Rubik: Knowledge guided tensor factorization and completion for health data analytics

Yichen Wang, Robert Chen, Joydeep Ghosh, Joshua C. Denny, Abel Kho, You Chen, Bradley A. Malin, Jimeng Sun

Research output: Chapter in Book/Report/Conference proceedingConference contribution

79 Scopus citations

Abstract

Computational phenotyping is the process of converting heterogeneous electronic health records (EHRs) into meaningful clinical concepts. Unsupervised phenotyping methods have the potential to leverage a vast amount of labeled EHR data for phenotype discovery. However, existing unsupervised phenotyping methods do not incorporate current medical knowledge and cannot directly handle missing, or noisy data. We propose Rubik, a constrained non-negative tensor factorization and completion method for phenotyping. Rubik incorporates 1) guidance constraints to align with existing medical knowledge, and 2) pairwise constraints for obtaining distinct, non-overlapping phenotypes. Rubik also has built-in tensor completion that can significantly alleviate the impact of noisy and missing data. We utilize the Alternating Direction Method of Multipliers (ADMM) framework to tensor factorization and completion, which can be easily scaled through parallel computing. We evaluate Rubik on two EHR datasets, one of which contains 647,118 records for 7,744 patients from an outpatient clinic, the other of which is a public dataset containing 1,018,614 CMS claims records for 472,645 patients. Our results show that Rubik can discover more meaningful and distinct phenotypes than the baselines. In particular, by using knowledge guidance constraints, Rubik can also discover sub-phenotypes for several major diseases. Rubik also runs around seven times faster than current state-of-the-art tensor methods. Finally, Rubik is scalable to large datasets containing millions of EHR records.

Original languageEnglish (US)
Title of host publicationKDD 2015 - Proceedings of the 21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining
PublisherAssociation for Computing Machinery
Pages1265-1274
Number of pages10
ISBN (Electronic)9781450336642
DOIs
StatePublished - Aug 10 2015
Event21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, KDD 2015 - Sydney, Australia
Duration: Aug 10 2015Aug 13 2015

Publication series

NameProceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
Volume2015-August

Other

Other21st ACM SIGKDD Conference on Knowledge Discovery and Data Mining, KDD 2015
CountryAustralia
CitySydney
Period8/10/158/13/15

Keywords

  • Computational phenotyping
  • Constraint optimization
  • Healthcare analytics
  • Tensor analysis

ASJC Scopus subject areas

  • Software
  • Information Systems

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