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1. Update with Care: Testing Candidate Bug Fixes and Integrating Selective Updates through Binary Rewriting

   https://doi.org/https://doi.org/10.1016/j.jss.2022.111381  

   Saieva, Anthony ; Kaiser, Gail ( January 2022 , The Journal of systems and software)

   Enterprise software updates depend on the interaction between user and developer organizations. This interaction becomes especially complex when a single developer organization writes software that services hundreds of different user organizations. Miscommunication during patching and deployment efforts lead to insecure or malfunctioning software installations. While developers oversee the code, the update process starts and ends outside their control. Since developer test suites may fail to capture buggy behavior finding and fixing these bugs starts with user generated bug reports and 3rd party disclosures. The process ends when the fixed code is deployed in production. Any friction between user, and developer results in a delay patching critical bugs. Two common causes for friction are a failure to replicate user specific circumstances that cause buggy behavior and incompatible software releases that break critical functionality. Existing test generation techniques are insufficient. They fail to test candidate patches for post-deployment bugs and to test whether the new release adversely effects customer workloads. With existing test generation and deployment techniques, users can't choose (nor validate) compatible portions of new versions and retain their previous version's functionality. We present two new technologies to alleviate this friction. First, Test Generation for Ad Hoc Circumstances transforms buggy executions into test cases. Second, Binary Patch Decomposition allows users to select the compatible pieces of update releases. By sharing specific context around buggy behavior and developers can create specific test cases that demonstrate if their fixes are appropriate. When fixes are distributed by including extra context users can incorporate only updates that guarantee compatibility between buggy and fixed versions. We use change analysis in combination with binary rewriting to transform the old executable and buggy execution into a test case including the developer's prospective changes that let us generate and run targeted tests for the candidate patch. We also provide analogous support to users, to selectively validate and patch their production environments with only the desired bug-fixes from new version releases. This paper presents a new patching workflow that allows developers to validate prospective patches and users to select which updates they would like to apply, along with two new technologies that make it possible. We demonstrate our technique constructs tests cases more effectively and more efficiently than traditional test case generation on a collection of real world bugs compared to traditional test generation techniques, and provides the ability for flexible updates in real world scenarios. 

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2. On the effectiveness of unified debugging: an extensive study on 16 program repair systems

   https://doi.org/10.1145/3324884.3416566  

   Benton, Samuel ; Li, Xia ; Lou, Yiling ; Zhang, Lingming ( December 2020 , IEEE/ACM International Conference on Automated Software Engineering)

   null (Ed.)

   Automated debugging techniques, including fault localization and program repair, have been studied for over a decade. However, the only existing connection between fault localization and program repair is that fault localization computes the potential buggy elements for program repair to patch. Recently, a pioneering work, ProFL, explored the idea of unified debugging to unify fault localization and program repair in the other direction for the first time to boost both areas. More specifically, ProFL utilizes the patch execution results from one state-of-the-art repair system, PraPR, to help improve state-of-the-art fault localization. In this way, ProFL not only improves fault localization for manual repair, but also extends the application scope of automated repair to all possible bugs (not only the small ratio of bugs that can be automatically fixed). However, ProFL only considers one APR system (i.e., PraPR), and it is not clear how other existing APR systems based on different designs contribute to unified debugging. In this work, we perform an extensive study of the unified-debugging approach on 16 state-of-the-art program repair systems for the first time. Our experimental results on the widely studied Defects4J benchmark suite reveal various practical guidelines for unified debugging, such as (1) nearly all the studied 16 repair systems can positively contribute to unified debugging despite their varying repairing capabilities, (2) repair systems targeting multi-edit patches can bring extraneous noise into unified debugging, (3) repair systems with more executed/plausible patches tend to perform better for unified debugging, and (4) unified debugging effectiveness does not rely on the availability of correct patches in automated repair. Based on our results, we further propose an advanced unified debugging technique, UniDebug++, which can localize over 20% more bugs within Top-1 positions than state-of-the-art unified debugging technique, ProFL. 

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3. 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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4. Practical program repair via bytecode mutation

   https://doi.org/10.1145/3293882.3330559  

   Ghanbari, Ali ; Benton, Samuel ; Zhang, Lingming ( January 2019 , ACM SIGSOFT International Symposium on Software Testing and Analysis)

   Automated Program Repair (APR) is one of the most recent advances in automated debugging, and can directly fix buggy programs with minimal human intervention. Although various advanced APR techniques (including search-based or semantic-based ones) have been proposed, they mainly work at the source-code level and it is not clear how bytecode-level APR performs in practice. Also, empirical studies of the existing techniques on bugs beyond what has been reported in the original papers are rather limited. In this paper, we implement the first practical bytecode-level APR technique, PraPR, and present the first extensive study on fixing real-world bugs (e.g., Defects4J bugs) using JVM bytecode mutation. The experimental results show that surprisingly even PraPR with only the basic traditional mutators can produce genuine fixes for 17 bugs; with simple additional commonly used APR mutators, PraPR is able to produce genuine fixes for 43 bugs, significantly outperforming state-of-the-art APR, while being over 10X faster. Furthermore, we performed an extensive study of PraPR and other recent APR tools on a large number of additional real-world bugs, and demonstrated the overfitting problem of recent advanced APR tools for the first time. Lastly, PraPR has also successfully fixed bugs for other JVM languages (e.g., for the popular Kotlin language), indicating PraPR can greatly complement existing source-code-level APR. 

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5. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

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