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1. Permchecker: a toolchain for debugging memory managers with typestate

   https://doi.org/10.1145/3485526  

   Cronburg, Karl ; Guyer, Samuel Z. ( October 2021 , Proceedings of the ACM on Programming Languages)

   Dynamic memory managers are a crucial component of almost every modern software system. In addition to implementing efficient allocation and reclamation, memory managers provide the essential abstraction of memory as distinct objects, which underpins the properties of memory safety and type safety. Bugs in memory managers, while not common, are extremely hard to diagnose and fix. One reason is that their implementations often involve tricky pointer calculations, raw memory manipulation, and complex memory state invariants. While these properties are often documented, they are not specified in any precise, machine-checkable form. A second reason is that memory manager bugs can breakmore »the client application in bizarre ways that do not immediately implicate the memory manager at all. A third reason is that existing tools for debugging memory errors, such as Memcheck, cannot help because they rely on correct allocation and deallocation information to work. In this paper we present Permchecker, a tool designed specifically to detect and diagnose bugs in memory managers. The key idea in Permchecker is to make the expected structure of the heap explicit by associating typestates with each piece of memory. Typestate captures elements of both type (e.g., page, block, or cell) and state (e.g., allocated, free, or forwarded). Memory manager developers annotate their implementation with information about the expected typestates of memory and how heap operations change those typestates. At runtime, our system tracks the typestates and ensures that each memory access is consistent with the expected typestates. This technique detects errors quickly, before they corrupt the application or the memory manager itself, and it often provides accurate information about the reason for the error. The implementation of Permchecker uses a combination of compile-time annotation and instrumentation, and dynamic binary instrumentation (DBI). Because the overhead of DBI is fairly high, Permchecker is suitable for a testing and debugging setting and not for deployment. It works on a wide variety of existing systems, including explicit malloc/free memory managers and garbage collectors, such as those found in JikesRVM and OpenJDK. Since bugs in these systems are not numerous, we developed a testing methodology in which we automatically inject bugs into the code using bug patterns derived from real bugs. This technique allows us to test Permchecker on hundreds or thousands of buggy variants of the code. We find that Permchecker effectively detects and localizes errors in the vast majority of cases; without it, these bugs result in strange, incorrect behaviors usually long after the actual error occurs.« less
2. The Deep Learning Epilepsy Detection Challenge: Design, Implementation, and Test of a New Crowd-Sourced AI Challenge Ecosystem

   Kiral, Isabell ; Roy, Subhrajit ; Mummert, Todd ; Braz, Alan ; Tsay, Jason ; Tang, Jianbin ; Asif, Umar ; Schaffter, Thomas ; Mehmet, Eren ; Picone, Joseph ; et al ( April 2019 , Challenges in Machine Learning Competitions for All (CiML))

