Bertrand Clarke

Portrait of Bertrand Clarke

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Department Chair, Professor

Areas of expertise:

Data mining and machine learning, prediction,statistical techniques for complex or high-dimensional data, model bias and uncertainty.

Publications

Statistics

Clarke, B. (2019) "Discussion of ‘Prior-based Bayesian Information Criterion (PBIC)’." Statistical Theory and Related Fields 3.1: 26-29.

Yu, C. W., & Clarke, B. (2015). Regular, median and Huber cross‐validation: A computational comparison. Statistical Analysis and Data Mining: The ASA Data Science Journal8(1), 14-33.

Clarke, B. and Clarke, J. (2014) “Estimating proportions in a mixed sample using transcriptomics.”STAT, Vol. 3, 313-325.(pdf)

Clarke, B., Clarke, J. and Yu, C.-W. (2014) Statistical problem classes and their links to information theory. Econ. Reviews, Zellner Memorial Issue, Vol. 33, 337-371(pdf)

Clarke, B. and Clarke, J. (2012) `How to Predict in Several Conventional Settings’.Statistics Surveys, Vol. 6, 1-73(pdf)

Fokoue, E. and Clarke, B. (2011) “Variance Bias Tradeoff for Prequential Model List Selection”.Stat. Papers, Vol. 52, 813-833(pdf)

Clarke, B. and Yuan, A. (2010) “Reference Priors for Empirical Likelihoods.” in: Frontiers of Statistical Decision Making and Bayesian Analysis. Co-Editors: Chen, M., Dey, D., Mueller, P. Sun, D. and Ye, K. Springer, New York, p. 56-68.(pdf)

Yu, C-W and Clarke, B. (2010) “Median Loss Decision Theory”. J. Stat. Planning and Inference, Vol 141, 611-623.(pdf)

Yu, C-W and Clarke, B. (2010) “Asymptotics of Bayesian Median Loss Estimation”J. Mult. Analysis, Vol. 101, No.9, 1950-1958.(pdf)

Clarke, B. (2010) “Desiderata for a Predictive Theory for Statistics”. Bayesian Analysis, Vol. 5, No. 2, 283-318.(pdf)

Clarke, J. and Clarke, B. (2009) “Prequential Analysis of Complex Data with Adaptive Model Reselection”. Stat. Analysis and Data Mining, Vol. 2, No. 4, 274-290.(pdf)

Datta, G., Bhattacharya, A. and Clarke, B. (2008) “Bayesian Tests for the Zero Inflated Poisson Model”. In: Beyond Parametrics in Interdisciplinary Research: Festschrift in Honor of P. K. Sen, Balakrishnan, A., Pena, E, and Silvapulle, M. Eds. p. 89-104.(pdf)

Lin, X., Pittman, J. and Clarke, B. (2007). “Information Conversion, Effective Samples & Parametric Size”. Information Theory Transactions. Vol. 53, No. 12, 4438-4456.(pdf)

Clarke, B. (2007). “Information Optimality and Bayes Models”.Journal of Econometrics, Vol. 138, No. 2, 405-429.(pdf)

Clarke, B. and Yuan, A. (2006). “Closed Form Expressions for Bayesian Sample Sizes”. Annals of Statistics, Vol. 34, No. 3, 1293-1330.(pdf)

Clarke, B. and Song, X. (2004). “Approximating the Dependence Structure of Discrete and Continuous Stochastic Processes”. Sankhya A Vol. 66, No. 3, 536-547.(pdf)

Wong, H. and Clarke, B. (2004). “Characterizing Model Weights Given Partial Information in Normal Models”. Statistics and Probability Letters. Vol. 68, No. 1, 27-37.(pdf)

Wong, H. and Clarke, B. (2004). “Improvement over Bayes Prediction in Small Samples in the Presence of Model Uncertainty”.Canadian Journal of Statistics, Vol. 32, No. 3,269-283.(pdf)

Yuan, A. and Clarke, B. (2004). “Asymptotic Normality of the Posterior Given a Statistic”. Canadian Journal of Statistics, Vol. 32, No. 2, 119-137. .(pdf)

Clarke, B. and Yuan, A. (2004). “Partial Information Reference Priors: Derivation and Interpretations”. Journal of Statistical Planning and Inference, Vol. 123, No. 2, 313-345.(pdf)

