We study the top-k set similarity search problem using semantic overlap. While vanilla overlap requires exact matches between set elements, semantic overlap allows elements that are syntactically different but semantically related to increase the overlap. The semantic overlap is the maximum matching score of a bipartite graph, where an edge weight between two set elements is defined by a user-defined similarity function, e.g., cosine similarity between embeddings. Common techniques like token indexes fail for semantic search since similar elements may be unrelated at the character level. Further, verifying candidates is expensive (cubic versus linear for syntactic overlap), calling for highly selective filters. We propose Koios, the first exact and efficient algorithm for semantic overlap search. Koios leverages sophisticated filters to minimize the number of required graph-matching calculations. Our experiments show that for medium to large sets less than 5% of the candidate sets need verification, and more than half of those sets are further pruned without requiring the expensive graph matching. We show the efficiency of our algorithm on four real datasets and demonstrate the improved result quality of semantic over vanilla set similarity search.
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REFORM: Fast and Adaptive Solution for Subteam Replacement
Subteam Replacement: given a team of people em- bedded in a social network to complete a certain task, and a subset of members (i.e., subteam) in this team which have become unavailable, find another set of people who can perform the subteam’s role in the larger team. We conjecture that a good candidate subteam should have high skill and structural similarity with the replaced subteam while sharing a similar connection with the larger team as a whole. Based on this conjecture, we propose a novel graph kernel which evaluates the goodness of candidate subteams in this holistic way freely adjustable to the need of the situation. To tackle the significant computational difficulties, we equip our kernel with a fast approximation algorithm which (a) employs effective pruning strategies, (b) exploits the similarity between candidate team structures to reduce kernel computations, and (c) features a solid theoretical bound on the quality of the obtained solution. We extensively test our solution on both synthetic and real datasets to demonstrate its effectiveness and efficiency. Our proposed graph kernel outputs more human-agreeable recommendations compared to metrics used in previous work, and our algorithm consistently outperforms alternative choices by finding near- optimal solutions while scaling linearly with the size of the replaced subteam.
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- NSF-PAR ID:
- 10332508
- Date Published:
- Journal Name:
- REFORM: Fast and Adaptive Solution for Subteam Replacement
- Page Range / eLocation ID:
- 350 to 358
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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. 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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. 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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/BigData52589.2021.9671359
