faster with no loss in accuracy while reporting higher scores for usability, learnability, and overall satisfaction. The contribution of this work is showing the potential for using block-based programming to make powerful technologies accessible to a wider audience.

Integrated development environments (IDEs) provide features to help developers both create and understand code. As maintenance and bug repair are time-consuming and costly activities, IDEs have long integrated debugging features to simplify these tasks. In this paper we investigate the impact of using IDE debugger features on different aspects of programming and debugging. Using the data set provided by MSR challenge track, we compared debugging tasks performed with or without the IDE debugger. We find, on average, that developers spend more time and effort on debugging when they use the debugger. Typically, developers start using the debugger early, at the beginning of a debugging session, and that their editing behavior does not appear to significantly change when they are debugging regardless of whether debugging features are in use.

Many robotic tasks in small manufacturing sites are quite simple. For example, a pick and place task requires only a few common commands. Unfortunately, the standard languages and programming environments for industrial robots are complex, making even these simple tasks nearly impossible for novices. To enable novices to program simple tasks we created a block-based programming language and environment focused on usability, learnability, and understandability and embedded its programming environment in a state-of-the-art robot simulator. By using this high-fidelity prototype over the course of a year in a case study, a user study, and for countless demonstrations we have gained many concrete insights. In this paper we discuss the details of the language, the design of its programming environment, and concrete insights gained via longitudinal usage.

Robots and autonomous systems are finding their way to interact with the public and failures in these systems could be extremely expensive, even deadly. However, low-cost software-based simulation could be a promising approach to systematically test robotics systems and prevent failures as early as possible. In our early work, we showed that the majority of bugs could actually be reproduced and discovered using low-fidelity simulation environment. We created a high-level framework for automated testing of popular ArduPilot systems. In this work, I propose novel approaches to automatically infer powerful representation of system models, and generate test suites with the purpose of enhancing automated fault localization performance and describing the root cause of failures. Finally, I propose to use those novel approaches to inform the construction of automated program repair techniques for autonomous systems.