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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. Pre-Training Multi-Modal Dense Retrievers for Outside-Knowledge Visual Question Answering

   Salemi, Alireza ; Rafiee, Mahta ; Zamani, Hamed ( July 2023 , Proceedings of The 13th International Conference on the Theory of Information Retrieval (ICTIR 2023))

   This paper studies a category of visual question answering tasks, in which accessing external knowledge is necessary for answering the questions. This category is called outside-knowledge visual question answering (OK-VQA). A major step in developing OKVQA systems is to retrieve relevant documents for the given multimodal query. Current state-of-the-art dense retrieval model for this task uses an asymmetric architecture with a multi-modal query encoder and a uni-modal document encoder. Such an architecture requires a large amount of training data for effective performance. We propose an automatic data generation pipeline for pre-training passage retrieval models for OK-VQA tasks. The proposed approach leads to 26.9% Precision@5 improvements compared to the current state-of-the-art. Additionally, the proposed pre-training approach exhibits a good ability in zero-shot retrieval scenarios. 

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3. Efficient Implicit Unsupervised Text Hashing using Adversarial Autoencoder

   https://doi.org/10.1145/3366423.3380150  

   Doan, Khoa ; Reddy, Chandan K. ( April 2020 , Proceedings of The Web Conference (WWW))

   Searching for documents with semantically similar content is a fundamental problem in the information retrieval domain with various challenges, primarily, in terms of efficiency and effectiveness. Despite the promise of modeling structured dependencies in documents, several existing text hashing methods lack an efficient mechanism to incorporate such vital information. Additionally, the desired characteristics of an ideal hash function, such as robustness to noise, low quantization error and bit balance/uncorrelation, are not effectively learned with existing methods. This is because of the requirement to either tune additional hyper-parameters or optimize these heuristically and explicitly constructed cost functions. In this paper, we propose a Denoising Adversarial Binary Autoencoder (DABA) model which presents a novel representation learning framework that captures structured representation of text documents in the learned hash function. Also, adversarial training provides an alternative direction to implicitly learn a hash function that captures all the desired characteristics of an ideal hash function. Essentially, DABA adopts a novel single-optimization adversarial training procedure that minimizes the Wasserstein distance in its primal domain to regularize the encoder’s output of either a recurrent neural network or a convolutional autoencoder.We empirically demonstrate the effectiveness of our proposed method in capturing the intrinsic semantic manifold of the related documents. The proposed method outperforms the current state-of-the-art shallow and deep unsupervised hashing methods for the document retrieval task on several prominent document collections. 

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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. FIXMYPOSE: Pose Correctional Captioning and Retrieval

   Kim, Hyounghun ; Zala, Abhay ; Burri, Graham ; Bansal, Mohit ( February 2021 , Proceedings of the AAAI Conference on Artificial Intelligence)

   null (Ed.)

   Interest in physical therapy and individual exercises such as yoga/dance has increased alongside the well-being trend, and people globally enjoy such exercises at home/office via video streaming platforms. However, such exercises are hard to follow without expert guidance. Even if experts can help, it is almost impossible to give personalized feedback to every trainee remotely. Thus, automated pose correction systems are required more than ever, and we introduce a new captioning dataset named FixMyPose to address this need. We collect natural language descriptions of correcting a “current” pose to look like a “target” pose. To support a multilingual setup, we collect descriptions in both English and Hindi. The collected descriptions have interesting linguistic properties such as egocentric relations to the environment objects, analogous references, etc., requiring an understanding of spatial relations and commonsense knowledge about postures. Further, to avoid ML biases, we maintain a balance across characters with diverse demographics, who perform a variety of movements in several interior environments (e.g., homes, offices). From our FixMyPose dataset, we introduce two tasks: the pose-correctional-captioning task and its reverse, the target-pose-retrieval task. During the correctional-captioning task, models must generate the descriptions of how to move from the current to the target pose image, whereas in the retrieval task, models should select the correct target pose given the initial pose and the correctional description. We present strong cross-attention baseline models (uni/multimodal, RL, multilingual) and also show that our baselines are competitive with other models when evaluated on other image-difference datasets. We also propose new task-specific metrics (object-match, body-part-match, direction-match) and conduct human evaluation for more reliable evaluation, and we demonstrate a large human-model performance gap suggesting room for promising future work. Finally, to verify the sim-to-real transfer of our FixMyPose dataset, we collect a set of real images and show promising performance on these images. Data and code are available: https://fixmypose-unc.github.io. 

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