Gustafson, P. and Clarke, B. (2004). “A Decomposition for the Posterior Variance”.Journal of Statistical Planning and Inference, Vol. 119, No. 2, 311-327.(pdf)

Clarke, B. (2001). “Combining Model Selection Procedures for Online Prediction”. Sankhya, Ser. A, Vol. 63, Part 2, 229-249.(pdf)

Yuan, A. and Clarke, B. (2001). “Manifest Characterization and Testing for Two Latent Traits”.Annals of Statistics., Vol. 29, No. 3, 876-898.(pdf)

Yuan, A. and Clarke, B. (1999). “A Minimally Informative Likelihood for Decision Analysis: Illustration and Robustness”. Canadian Journal of Statistics, Vol. 27, No. 3,649-665.(pdf)

Clarke, B. and Sun, D. (1999). "Asymptotics of the Expected Posterior". Annals of the Institute of Statistical Mathematics, Vol. 51, No. 1, 163-185.(pdf)

Clarke, B. and Gustafson, P. (1998). "On the overall sensitivity of the posterior distribution to its inputs”. Journal of Statistical Planning and Inference, 71: 137-150.(pdf)

Clarke, B. and Sun, D. (1997). "Reference Priors Under the Chi-Square Distance".Sankhya Series A, Vol. 59, Part II, 215-231.(pdf)

Clarke, B. (1996). "Implications of Reference Priors for Prior Information and Sample Size." Journal of the American Statistical Association, 91, 173-184.(pdf)

Clarke, B. and Ghosh, J. K. (1995). "Posterior Convergence Given the Mean."The Annals of Statistics, 23, 2116-2144.(pdf)

Clarke, B. and Barron, A. (1994). "Jeffreys' Prior is Asymptotically Least Favourable Under Entropy Risk." The Journal of Statistical Planning and Inference, 41, 37-60.(pdf)

.Clarke, B. and Wasserman, L. (1993). "Non Informative Priors and Nuisance Parameters."Journal of the American Statistical Association, 88, 1427-1432.(pdf)

Clarke, B. and Barron, A. (1990). "Information Theoretic Asymptotics of Bayes Methods." IEEE Transactions on Information Theory, 36, 453-471.(pdf)

Data Mining and Machine Learning

Clarke, B. and Mpoudeu, M. (2019) "Model Selection via the VC Dimension," Journal of Machine Learning Research, 20, 1-26

Amiri, S., Clarke, B., Clarke, J., and Koepke, H.  (2019) A General Hybrid Clustering Technique, Journal of Computational and Graphical Statistics, 28:3, 540-551

Le, T., & Clarke, B. (2018). On the interpretation of ensemble classifiers in terms of Bayes classifiers. Journal of Classification35(2), 198-229.

Amiri, S., Clarke, B., and Clarke, J.  (2018) Clustering Categorical Data via Ensembling Dissimilarity Matrices, Journal of Computational and Graphical Statistics, 27:1, 195-208

Clarke, B. and Chu, J. (2014) “‘Generic feature selection with short, fat data’. Invited paper for Special Issue of J. Ind. Soc. Ag. Stat. Vol. 68, 145-162. (pdf)

Yu, C.-W., Clarke, B. and Clarke, J. (2013) “Bayes Prediction in the M-complete problem class with moderate sample size” Bayes Analysis, Vol. 8, 647-690 (pdf)

Koepke, H. and Clarke, B. (2013) “A Bayesian Criterion for Clustering Stability.”Statistical Analysis and Data Mining, Vol. 4, 346-374 (pdf)

Koepke, H. and Clarke, B. (2011)“On The Limits of Clustering in High Dimensions viaCost Functions”.Stat. Anal. and Data Mining, Vol. 4, 30-53.(pdf)

Clarke, B. (2003). “Comparing Bayes and Non-Bayes Model Averaging When Model Approximation Error Cannot Be Ignored”.Journal of Machine Learning Research.4,683-712.(pdf)

Yuan, A. and Clarke, B. (1999). “An Information Criterion for Likelihood Selection”.IEEETransactions on Information Theory. Vol. 45, No. 2, 562-571.(pdf)

Clarke, B. (1999). "Asymptotic Normality of the Posterior in Relative Entropy”.IEEE Transactions on Information Theory, 45, No. 1, 165-176. (pdf)

Biomedical

Dobra, A., Valdes, C., Ajdic, D., Clarke, B., & Clarke, J. (2019). Modeling association in microbial communities with clique loglinear models. Annals of Applied Statistics13(2), 931-957.

