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1. Scholarly Very Large Data: Challenges For Digital Libraries

   Jian Wu, C Lee ( April 2020 , Large Scale Networking (LSN) Workshop on Huge Data: A Computing, Networking and Distributed Systems Perspective)

   The volume of scholarly data has been growing exponentially over the last 50 years. The total size of the open access documents is estimated to be 35 million by 2022. The total amount of data to be handled, including crawled documents, production repository, metadata, extracted content, and their replications, can be as high as 350TB. Academic digital library search engines face significant challenges in maintaining sustainable services. We discuss these challenges and propose feasible solutions to key modules in the digital library architecture including the document storage, data extraction, database and index. We use CiteSeerX as a case study. 

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2. Scholarly Very Large Data: Challenges For Digital Libraries

   Jian Wu, C Lee ( April 2020 , Challenges For Large Scale Networking (LSN) Workshop on Huge Data: A Computing, Networking and Distributed Systems Perspective)

   The volume of scholarly data has been growing exponentially over the last 50 years. The total size of the open access documents is estimated to be 35 million by 2022. The total amount of data to be handled, including crawled documents, production repository, metadata, extracted content, and their replications, can be as high as 350TB. Academic digital library search engines face signi cant challenges in maintaining sustainable services. We discuss these challenges and propose feasible solutions to key modules in the digital library architecture including the document storage, data extraction, database and index. We use CiteSeerX as a case study. 

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3. Capturing and Operationalizing Participation in Pediatric Re/Habilitation Research Using Artificial Intelligence: A Scoping Review

   https://doi.org/10.3389/fresc.2022.855240  

   Kaelin, Vera C. ; Valizadeh, Mina ; Salgado, Zurisadai ; Sim, Julia G. ; Anaby, Dana ; Boyd, Andrew D. ; Parde, Natalie ; Khetani, Mary A. ( April 2022 , Frontiers in Rehabilitation Sciences)

   Background There is increased interest in using artificial intelligence (AI) to provide participation-focused pediatric re/habilitation. Existing reviews on the use of AI in participation-focused pediatric re/habilitation focus on interventions and do not screen articles based on their definition of participation. AI-based assessments may help reduce provider burden and can support operationalization of the construct under investigation. To extend knowledge of the landscape on AI use in participation-focused pediatric re/habilitation, a scoping review on AI-based participation-focused assessments is needed. Objective To understand how the construct of participation is captured and operationalized in pediatric re/habilitation using AI. Methods We conducted a scoping review of literature published in Pubmed, PsycInfo, ERIC, CINAHL, IEEE Xplore, ACM Digital Library, ProQuest Dissertation and Theses, ACL Anthology, AAAI Digital Library, and Google Scholar. Documents were screened by 2–3 independent researchers following a systematic procedure and using the following inclusion criteria: (1) focuses on capturing participation using AI; (2) includes data on children and/or youth with a congenital or acquired disability; and (3) published in English. Data from included studies were extracted [e.g., demographics, type(s) of AI used], summarized, and sorted into categories of participation-related constructs. Results Twenty one out of 3,406 documents were included. Included assessment approaches mainly captured participation through annotated observations ( n = 20; 95%), were administered in person ( n = 17; 81%), and applied machine learning ( n = 20; 95%) and computer vision ( n = 13; 62%). None integrated the child or youth perspective and only one included the caregiver perspective. All assessment approaches captured behavioral involvement, and none captured emotional or cognitive involvement or attendance. Additionally, 24% ( n = 5) of the assessment approaches captured participation-related constructs like activity competencies and 57% ( n = 12) captured aspects not included in contemporary frameworks of participation. Conclusions Main gaps for future research include lack of: (1) research reporting on common demographic factors and including samples representing the population of children and youth with a congenital or acquired disability; (2) AI-based participation assessment approaches integrating the child or youth perspective; (3) remotely administered AI-based assessment approaches capturing both child or youth attendance and involvement; and (4) AI-based assessment approaches aligning with contemporary definitions of participation. 

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4. Keyphrase Extraction in Scholarly Digital Library Search Engines

   https://doi.org/10.1007/978-3-030-59618-7_12  

   Patel, K. ; Caragea, C. ; Wu, J ; Giles, C.L. ( September 2020 , International Conference on Web Services)

   Scholarly digital libraries provide access to scientific publications and comprise useful resources for researchers who search for literature on specific subject areas. CiteSeerX is an example of such a digital library search engine that provides access to more than 10 million academic documents and has nearly one million users and three million hits per day. Artificial Intelligence (AI) technologies are used in many components of CiteSeerX including Web crawling, document ingestion, and metadata extraction. CiteSeerX also uses an unsupervised algorithm called noun phrase chunking (NP-Chunking) to extract keyphrases out of documents. However, often NP-Chunking extracts many unimportant noun phrases. In this paper, we investigate and contrast three supervised keyphrase extraction models to explore their deployment in CiteSeerX for extracting high quality keyphrases. To perform user evaluations on the keyphrases predicted by different models, we integrate a voting interface into CiteSeerX. We show the development and deployment of the keyphrase extraction models and the maintenance requirements. 

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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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