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1. Skyhook: Towards an Arrow-Native Storage System

   https://doi.org/10.1109/CCGrid54584.2022.00017  

   Chakraborty, Jayjeet ; Jimenez, Ivo ; Rodriguez, Sebastiaan Alvarez ; Uta, Alexandru ; LeFevre, Jeff ; Maltzahn, Carlos ( May 2022 , The 22nd IEEE/ACM Interna- tional Symposium on Cluster, Cloud and Internet Computing (CCGrid22))

   With the ever-increasing dataset sizes, several file formats such as Parquet, ORC, and Avro have been developed to store data efficiently, save the network, and interconnect bandwidth at the price of additional CPU utilization. However, with the advent of networks supporting 25-100 Gb/s and storage devices delivering 1,000,000 reqs/sec, the CPU has become the bottleneck trying to keep up feeding data in and out of these fast devices. The result is that data access libraries executed on single clients are often CPU-bound and cannot utilize the scale-out benefits of distributed storage systems. One attractive solution to this problem is to offload data-reducing processing and filtering tasks to the storage layer. However, modifying legacy storage systems to support compute offloading is often tedious and requires an extensive understanding of the system internals. Previous approaches re-implemented functionality of data processing frameworks and access libraries for a particular storage system, a duplication of effort that might have to be repeated for different storage systems. This paper introduces a new design paradigm that allows extending programmable object storage systems to embed existing, widely used data processing frameworks and access libraries into the storage layer with no modifications. In this approach, data processing frameworks and access libraries can evolve independently from storage systems while leveraging distributed storage systems’ scale-out and availability properties. We present Skyhook, an example implementation of our design paradigm using Ceph, Apache Arrow, and Parquet. We provide a brief performance evaluation of Skyhook and discuss key results. 

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2. Spatial parquet: a column file format for geospatial data lakes

   https://doi.org/10.1145/3557915.3561038  

   Saeedan, Majid ; Eldawy, Ahmed ( November 2022 , he 30th International Conference on Advances in Geographic Information Systems)

   Modern data analytics applications prefer to use column-storage formats due to their improved storage efficiency through encoding and compression. Parquet is the most popular file format for col- umn data storage that provides several of these benefits out of the box. However, geospatial data is not readily supported by Parquet. This paper introduces Spatial Parquet, a Parquet extension that efficiently supports geospatial data. Spatial Parquet inherits all the advantages of Parquet for non-spatial data, such as rich data types, compression, and column/row filtering. Additionally, it adds three new features to accommodate geospatial data. First, it introduces a geospatial data type that can encode all standard spatial geome- tries in a column format compatible with Parquet. Second, it adds a new lossless and efficient encoding method, termed FP-delta, that is customized to efficiently store geospatial coordinates stored in floating-point format. Third, it adds a light-weight spatial index that allows the reader to skip non-relevant parts of the file for increased read efficiency. Experiments on large-scale real data showed that Spatial Parquet can reduce the data size by a factor of three even without compression. Compression can further reduce the storage size. Additionally, Spatial Parquet can reduce the reading time by two orders of magnitude when the light-weight index is applied. This initial prototype can open new research directions to further improve geospatial data storage in column format. 

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3. US State Tourism Websites

   Shere, Danya ; Ayub, Ahmad ; Mueller, Rebecca ; Fabian, Lexi ; Shah, Akshat ; Fox, Edward A. ( May 2020 , Multimedia, Hypertext, and Information Access)

   null (Ed.)

