Literature DB >> 29531060

Training replicable predictors in multiple studies.

Prasad Patil1,2, Giovanni Parmigiani3,2.   

Abstract

This article considers replicability of the performance of predictors across studies. We suggest a general approach to investigating this issue, based on ensembles of prediction models trained on different studies. We quantify how the common practice of training on a single study accounts in part for the observed challenges in replicability of prediction performance. We also investigate whether ensembles of predictors trained on multiple studies can be combined, using unique criteria, to design robust ensemble learners trained upfront to incorporate replicability into different contexts and populations.

Keywords:  cross-study validation; ensemble learning; machine learning; replicability; validation

Mesh:

Year:  2018        PMID: 29531060      PMCID: PMC5856504          DOI: 10.1073/pnas.1708283115

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  22 in total

1.  Cross-study validation and combined analysis of gene expression microarray data.

Authors:  Elizabeth Garrett-Mayer; Giovanni Parmigiani; Xiaogang Zhong; Leslie Cope; Edward Gabrielson
Journal:  Biostatistics       Date:  2007-09-14       Impact factor: 5.899

2.  Gene expression profiling predicts clinical outcome of breast cancer.

Authors:  Laura J van 't Veer; Hongyue Dai; Marc J van de Vijver; Yudong D He; Augustinus A M Hart; Mao Mao; Hans L Peterse; Karin van der Kooy; Matthew J Marton; Anke T Witteveen; George J Schreiber; Ron M Kerkhoven; Chris Roberts; Peter S Linsley; René Bernards; Stephen H Friend
Journal:  Nature       Date:  2002-01-31       Impact factor: 49.962

3.  Test set bias affects reproducibility of gene signatures.

Authors:  Prasad Patil; Pierre-Olivier Bachant-Winner; Benjamin Haibe-Kains; Jeffrey T Leek
Journal:  Bioinformatics       Date:  2015-03-18       Impact factor: 6.937

4.  Regularization Paths for Generalized Linear Models via Coordinate Descent.

Authors:  Jerome Friedman; Trevor Hastie; Rob Tibshirani
Journal:  J Stat Softw       Date:  2010       Impact factor: 6.440

5.  Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

Authors:  Markus Riester; Wei Wei; Levi Waldron; Aedin C Culhane; Lorenzo Trippa; Esther Oliva; Sung-Hoon Kim; Franziska Michor; Curtis Huttenhower; Giovanni Parmigiani; Michael J Birrer
Journal:  J Natl Cancer Inst       Date:  2014-04-03       Impact factor: 13.506

Review 6.  Systematic review: gene expression profiling assays in early-stage breast cancer.

Authors:  Luigi Marchionni; Renee F Wilson; Antonio C Wolff; Spyridon Marinopoulos; Giovanni Parmigiani; Eric B Bass; Steven N Goodman
Journal:  Ann Intern Med       Date:  2008-02-04       Impact factor: 25.391

Review 7.  Public data and open source tools for multi-assay genomic investigation of disease.

Authors:  Lavanya Kannan; Marcel Ramos; Angela Re; Nehme El-Hachem; Zhaleh Safikhani; Deena M A Gendoo; Sean Davis; David Gomez-Cabrero; Robert Castelo; Kasper D Hansen; Vincent J Carey; Martin Morgan; Aedín C Culhane; Benjamin Haibe-Kains; Levi Waldron
Journal:  Brief Bioinform       Date:  2015-10-12       Impact factor: 11.622

8.  curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.

Authors:  Benjamin Frederick Ganzfried; Markus Riester; Benjamin Haibe-Kains; Thomas Risch; Svitlana Tyekucheva; Ina Jazic; Xin Victoria Wang; Mahnaz Ahmadifar; Michael J Birrer; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron
Journal:  Database (Oxford)       Date:  2013-04-02       Impact factor: 3.451

9.  Wisdom of crowds for robust gene network inference.

Authors:  Daniel Marbach; James C Costello; Robert Küffner; Nicole M Vega; Robert J Prill; Diogo M Camacho; Kyle R Allison; Manolis Kellis; James J Collins; Gustavo Stolovitzky
Journal:  Nat Methods       Date:  2012-07-15       Impact factor: 28.547

10.  Cross-study validation for the assessment of prediction algorithms.

Authors:  Christoph Bernau; Markus Riester; Anne-Laure Boulesteix; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron; Lorenzo Trippa
Journal:  Bioinformatics       Date:  2014-06-15       Impact factor: 6.937

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  8 in total

1.  Reproducibility of research: Issues and proposed remedies.

Authors:  David B Allison; Richard M Shiffrin; Victoria Stodden
Journal:  Proc Natl Acad Sci U S A       Date:  2018-03-12       Impact factor: 11.205

2.  A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer.

Authors:  Ifeanyichukwu O Nwosu; Stephen R Piccolo
Journal:  Cancer Biol Ther       Date:  2021-08-19       Impact factor: 4.875

3.  The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.

Authors:  Yuqing Zhang; Christoph Bernau; Giovanni Parmigiani; Levi Waldron
Journal:  Biostatistics       Date:  2020-04-01       Impact factor: 5.899

4.  Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality.

Authors:  Xinyu Zhang; Ying Hu; Bradley E Aouizerat; Gang Peng; Vincent C Marconi; Michael J Corley; Todd Hulgan; Kendall J Bryant; Hongyu Zhao; John H Krystal; Amy C Justice; Ke Xu
Journal:  Clin Epigenetics       Date:  2018-12-13       Impact factor: 6.551

5.  Tree-Weighting for Multi-Study Ensemble Learners.

Authors:  Maya Ramchandran; Prasad Patil; Giovanni Parmigiani
Journal:  Pac Symp Biocomput       Date:  2020

6.  Universal adaptability: Target-independent inference that competes with propensity scoring.

Authors:  Michael P Kim; Christoph Kern; Shafi Goldwasser; Frauke Kreuter; Omer Reingold
Journal:  Proc Natl Acad Sci U S A       Date:  2022-01-25       Impact factor: 11.205

7.  SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.

Authors:  Mingyi Wang; Wen Luo; Kristine Jones; Xiaopeng Bian; Russell Williams; Herbert Higson; Dongjing Wu; Belynda Hicks; Meredith Yeager; Bin Zhu
Journal:  Sci Rep       Date:  2020-07-30       Impact factor: 4.996

8.  Epigenomic Assessment of Cardiovascular Disease Risk and Interactions With Traditional Risk Metrics.

Authors:  Kenneth Westerman; Alba Fernández-Sanlés; Prasad Patil; Paola Sebastiani; Paul Jacques; John M Starr; Ian J Deary; Qing Liu; Simin Liu; Roberto Elosua; Dawn L DeMeo; José M Ordovás
Journal:  J Am Heart Assoc       Date:  2020-04-20       Impact factor: 5.501

  8 in total

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