Valdes, C., Brennan, M., Clarke, B., & Clarke, J. (2015). Detecting bacterial genomes in a metagenomic sample using NGS reads. Statistics and Its Interface8(4), 477-494.

Clarke, B., Valdes, C., Dobra, A., & Clarke, J. (2015). A Bayes testing approach to metagenomic profiling in bacteria. Statistics and Its Interface8(2), 173-185.

Clarke, J., Seo, P. and Clarke, B. (2010). “Statistical expression deconvolution from mixed tissue samples.” Bionformatics, Vol. 26, No. 8, 1043-1049.(pdf)

Clarke, B., Mittenthal, J. and Fawcett, G. (2004). “Netscan: An Algorithm for Assembling Molecular Networks”. Journal of Theoretical Biology, Vol. 230, No. 4, 591-602.(pdf)

Mittenthal, J.E., Clarke, B., Waddell, T., and Fawcett, G. (2001). “A New Method for Assembling Metabolic Networks, with Application to the Krebs Citric Acid Cycle.” Journal of Theoretical Biology, Vol. 208, No. 3, 361-382.(pdf)

Mittenthal, J.E., Yuan, A., Clarke, B., and Scheeline, A. (1998). “Designing Metabolism: Alternative Connectivities for the Pentose Phosphate Pathway”. Bulletin of Mathematical Biology, Vol. 60, 815-856.(pdf)

Clarke, B., McKay, I., Grigliatti, T., Lloyd, V., Yuan, A. (1996). "A Markov Model for the Assembly of Heterochromatic Regions in Position-Effect Variegation." Journal of Theoretical Biology, 181, 137-155.(pdf)

Predictive

Books

 

Presentations

Research interests:

My main interest these days is in prediction. This is broader than it sounds because prediction brings in questions about model uncertainty (Which model, if any, is true?) model mis-specification (If no model is true, what’s the least bad one?), model complexity (When is more complex modeling better than a simple approach?) and the other sources of variability and bias that have to be small enough for a prediction is useful. Obviously, different model classes can be used to generate predictors but there are also predictors that are not based on any model class. This is the case, for instance, with many machine learning methods such as bagging, boosting, kernel methods, and ensemble methods more generally. In these cases, it is reasonable to ask what the predictor means, i.e., what does a good predictor say about the properties of the phenomenon being predicted? Complex and high dimensional data are the natural places to use predictive techniques since model identification is so hard – even if one believes a model exists (often a dubious assumption). So, I tend to be interested in genomic or other types of complex data where useful formal theory is rare but statistical principles (variance-bias, robustness, complexity minimization, etc.) still provide helpful guidance. Analyzing complex data, or better, developing and understanding good predictors for complex data, often includes clustering, dimension reduction, complexity concepts, ensemble methods – and much else. Indeed, the predictive approach can be regarded as providing an overall conceptualization of the statistical problem in much the same way as Bayes, frequentist, survey sampling, or decision theory does.

Biosketch:

Bertrand Clarke earned his PhD in Statistics at the University of Illinois-Champaign-Urbana in 1989.His thesis work was given the Browder J. Thompson award for authors under age 30 of papers in IEEE journals. He spent three years as an Assistant Professor at Purdue University before moving to the University of British Columbia where he worked from 1992-2008. His early research focused on asymptotics, prior selection in Bayesian statistics, and mathematical modeling of biological systems. His first sabbatical was at University College London and his second sabbatical was at Duke University where he was a visiting scholar in the `Large P Small N’ program at SAMSI. In addition, in 2008 he spent three months at the Newton Institute at Cambridge University. He moved to the University of Miami in 2008 and worked for five years at the medical school where he started their MS and PhD programs in biostatistics before coming to Chair the Department of Statistics at the University of Nebraska-Lincoln. His current foci of research are predictive statistics and statistical methodology in genomic data. He has been an associate editor for four different journals, served three years on the Savage Award Committee (best thesis prize in Bayesian statistics), has published numerous papers over several fields, and was made a Fellow of the ASA in 2014. He has also authored one PhD level textbook on data mining and machine learning for Springer, with a complete solutions manual (available to instructors on request).