   In the United States, every state has a tourism website. These sites highlight the main attractions of the state, travel tips, and blog posts among other relevant information. The funding for these websites often comes from occupancy taxes, a form of taxes that comes from tourists who stay in hotels and visit attractions. Therefore, current and past tourists fund the efforts to draw future tourists into the state. Since state tourism is funded by the success of past tourism efforts, it is important for researchers to spend their time and resources on finding out what efforts were successful and which weren’t. With this comes the importance of seeing trends in past tourism endeavors. By examining past tourism websites, patterns can be drawn about information that changed, from season to season and year to year. These patterns can be used to see what researchers deemed as successful tourism efforts, and help guide future state tourism decisions. Our client, Dr. Florian Zach of the Howard Feiertag Department of Hospitality and Tourism Management, wants to use this historical analysis on state tourism information to help with his research on trends in state tourism website content. Iterations of the California state tourism website, among other sites, are stored as snapshots on the Internet Archive and can be accessed to see changes in websites over time. Our team was given Parquet files of these snapshots dating back to 2008. The goal of the project was to assist Dr. Zach by using the California state tourism website, visitcalifornia.com, and these snapshots as an avenue to explore data extraction and visualization techniques on tourism patterns to later be expanded to other states’ tourism websites. Python’s Pandas library was utilized to examine and extract relevant pieces of data from the given Parquet files. Once the data was extracted, we used Python’s Natural Language Processing Toolkit to remove non-English words, punctuation, and a set of unimportant “stop words”. With this refined data, we were able to make visualizations regarding the frequency of words in the headers and body of the website snapshots. The data was examined in its entirety as well as in groups of seasons and years. Microsoft Excel functions were utilized to examine and visualize the data in these formats. These data extraction and visualization techniques that we became familiar with will be passed down to a future team. The research on state tourism site information can be expanded to different metadata sets and to other states. 

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4. Code Synthesis for Sparse Tensor Format Conversion and Optimization

   https://doi.org/10.1145/3579990.3580021  

   Popoola, Tobi ; Zhao, Tuowen ; St. George, Aaron ; Bhetwal, Kalyan ; Strout, Michelle Mills ; Hall, Mary ; Olschanowsky, Catherine ( February 2023 , ACM)

   Many scientific applications compute using sparse data and store that data in a variety of sparse formats because each format has unique space and performance benefits. Optimizing applications that use sparse data involves translating the sparse data into the chosen format and transforming the computation to iterate over that format. This paper presents a formal definition of sparse tensor formats and an automated approach to synthesize the transformation between formats. This approach is unique in that it supports ordering constraints not supported by other approaches and synthesizes the transformation code in a high-level intermediate representation suitable for applying composable transformations such as loop fusion and temporary storage reduction. We demonstrate that the synthesized code for COO to CSR with optimizations is 2.85x faster than TACO, Intel MKL, and SPARSKIT while the more complex COO to DIA is 1.4x slower than TACO but faster than SPARSKIT and Intel MKL using the geometric average of execution time. 

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5. Recent Advances in the Temple University Digital Pathology Corpus