   The DeepLearningEpilepsyDetectionChallenge: design, implementation, andtestofanewcrowd-sourced AIchallengeecosystem Isabell Kiral*, Subhrajit Roy*, Todd Mummert*, Alan Braz*, Jason Tsay, Jianbin Tang, Umar Asif, Thomas Schaffter, Eren Mehmet, The IBM Epilepsy Consortium◊ , Joseph Picone, Iyad Obeid, Bruno De Assis Marques, Stefan Maetschke, Rania Khalaf†, Michal Rosen-Zvi† , Gustavo Stolovitzky† , Mahtab Mirmomeni† , Stefan Harrer† * These authors contributed equally to this work † Corresponding authors: rkhalaf@us.ibm.com, rosen@il.ibm.com, gustavo@us.ibm.com, mahtabm@au1.ibm.com, sharrer@au.ibm.com ◊ Members of the IBM Epilepsy Consortium are listed in the Acknowledgements section J. Picone and I. Obeid are with Temple University, USA. T. Schaffter is with Sage Bionetworks, USA. E. Mehmetmore »is with the University of Illinois at Urbana-Champaign, USA. All other authors are with IBM Research in USA, Israel and Australia. Introduction This decade has seen an ever-growing number of scientific fields benefitting from the advances in machine learning technology and tooling. More recently, this trend reached the medical domain, with applications reaching from cancer diagnosis [1] to the development of brain-machine-interfaces [2]. While Kaggle has pioneered the crowd-sourcing of machine learning challenges to incentivise data scientists from around the world to advance algorithm and model design, the increasing complexity of problem statements demands of participants to be expert data scientists, deeply knowledgeable in at least one other scientific domain, and competent software engineers with access to large compute resources. People who match this description are few and far between, unfortunately leading to a shrinking pool of possible participants and a loss of experts dedicating their time to solving important problems. Participation is even further restricted in the context of any challenge run on confidential use cases or with sensitive data. Recently, we designed and ran a deep learning challenge to crowd-source the development of an automated labelling system for brain recordings, aiming to advance epilepsy research. A focus of this challenge, run internally in IBM, was the development of a platform that lowers the barrier of entry and therefore mitigates the risk of excluding interested parties from participating. The challenge: enabling wide participation With the goal to run a challenge that mobilises the largest possible pool of participants from IBM (global), we designed a use case around previous work in epileptic seizure prediction [3]. In this “Deep Learning Epilepsy Detection Challenge”, participants were asked to develop an automatic labelling system to reduce the time a clinician would need to diagnose patients with epilepsy. Labelled training and blind validation data for the challenge were generously provided by Temple University Hospital (TUH) [4]. TUH also devised a novel scoring metric for the detection of seizures that was used as basis for algorithm evaluation [5]. In order to provide an experience with a low barrier of entry, we designed a generalisable challenge platform under the following principles: 1. No participant should need to have in-depth knowledge of the specific domain. (i.e. no participant should need to be a neuroscientist or epileptologist.) 2. No participant should need to be an expert data scientist. 3. No participant should need more than basic programming knowledge. (i.e. no participant should need to learn how to process fringe data formats and stream data efficiently.) 4. No participant should need to provide their own computing resources. In addition to the above, our platform should further • guide participants through the entire process from sign-up to model submission, • facilitate collaboration, and • provide instant feedback to the participants through data visualisation and intermediate online leaderboards. The platform The architecture of the platform that was designed and developed is shown in Figure 1. The entire system consists of a number of interacting components. (1) A web portal serves as the entry point to challenge participation, providing challenge information, such as timelines and challenge rules, and scientific background. The portal also facilitated the formation of teams and provided participants with an intermediate leaderboard of submitted results and a final leaderboard at the end of the challenge. (2) IBM Watson Studio [6] is the umbrella term for a number of services offered by IBM. Upon creation of a user account through the web portal, an IBM Watson Studio account was automatically created for each participant that allowed users access to IBM's Data Science Experience (DSX), the analytics engine Watson Machine Learning (WML), and IBM's Cloud Object Storage (COS) [7], all of which will be described in more detail in further sections. (3) The user interface and starter kit were hosted on IBM's Data Science Experience platform (DSX) and formed the main component for designing and testing models during the challenge. DSX allows for real-time collaboration on shared notebooks between team members. A starter kit in the form of a Python notebook, supporting the popular deep learning libraries TensorFLow [8] and PyTorch [9], was provided to all teams to guide them through the challenge process. Upon instantiation, the starter kit loaded necessary python libraries and custom functions for the invisible integration with COS and WML. In dedicated spots in the notebook, participants could write custom pre-processing code, machine learning models, and post-processing algorithms. The starter kit provided instant feedback about participants' custom routines through data visualisations. Using the notebook only, teams were able to run the code on WML, making use of a compute cluster of IBM's resources. The starter kit also enabled submission of the final code to a data storage to which only the challenge team had access. (4) Watson Machine Learning provided access to shared compute resources (GPUs). Code was bundled up automatically in the starter kit and deployed to and run on WML. WML in turn had access to shared storage from which it requested recorded data and to which it stored the participant's code and trained models. (5) IBM's Cloud Object Storage held the data for this challenge. Using the starter kit, participants could investigate their results as well as data samples in order to better design custom algorithms. (6) Utility Functions were loaded into the starter kit at instantiation. This set of functions included code to pre-process data into a more common format, to optimise streaming through the use of the NutsFlow and NutsML libraries [10], and to provide seamless access to the all IBM services used. Not captured in the diagram is the final code evaluation, which was conducted in an automated way as soon as code was submitted though the starter kit, minimising the burden on the challenge organising team. Figure 1: High-level architecture of the challenge platform Measuring success The competitive phase of the "Deep Learning Epilepsy Detection Challenge" ran for 6 months. Twenty-five teams, with a total number of 87 scientists and software engineers from 14 global locations participated. All participants made use of the starter kit we provided and ran algorithms on IBM's infrastructure WML. Seven teams persisted until the end of the challenge and submitted final solutions. The best performing solutions reached seizure detection performances which allow to reduce hundred-fold the time eliptologists need to annotate continuous EEG recordings. Thus, we expect the developed algorithms to aid in the diagnosis of epilepsy by significantly shortening manual labelling time. Detailed results are currently in preparation for publication. Equally important to solving the scientific challenge, however, was to understand whether we managed to encourage participation from non-expert data scientists. Figure 2: Primary occupation as reported by challenge participants Out of the 40 participants for whom we have occupational information, 23 reported Data Science or AI as their main job description, 11 reported being a Software Engineer, and 2 people had expertise in Neuroscience. Figure 2 shows that participants had a variety of specialisations, including some that are in no way related to data science, software engineering, or neuroscience. No participant had deep knowledge and experience in data science, software engineering and neuroscience. Conclusion Given the growing complexity of data science problems and increasing dataset sizes, in order to solve these problems, it is imperative to enable collaboration between people with differences in expertise with a focus on inclusiveness and having a low barrier of entry. We designed, implemented, and tested a challenge platform to address exactly this. Using our platform, we ran a deep-learning challenge for epileptic seizure detection. 87 IBM employees from several business units including but not limited to IBM Research with a variety of skills, including sales and design, participated in this highly technical challenge.« less
3. CS 5604 2020: Information Storage and Retrieval TWT - Tweet Collection Management Team

