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1. Fast and Precise On-the-fly Patch Validation for All

   Chen, Lingchao ; Ouyang, Yicheng ; Zhang, Lingming ( July 2021 , IEEE/ACM International Conference on Software Engineering)

   null (Ed.)

   Generate-and-validate (G&V) automated program repair (APR) techniques have been extensively studied during the past decade. Meanwhile, such techniques can be extremely time-consuming due to the manipulation of program code to fabricate a large number of patches and also the repeated test executions on patches to identify potential fixes. PraPR, a recent G&V APR technique, reduces such costs by modifying program code directly at the level of compiled JVM bytecode with on-the-fly patch validation, which directly allows multiple bytecode patches to be tested within the same JVM process. However, PraPR is limited due to its unique bytecode-repair design, and is basically unsound/imprecise as it assumes that patch executions do not change global JVM state and affect later patch executions on the same JVM process. In this paper, we propose a unified patch validation framework, named UniAPR, to perform the first empirical study of on-the-fly patch validation for state-of-the-art source-code-level APR techniques widely studied in the literature; furthermore, UniAPR addresses the imprecise patch validation issue by resetting the JVM global state via runtime bytecode transformation. We have implemented UniAPR as a publicly available fully automated Maven Plugin. Our study demonstrates for the first time that on-the-fly patch validation can often speed up state-of-the-art source-code-level APR by over an order of magnitude, enabling all existing APR techniques to explore a larger search space to fix more bugs in the near future. Furthermore, our study shows the first empirical evidence that vanilla on-the-fly patch validation can be imprecise/unsound, while UniAPR with JVM reset is able to mitigate such issues with negligible overhead. 

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2. Static automated program repair for heap properties

   https://doi.org/10.1145/3180155.3180250  

   van Tonder, Rijnard ; Le Goues, Claire ( January 2018 , Proceedings of the 40th International Conference on Software Engineering)

   Static analysis tools have demonstrated effectiveness at finding bugs in real world code. Such tools are increasingly widely adopted to improve software quality in practice. Automated Program Repair (APR) has the potential to further cut down on the cost of improving software quality. However, there is a disconnect between these effective bug-finding tools and APR. Recent advances in APR rely on test cases, making them inapplicable to newly discovered bugs or bugs difficult to test for deterministically (like memory leaks). Additionally, the quality of patches generated to satisfy a test suite is a key challenge. We address these challenges by adapting advances in practical static analysis and verification techniques to enable a new technique that finds and then accurately fixes real bugs without test cases. We present a new automated program repair technique using Separation Logic. At a high-level, our technique reasons over semantic effects of existing program fragments to fix faults related to general pointer safety properties: resource leaks, memory leaks, and null dereferences. The procedure automatically translates identified fragments into source-level patches, and verifies patch correctness with respect to reported faults. In this work we conduct the largest study of automatically fixing undiscovered bugs in real-world code to date. We demonstrate our approach by correctly fixing 55 bugs, including 11 previously undiscovered bugs, in 11 real-world projects. 

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3. 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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4. 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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5. Can automated program repair refine fault localization? a unified debugging approach

   https://doi.org/10.1145/3395363.3397351  

   Lou, Yiling ; Ghanbari, Ali ; Li, Xia ; Zhang, Lingming ; Zhang, Haotian ; Hao, Dan ; Zhang, Lu ( July 2020 , ACM SIGSOFT International Symposium on Software Testing and Analysis)

   A large body of research efforts have been dedicated to automated software debugging, including both automated fault localization and program repair. However, existing fault localization techniques have limited effectiveness on real-world software systems while even the most advanced program repair techniques can only fix a small ratio of real-world bugs. Although fault localization and program repair are inherently connected, their only existing connection in the literature is that program repair techniques usually use off-the-shelf fault localization techniques (e.g., Ochiai) to determine the potential candidate statements/elements for patching. In this work, we propose the unified debugging approach to unify the two areas in the other direction for the first time, i.e., can program repair in turn help with fault localization? In this way, we not only open a new dimension for more powerful fault localization, but also extend the application scope of program repair to all possible bugs (not only the bugs that can be directly automatically fixed). We have designed ProFL to leverage patch-execution results (from program repair) as the feedback information for fault localization. The experimental results on the widely used Defects4J benchmark show that the basic ProFL can already at least localize 37.61% more bugs within Top-1 than state-of-the-art spectrum and mutation based fault localization. Furthermore, ProFL can boost state-of-the-art fault localization via both unsupervised and supervised learning. Meanwhile, we have demonstrated ProFL's effectiveness under different settings and through a case study within Alipay, a popular online payment system with over 1 billion global users. 

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