   https://doi.org/10.1109/SPMB47826.2019.9037859  

   Hunt, I. ; Husain, S. ; Simon, J. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad ; Picone, Joseph ; Selesnick, Ivan (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing a large open source database of high-resolution digital pathology images known as the Temple University Digital Pathology Corpus (TUDP) [1]. Our long-term goal is to release one million images. We expect to release the first 100,000 image corpus by December 2020. The data is being acquired at the Department of Pathology at Temple University Hospital (TUH) using a Leica Biosystems Aperio AT2 scanner [2] and consists entirely of clinical pathology images. More information about the data and the project can be found in Shawki et al. [3]. We currently have a National Science Foundation (NSF) planning grant [4] to explore how best the community can leverage this resource. One goal of this poster presentation is to stimulate community-wide discussions about this project and determine how this valuable resource can best meet the needs of the public. The computing infrastructure required to support this database is extensive [5] and includes two HIPAA-secure computer networks, dual petabyte file servers, and Aperio’s eSlide Manager (eSM) software [6]. We currently have digitized over 50,000 slides from 2,846 patients and 2,942 clinical cases. There is an average of 12.4 slides per patient and 10.5 slides per case with one report per case. The data is organized by tissue type as shown below: Filenames: tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_0a001_00123456_lvl0001_s000.svs tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_00123456.docx Explanation: tudp: root directory of the corpus v1.0.0: version number of the release svs: the image data type gastro: the type of tissue 000001: six-digit sequence number used to control directory complexity 00123456: 8-digit patient MRN 2015_03_05: the date the specimen was captured 0s15_12345: the clinical case name 0s15_12345_0a001_00123456_lvl0001_s000.svs: the actual image filename consisting of a repeat of the case name, a site code (e.g., 0a001), the type and depth of the cut (e.g., lvl0001) and a token number (e.g., s000) 0s15_12345_00123456.docx: the filename for the corresponding case report We currently recognize fifteen tissue types in the first installment of the corpus. The raw image data is stored in Aperio’s “.svs” format, which is a multi-layered compressed JPEG format [3,7]. Pathology reports containing a summary of how a pathologist interpreted the slide are also provided in a flat text file format. A more complete summary of the demographics of this pilot corpus will be presented at the conference. Another goal of this poster presentation is to share our experiences with the larger community since many of these details have not been adequately documented in scientific publications. There are quite a few obstacles in collecting this data that have slowed down the process and need to be discussed publicly. Our backlog of slides dates back to 1997, meaning there are a lot that need to be sifted through and discarded for peeling or cracking. Additionally, during scanning a slide can get stuck, stalling a scan session for hours, resulting in a significant loss of productivity. Over the past two years, we have accumulated significant experience with how to scan a diverse inventory of slides using the Aperio AT2 high-volume scanner. We have been working closely with the vendor to resolve many problems associated with the use of this scanner for research purposes. This scanning project began in January of 2018 when the scanner was first installed. The scanning process was slow at first since there was a learning curve with how the scanner worked and how to obtain samples from the hospital. From its start date until May of 2019 ~20,000 slides we scanned. In the past 6 months from May to November we have tripled that number and how hold ~60,000 slides in our database. This dramatic increase in productivity was due to additional undergraduate staff members and an emphasis on efficient workflow. The Aperio AT2 scans 400 slides a day, requiring at least eight hours of scan time. The efficiency of these scans can vary greatly. When our team first started, approximately 5% of slides failed the scanning process due to focal point errors. We have been able to reduce that to 1% through a variety of means: (1) best practices regarding daily and monthly recalibrations, (2) tweaking the software such as the tissue finder parameter settings, and (3) experience with how to clean and prep slides so they scan properly. Nevertheless, this is not a completely automated process, making it very difficult to reach our production targets. With a staff of three undergraduate workers spending a total of 30 hours per week, we find it difficult to scan more than 2,000 slides per week using a single scanner (400 slides per night x 5 nights per week). The main limitation in achieving this level of production is the lack of a completely automated scanning process, it takes a couple of hours to sort, clean and load slides. We have streamlined all other aspects of the workflow required to database the scanned slides so that there are no additional bottlenecks. To bridge the gap between hospital operations and research, we are using Aperio’s eSM software. Our goal is to provide pathologists access to high quality digital images of their patients’ slides. eSM is a secure website that holds the images with their metadata labels, patient report, and path to where the image is located on our file server. Although eSM includes significant infrastructure to import slides into the database using barcodes, TUH does not currently support barcode use. Therefore, we manage the data using a mixture of Python scripts and manual import functions available in eSM. The database and associated tools are based on proprietary formats developed by Aperio, making this another important point of community-wide discussion on how best to disseminate such information. Our near-term goal for the TUDP Corpus is to release 100,000 slides by December 2020. We hope to continue data collection over the next decade until we reach one million slides. We are creating two pilot corpora using the first 50,000 slides we have collected. The first corpus consists of 500 slides with a marker stain and another 500 without it. This set was designed to let people debug their basic deep learning processing flow on these high-resolution images. We discuss our preliminary experiments on this corpus and the challenges in processing these high-resolution images using deep learning in [3]. We are able to achieve a mean sensitivity of 99.0% for slides with pen marks, and 98.9% for slides without marks, using a multistage deep learning algorithm. While this dataset was very useful in initial debugging, we are in the midst of creating a new, more challenging pilot corpus using actual tissue samples annotated by experts. The task will be to detect ductal carcinoma (DCIS) or invasive breast cancer tissue. There will be approximately 1,000 images per class in this corpus. Based on the number of features annotated, we can train on a two class problem of DCIS or benign, or increase the difficulty by increasing the classes to include DCIS, benign, stroma, pink tissue, non-neoplastic etc. Those interested in the corpus or in participating in community-wide discussions should join our listserv, nedc_tuh_dpath@googlegroups.com, to be kept informed of the latest developments in this project. You can learn more from our project website: https://www.isip.piconepress.com/projects/nsf_dpath. 

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