   Baadkar, Hitesh ; Chimote, Pranav ; Hicks, Megan ; Juneja, Ikjot ; Kusuma, Manisha ; Mehta, Ujjval ; Patil, Akash ; Sharma, Irith ; Wang, Xinyue ; Fox, Edward A. ( December 2020 , Information storage and retrieval)

   The Tweet Collection Management (TWT) Team aims to ingest 5 billion tweets, clean this data, analyze the metadata present, extract key information, classify tweets into categories, and finally, index these tweets into Elasticsearch to browse and query. The main deliverable of this project is a running software application for searching tweets and for viewing Twitter collections from Digital Library Research Laboratory (DLRL) event archive projects. As a starting point, we focused on two development goals: (1) hashtag-based and (2) username-based search for tweets. For IR1, we completed extraction of two fields within our sample collection: hashtags and username. Sample codemore »for TwiRole, a user-classification program, was investigated for use in our project. We were able to sample from multiple collections of tweets, spanning topics like COVID-19 and hurricanes. Initial work encompassed using a sample collection, provided via Google Drive. An NFS-based persistent storage was later involved to allow access to larger collections. In total, we have developed 9 services to extract key information like username, hashtags, geo-location, and keywords from tweets. We have also developed services to allow for parsing and cleaning of raw API data, and backup of data in an Apache Parquet filestore. All services are Dockerized and added to the GitLab Container Registry. The services are deployed in the CS cloud cluster to integrate services into the full search engine workflow. A service is created to convert WARC files to JSON for reading archive files into the application. Unit testing of services is complete and end-to-end tests have been conducted to improve system robustness and avoid failure during deployment. The TWT team has indexed 3,200 tweets into the Elasticsearch index. Future work could involve parallelization of the extraction of metadata, an alternative feature-flag approach, advanced geo-location inference, and adoption of the DMI-TCAT format. Key deliverables include a data body that allows for search, sort, filter, and visualization of raw tweet collections and metadata analysis; a running software application for searching tweets and for viewing Twitter collections from Digital Library Research Laboratory (DLRL) event archive projects; and a user guide to assist those using the system.« less
4. ConPredictor: Concurrency Defect Prediction in Real-World Applications

   https://doi.org/10.1109/TSE.2018.2791521  

   Yu, Tingting ; Wen, Wei ; Han, Xue ; Hayes, Jane ( January 2018 , IEEE Transactions on Software Engineering)

   Concurrent programs are difficult to test due to their inherent non-determinism. To address this problem, testing often requires the exploration of thread schedules of a program; this can be time-consuming when applied to real-world programs. Software defect prediction has been used to help developers find faults and prioritize their testing efforts. Prior studies have used machine learning to build such predicting models based on designed features that encode the characteristics of programs. However, research has focused on sequential programs; to date, no work has considered defect prediction for concurrent programs, with program characteristics distinguished from sequential programs. In this paper,more »we present ConPredictor, an approach to predict defects specific to concurrent programs by combining both static and dynamic program metrics. Specifically, we propose a set of novel static code metrics based on the unique properties of concurrent programs. We also leverage additional guidance from dynamic metrics constructed based on mutation analysis. Our evaluation on four large open source projects shows that ConPredictor improved both within-project defect prediction and cross-project defect prediction compared to traditional features.« less
5. Efficient dependency detection for safe Java test acceleration

   https://doi.org/10.1145/2786805.2786823  

   Bell, Jonathan ; Kaiser, Gail ; Melski, Eric ; Dattatreya, Mohan ( August 2015 , 10th Joint Meeting of the European Software Engineering Conference and the ACM SIGSOFT Symposium on the Foundations of Software Engineering (ESEC/FSE))

   Slow builds remain a plague for software developers. The frequency with which code can be built (compiled, tested and packaged) directly impacts the productivity of developers: longer build times mean a longer wait before determining if a change to the application being built was successful. We have discovered that in the case of some languages, such as Java, the majority of build time is spent running tests, where dependencies between individual tests are complicated to discover, making many existing test acceleration techniques unsound to deploy in practice. Without knowledge of which tests are dependent on others, we cannot safely parallelizemore »the execution of the tests, nor can we perform incremental testing (i.e., execute only a subset of an application's tests for each build). The previous techniques for detecting these dependencies did not scale to large test suites: given a test suite that normally ran in two hours, the best-case running scenario for the previous tool would have taken over 422 CPU days to find dependencies between all test methods (and would not soundly find all dependencies) — on the same project the exhaustive technique (to find all dependencies) would have taken over 1e300 years. We present a novel approach to detecting all dependencies between test cases in large projects that can enable safe exploitation of parallelism and test selection with a modest analysis cost.« less