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1. On Using GUI Interaction Data to Improve Text Retrieval-based Bug Localization

   Mahmud, Junayed ; De Silva, Nadeeshan ; Ali Khan, Safwat ; Mostafavi, Seyed Hooman ; Mansur, SM Hasan ; Chaparro, Oscar ; Marcus, Andrian ; Moran, Kevin ( January 2024 , 2024 IEEE/ACM 46th International Conference on Software Engineering (ICSE))

   One of the most important tasks related to managing bug reports is localizing the fault so that a fix can be applied. As such, prior work has aimed to automate this task of bug localization by formulating it as an information retrieval problem, where potentially buggy files are retrieved and ranked according to their textual similarity with a given bug report. However, there is often a notable semantic gap between the information contained in bug reports and identifiers or natural language contained within source code files. For user-facing software, there is currently a key source of information that could aid in bug localization, but has not been thoroughly investigated - information from the GUI. We investigate the hypothesis that, for end user-facing applications, connecting information in a bug report with information from the GUI, and using this to aid in retrieving potentially buggy files, can improve upon existing techniques for bug localization. To examine this phenomenon, we conduct a comprehensive empirical study that augments four baseline techniques for bug localization with GUI interaction information from a reproduction scenario to (i) filter out potentially irrelevant files, (ii) boost potentially relevant files, and (iii) reformulate text-retrieval queries. To carry out our study, we source the current largest dataset of fully-localized and reproducible real bugs for Android apps, with corresponding bug reports, consisting of 80 bug reports from 39 popular open-source apps. Our results illustrate that augmenting traditional techniques with GUI information leads to a marked increase in effectiveness across multiple metrics, including a relative increase in Hits@10 of 13-18%. Additionally, through further analysis, we find that our studied augmentations largely complement existing techniques. 

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2. Toward Optimal Selection of Information Retrieval Models for Software Engineering Tasks

   Rahman, Md Masudur ; Chakraborty, Saikat ; Kaiser, Gail ; Ray, Baishakhi ( September 2019 , 19th IEEE International Working Conference on Source Code Analysis and Manipulation (SCAM))

   Information Retrieval (IR) plays a pivotal role indiverse Software Engineering (SE) tasks, e.g., bug localization and triaging, bug report routing, code retrieval, requirements analysis, etc. SE tasks operate on diverse types of documents including code, text, stack-traces, and structured, semi-structured and unstructured meta-data that often contain specialized vocabularies. As the performance of any IR-based tool critically depends on the underlying document types, and given the diversity of SE corpora, it is essential to understand which models work best for which types of SE documents and tasks.We empirically investigate the interaction between IR models and document types for two representative SE tasks (bug localization and relevant project search), carefully chosen as they require a diverse set of SE artifacts (mixtures of code and text),and confirm that the models’ performance varies significantly with mix of document types. Leveraging this insight, we propose a generalized framework, SRCH, to automatically select the most favorable IR model(s) for a given SE task. We evaluate SRCH w.r.t. these two tasks and confirm its effectiveness. Our preliminary user study shows that SRCH’s intelligent adaption of the IR model(s) to the task at hand not only improves precision and recall for SE tasks but may also improve users’ satisfaction. 

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3. 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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4. 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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5. Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods

   https://doi.org/10.1186/s12911-022-01996-2  

   Yu, Zehao ; Yang, Xi ; Sweeting, Gianna L. ; Ma, Yinghan ; Stolte, Skylar E. ; Fang, Ruogu ; Wu, Yonghui ( September 2022 , BMC Medical Informatics and Decision Making)

   Abstract Background Diabetic retinopathy (DR) is a leading cause of blindness in American adults. If detected, DR can be treated to prevent further damage causing blindness. There is an increasing interest in developing artificial intelligence (AI) technologies to help detect DR using electronic health records. The lesion-related information documented in fundus image reports is a valuable resource that could help diagnoses of DR in clinical decision support systems. However, most studies for AI-based DR diagnoses are mainly based on medical images; there is limited studies to explore the lesion-related information captured in the free text image reports. Methods In this study, we examined two state-of-the-art transformer-based natural language processing (NLP) models, including BERT and RoBERTa, compared them with a recurrent neural network implemented using Long short-term memory (LSTM) to extract DR-related concepts from clinical narratives. We identified four different categories of DR-related clinical concepts including lesions, eye parts, laterality, and severity, developed annotation guidelines, annotated a DR-corpus of 536 image reports, and developed transformer-based NLP models for clinical concept extraction and relation extraction. We also examined the relation extraction under two settings including ‘gold-standard’ setting—where gold-standard concepts were used–and end-to-end setting. Results For concept extraction, the BERT model pretrained with the MIMIC III dataset achieve the best performance (0.9503 and 0.9645 for strict/lenient evaluation). For relation extraction, BERT model pretrained using general English text achieved the best strict/lenient F1-score of 0.9316. The end-to-end system, BERT_general_e2e, achieved the best strict/lenient F1-score of 0.8578 and 0.8881, respectively. Another end-to-end system based on the RoBERTa architecture, RoBERTa_general_e2e, also achieved the same performance as BERT_general_e2e in strict scores. Conclusions This study demonstrated the efficiency of transformer-based NLP models for clinical concept extraction and relation extraction. Our results show that it’s necessary to pretrain transformer models using clinical text to optimize the performance for clinical concept extraction. Whereas, for relation extraction, transformers pretrained using general English text perform better. 

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