Literature DB >> 31198618

CP Tensor Decomposition with Cannot-Link Intermode Constraints.

Jette Henderson1,2,3,4,5, Bradley A Malin1, Joshua C Denny1, Abel N Kho2, Jimeng Sun3, Joydeep Ghosh4, Joyce C Ho5.   

Abstract

Tensor factorization is a methodology that is applied in a variety of fields, ranging from climate modeling to medical informatics. A tensor is an n-way array that captures the relationship between n objects. These multiway arrays can be factored to study the underlying bases present in the data. Two challenges arising in tensor factorization are 1) the resulting factors can be noisy and highly overlapping with one another and 2) they may not map to insights within a domain. However, incorporating supervision to increase the number of insightful factors can be costly in terms of the time and domain expertise necessary for gathering labels or domain-specific constraints. To meet these challenges, we introduce CANDECOMP/PARAFAC (CP) tensor factorization with Cannot-Link Intermode Constraints (CP-CLIC), a framework that achieves succinct, diverse, interpretable factors. This is accomplished by gradually learning constraints that are verified with auxiliary information during the decomposition process. We demonstrate CP-CLIC's potential to extract sparse, diverse, and interpretable factors through experiments on simulated data and a real-world application in medical informatics.

Entities:  

Year:  2019        PMID: 31198618      PMCID: PMC6563811          DOI: 10.1137/1.9781611975673.80

Source DB:  PubMed          Journal:  Proc SIAM Int Conf Data Min


  8 in total

1.  Electronic health records-driven phenotyping: challenges, recent advances, and perspectives.

Authors:  Jyotishman Pathak; Abel N Kho; Joshua C Denny
Journal:  J Am Med Inform Assoc       Date:  2013-12       Impact factor: 4.497

2.  Tensor factorization toward precision medicine.

Authors:  Yuan Luo; Fei Wang; Peter Szolovits
Journal:  Brief Bioinform       Date:  2017-05-01       Impact factor: 11.622

3.  Clinical phenotyping in selected national networks: demonstrating the need for high-throughput, portable, and computational methods.

Authors:  Rachel L Richesson; Jimeng Sun; Jyotishman Pathak; Abel N Kho; Joshua C Denny
Journal:  Artif Intell Med       Date:  2016-06-25       Impact factor: 5.326

4.  Limestone: high-throughput candidate phenotype generation via tensor factorization.

Authors:  Joyce C Ho; Joydeep Ghosh; Steve R Steinhubl; Walter F Stewart; Joshua C Denny; Bradley A Malin; Jimeng Sun
Journal:  J Biomed Inform       Date:  2014-07-16       Impact factor: 6.317

5.  Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data.

Authors:  Joshua C Denny; Lisa Bastarache; Marylyn D Ritchie; Robert J Carroll; Raquel Zink; Jonathan D Mosley; Julie R Field; Jill M Pulley; Andrea H Ramirez; Erica Bowton; Melissa A Basford; David S Carrell; Peggy L Peissig; Abel N Kho; Jennifer A Pacheco; Luke V Rasmussen; David R Crosslin; Paul K Crane; Jyotishman Pathak; Suzette J Bielinski; Sarah A Pendergrass; Hua Xu; Lucia A Hindorff; Rongling Li; Teri A Manolio; Christopher G Chute; Rex L Chisholm; Eric B Larson; Gail P Jarvik; Murray H Brilliant; Catherine A McCarty; Iftikhar J Kullo; Jonathan L Haines; Dana C Crawford; Daniel R Masys; Dan M Roden
Journal:  Nat Biotechnol       Date:  2013-12       Impact factor: 54.908

6.  Discriminative and Distinct Phenotyping by Constrained Tensor Factorization.

Authors:  Yejin Kim; Robert El-Kareh; Jimeng Sun; Hwanjo Yu; Xiaoqian Jiang
Journal:  Sci Rep       Date:  2017-04-25       Impact factor: 4.379

7.  Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature.

Authors:  Jette Henderson; Junyuan Ke; Joyce C Ho; Joydeep Ghosh; Byron C Wallace
Journal:  J Med Internet Res       Date:  2018-05-04       Impact factor: 5.428

8.  Learning Low-Dimensional Representations of Medical Concepts.

Authors:  Youngduck Choi; Chill Yi-I Chiu; David Sontag
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2016-07-20
  8 in total
  1 in total

1.  3D Tensor Based Nonlocal Low Rank Approximation in Dynamic PET Reconstruction.

Authors:  Nuobei Xie; Yunmei Chen; Huafeng Liu
Journal:  Sensors (Basel)       Date:  2019-12-01       Impact factor: 3.576

  1 in total

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