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research-article

Exaflops biomedical knowledge graph analytics

Authors:

Ramakrishnan Kannan,

Gundolf Schenk,

Seung-Hwan Lim,

Sergio E. Baranzini,

Thomas PotokAuthors Info & Claims

SC '22: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis

Article No.: 6, Pages 1 - 11

Published: 18 November 2022 Publication History

Abstract

We are motivated by newly proposed methods for mining large-scale corpora of scholarly publications (e.g., full biomedical literature), which consists of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover relationships among concepts. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as an all-pairs shortest paths (APSP) and validate connective paths against curated biomedical knowledge graphs (e.g., Spoke). In this context, we present Coast (Exascale Communication-Optimized All-Pairs Shortest Path) and demonstrate 1.004 EF/s on 9,200 Frontier nodes (73,600 GCDs). We develop hyperbolic performance models (HyPerMod), which guide optimizations and parametric tuning. The proposed Coast algorithm achieved the memory constant parallel efficiency of 99% in the single-precision tropical semiring. Looking forward, Coast will enable the integration of scholarly corpora like PubMed into the Spoke biomedical knowledge graph.

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References

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Cited By

Lu HSao PMatheson MKannan RWang FPotok T(2023)Optimizing Communication in 2D Grid-Based MPI Applications at ExascaleProceedings of the 30th European MPI Users' Group Meeting10.1145/3615318.3615327(1-11)Online publication date: 11-Sep-2023
https://dl.acm.org/doi/10.1145/3615318.3615327

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Information & Contributors

Information

Published In

cover image ACM Conferences

SC '22: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis

November 2022

1277 pages

ISBN:9784665454445

Conference Chairs:
Felix Wolf,
Sameer Shende,
General Chair:
Candace Culhane,
Program Chairs:
Sadaf Alam,
Heike Jagode

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SIGHPC: ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing

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IEEE CS

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IEEE Press

Publication History

Published: 18 November 2022

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SC '22

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SIGHPC

SC '22: The International Conference for High Performance Computing, Networking, Storage and Analysis

November 13 - 18, 2022

Texas, Dallas

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Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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Cited By

Lu HSao PMatheson MKannan RWang FPotok T(2023)Optimizing Communication in 2D Grid-Based MPI Applications at ExascaleProceedings of the 30th European MPI Users' Group Meeting10.1145/3615318.3615327(1-11)Online publication date: 11-Sep-2023
https://dl.acm.org/doi/10.1145/3615318.3615327

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