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Title: Exaflops Biomedical Knowledge Graph Analytics

Conference ·

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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
DOE Contract Number:
Resource Relation:
Conference: The International Conference for High Performance Computing, Networking, Storage, and Analysis (SC22) - Dallas, Texas, United States of America - 11/13/2022 10:00:00 AM-11/18/2022 5:00:00 AM
Country of Publication:
United States