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1. Repairing Deep Neural Networks: Fix Patterns and Challenges

   https://doi.org/10.1145/3377811.3380378  

   Islam, Md Johirul ; Pan, Rangeet ; Nguyen, Giang ; Rajan, Hridesh ( July 2020 , ICSE'20: The 42nd International Conference on Software Engineering)

   Significant interest in applying Deep Neural Network (DNN) has fueled the need to support engineering of software that uses DNNs. Repairing software that uses DNNs is one such unmistakable SE need where automated tools could be very helpful; however, we do not fully understand challenges to repairing and patterns that are utilized when manually repairing them. What challenges should automated repair tools address? What are the repair patterns whose automation could help developers? Which repair patterns should be assigned a higher priority for automation? This work presents a comprehensive study of bug fix patterns to address these questions. We have studied 415 repairs from Stack Overflow and 555 repairs from GitHub for five popular deep learning libraries Caffe, Keras, Tensorflow, Theano, and Torch to understand challenges in repairs and bug repair patterns. Our key findings reveal that DNN bug fix patterns are distinctive compared to traditional bug fix patterns; the most common bug fix patterns are fixing data dimension and neural network connectivity; DNN bug fixes have the potential to introduce adversarial vulnerabilities; DNN bug fixes frequently introduce new bugs; and DNN bug localization, reuse of trained model, and coping with frequent releases are major challenges faced by developers when fixing bugs. We also contribute a benchmark of 667 DNN (bug, repair) instances. 

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2. DeepLocalize: Fault Localization for Deep Neural Networks

   https://doi.org/10.1109/ICSE43902.2021.00034  

   Wardat, Mohammad ; Le, Wei ; Rajan, Hridesh ( May 2021 , 2021 IEEE/ACM 43rd International Conference on Software Engineering (ICSE))

   null (Ed.)

   Deep Neural Networks (DNNs) are becoming an integral part of most software systems. Previous work has shown that DNNs have bugs. Unfortunately, existing debugging techniques don't support localizing DNN bugs because of the lack of understanding of model behaviors. The entire DNN model appears as a black box. To address these problems, we propose an approach and a tool that automatically determines whether the model is buggy or not, and identifies the root causes for DNN errors. Our key insight is that historic trends in values propagated between layers can be analyzed to identify faults, and also localize faults. To that end, we first enable dynamic analysis of deep learning applications: by converting it into an imperative representation and alternatively using a callback mechanism. Both mechanisms allows us to insert probes that enable dynamic analysis over the traces produced by the DNN while it is being trained on the training data. We then conduct dynamic analysis over the traces to identify the faulty layer or hyperparameter that causes the error. We propose an algorithm for identifying root causes by capturing any numerical error and monitoring the model during training and finding the relevance of every layer/parameter on the DNN outcome. We have collected a benchmark containing 40 buggy models and patches that contain real errors in deep learning applications from Stack Overflow and GitHub. Our benchmark can be used to evaluate automated debugging tools and repair techniques. We have evaluated our approach using this DNN bug-and-patch benchmark, and the results showed that our approach is much more effective than the existing debugging approach used in the state-of-the-practice Keras library. For 34/40 cases, our approach was able to detect faults whereas the best debugging approach provided by Keras detected 32/40 faults. Our approach was able to localize 21/40 bugs whereas Keras did not localize any faults. 

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3. A Comprehensive Study of Autonomous Vehicle Bugs

   https://doi.org/10.1145/3377811.3380397  

   Garcia, Joshua ; Feng, Yang ; Shen, Junjie ; Almanee, Sumaya ; Xia, Yuan ; Chen, Qi Alfred ( May 2020 , 2020 IEEE/ACM 42nd International Conference on Software Engineering (ICSE))

   Self-driving cars, or Autonomous Vehicles (AVs), are increasingly becoming an integral part of our daily life. About 50 corporations are actively working on AVs, including large companies such as Google, Ford, and Intel. Some AVs are already operating on public roads, with at least one unfortunate fatality recently on record. As a result, understanding bugs in AVs is critical for ensuring their security, safety, robustness, and correctness. While previous studies have focused on a variety of domains (e.g., numerical software; machine learning; and error-handling, concurrency, and performance bugs) to investigate bug characteristics, AVs have not been studied in a similar manner. Recently, two software systems for AVs, Baidu Apollo and Autoware, have emerged as frontrunners in the opensource community and have been used by large companies and governments (e.g., Lincoln, Volvo, Ford, Intel, Hitachi, LG, and the US Department of Transportation). From these two leading AV software systems, this paper describes our investigation of 16,851 commits and 499 AV bugs and introduces our classification of those bugs into 13 root causes, 20 bug symptoms, and 18 categories of software components those bugs often affect. We identify 16 major findings from our study and draw broader lessons from them to guide the research community towards future directions in software bug detection, localization, and repair. 

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4. Evaluating Synthetic Bugs

   https://doi.org/10.1145/3433210.3453096  

   Bundt, Joshua ; Fasano, Andrew ; Dolan-Gavitt, Brendan ; Robertson, William ; Leek, Tim ( May 2021 , ASIA CCS '21: Proceedings of the 2021 ACM Asia Conference on Computer and Communications Security)

   null (Ed.)

   Fuzz testing has been used to find bugs in programs since the 1990s, but despite decades of dedicated research, there is still no consensus on which fuzzing techniques work best. One reason for this is the paucity of ground truth: bugs in real programs with known root causes and triggering inputs are difficult to collect at a meaningful scale. Bug injection technologies that add synthetic bugs into real programs seem to offer a solution, but the differences in finding these synthetic bugs versus organic bugs have not previously been explored at a large scale. Using over 80 years of CPU time, we ran eight fuzzers across 20 targets from the Rode0day bug-finding competition and the LAVA-M corpus. Experiments were standardized with respect to compute resources and metrics gathered. These experiments show differences in fuzzer performance as well as the impact of various configuration options. For instance, it is clear that integrating symbolic execution with mutational fuzzing is very effective and that using dictionaries improves performance. Other conclusions are less clear-cut; for example, no one fuzzer beat all others on all tests. It is noteworthy that no fuzzer found any organic bugs (i.e., one reported in a CVE), despite 50 such bugs being available for discovery in the fuzzing corpus. A close analysis of results revealed a possible explanation: a dramatic difference between where synthetic and organic bugs live with respect to the "main path" discovered by fuzzers. We find that recent updates to bug injection systems have made synthetic bugs more difficult to discover, but they are still significantly easier to find than organic bugs in our target programs. Finally, this study identifies flaws in bug injection techniques and suggests a number of axes along which synthetic bugs should be improved. 

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5. 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))

   null (Ed.)

   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. Mehmet 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. 

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