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1. Resurgence of Regression Test Selection for C++

   Fu, Ben ; Misailovic, Sasa ; Gligoric, Milos ( April 2019 , 12th IEEE Conference on Software Testing, Validation, and Verification (ICST 2019))

   Regression testing - running available tests after each project change - is widely practiced in industry. Despite its widespread use and importance, regression testing is a costly activity. Regression test selection (RTS) optimizes regression testing by selecting only tests affected by project changes. RTS has been extensively studied and several tools have been deployed in large projects. However, work on RTS over the last decade has mostly focused on languages with abstract computing machines(e.g., JVM). Meanwhile development practices (e.g., frequency of commits, testing frameworks, compilers) in C++ projects have dramatically changed and the way we should design and implement RTS tools and the benefits of those tools is unknown. We present a design and implementation of an RTS technique, dubbed RTS++, that targets projects written in C++, which compile to LLVM IR and use the Google Test testing framework. RTS++ uses static analysis of a function call graph to select tests. RTS++ integrates with many existing build systems, including AutoMake, CMake, and Make. We evaluated RTS++ on 11 large open-source projects, totaling 3,811,916 lines of code. To the best of our knowledge, this is the largest evaluation of an RTS technique for C++. We measured the benefits of RTS++compared to running all available tests (i.e., retest-all). Our results show that RTS++ reduces the number of executed tests and end-to-end testing time by 88% and 61% on average. 

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2. 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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3. One-off events? An empirical study of hackathon code creation and reuse

   https://doi.org/10.1007/s10664-022-10201-x  

   Mahmoud, Ahmed Samir Imam ; Dey, Tapajit ; Nolte, Alexander ; Mockus, Audris ; Herbsleb, James D. ( September 2022 , Empirical Software Engineering)

   Hackathons have become popular events for teams to collaborate on projects and develop software prototypes. Most existing research focuses on activities during an event with limited attention to the evolution of the hackathon code.

   We aim to understand the evolution of code used in and created during hackathon events, with a particular focus on the code blobs, specifically, how frequently hackathon teams reuse pre-existing code, how much new code they develop, if that code gets reused afterwards, and what factors affect reuse.

   We collected information about 22,183 hackathon projects from Devpost and obtained related code blobs, authors, project characteristics, original author, code creation time, language, and size information from World of Code. We tracked the reuse of code blobs by identifying all commits containing blobs created during hackathons and identifying all projects that contain those commits. We also conducted a series of surveys in order to gain a deeper understanding of hackathon code evolution that we sent out to hackathon participants whose code was reused, whose code was not reused, and developers who reused some hackathon code.

   9.14% of the code blobs in hackathon repositories and 8% of the lines of code (LOC) are created during hackathons and around a third of the hackathon code gets reused in other projects by both blob count and LOC. The number of associated technologies and the number of participants in hackathons increase reuse probability.

   The results of our study demonstrates hackathons are not always “one-off” events as the common knowledge dictates and it can serve as a starting point for further studies in this area.

    

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4. The Secret Life of Hackathon Code Where does it come from and where does it go?

   https://doi.org/10.1109/MSR52588.2021.00020  

   Imam, Ahmed ; Dey, Tapajit ; Nolte, Alexander ; Mockus, Audris ; Herbsleb, James D. ( May 2021 , Mining Software Repositories)

   null (Ed.)

   Background: Hackathons have become popular events for teams to collaborate on projects and develop software prototypes. Most existing research focuses on activities during an event with limited attention to the evolution of the code brought to or created during a hackathon. Aim: We aim to understand the evolution of hackathon-related code, specifically, how much hackathon teams rely on pre-existing code or how much new code they develop during a hackathon. Moreover, we aim to understand if and where that code gets reused, and what factors affect reuse. Method: We collected information about 22,183 hackathon projects from DEVPOST– a hackathon database – and obtained related code (blobs), authors, and project characteristics from the WORLD OF CODE. We investigated if code blobs in hackathon projects were created before, during, or after an event by identifying the original blob creation date and author, and also checked if the original author was a hackathon project member. We tracked code reuse by first identifying all commits containing blobs created during an event before determining all projects that contain those commits. Result: While only approximately 9.14% of the code blobs are created during hackathons, this amount is still significant considering time and member constraints of such events. Approximately a third of these code blobs get reused in other projects. The number of associated technologies and the number of participants in a project increase reuse probability. Conclusion: Our study demonstrates to what extent pre-existing code is used and new code is created during a hackathon and how much of it is reused elsewhere afterwards. Our findings help to better understand code reuse as a phenomenon and the role of hackathons in this context and can serve as a starting point for further studies in this area. 

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5. "Did you miss my comment or what?": understanding toxicity in open source discussions

   https://doi.org/10.1145/3510003.3510111  

   Miller, Courtney ; Cohen, Sophie ; Klug, Daniel ; Vasilescu, Bogdan ; KaUstner, Christian ( May 2022 , International Conference on Software Engineering)

   Online toxicity is ubiquitous across the internet and its negative impact on the people and that online communities that it effects has been well documented. However, toxicity manifests differently on various platforms and toxicity in open source communities, while frequently discussed, is not well understood. We take a first stride at understanding the characteristics of open source toxicity to better inform future work on designing effective intervention and detection methods. To this end, we curate a sample of 100 toxic GitHub issue discussions combining multiple search and sampling strategies. We then qualitatively analyze the sample to gain an understanding of the characteristics of open-source toxicity. We find that the pervasive forms of toxicity in open source differ from those observed on other platforms like Reddit or Wikipedia. In our sample, some of the most prevalent forms of toxicity are entitled, demanding, and arrogant comments from project users as well as insults arising from technical disagreements. In addition, not all toxicity was written by people external to the projects; project members were also common authors of toxicity. We also discuss the implications of our findings. Among others we hope that our findings will be useful for future detection work. 

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