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High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.

ABSTRACT: Survival analysis endures as an old, yet active research field with applications that spread across many domains. Continuing improvements in data acquisition techniques pose constant challenges in applying existing survival analysis methods to these emerging data sets. In this paper, we present tools for fitting regularized Cox survival analysis models on high-dimensional, massive sample-size (HDMSS) data using a variant of the cyclic coordinate descent optimization technique tailored for the sparsity that HDMSS data often present. Experiments on two real data examples demonstrate that efficient analyses of HDMSS data using these tools result in improved predictive performance and calibration.

SUBMITTER: Mittal S

PROVIDER: S-EPMC3944969 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.

Mittal Sushil S Madigan David D Burd Randall S RS Suchard Marc A MA

Biostatistics (Oxford, England) 20131004 2

Survival analysis endures as an old, yet active research field with applications that spread across many domains. Continuing improvements in data acquisition techniques pose constant challenges in applying existing survival analysis methods to these emerging data sets. In this paper, we present tools for fitting regularized Cox survival analysis models on high-dimensional, massive sample-size (HDMSS) data using a variant of the cyclic coordinate descent optimization technique tailored for the sp ...[more]

PMID: 24096388

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Project description:From March through August 2015, nearly 60 teams from around the world participated in the Prostate Cancer Dream Challenge (PCDC). Participating teams were faced with the task of developing prediction models for patient survival and treatment discontinuation using baseline clinical variables collected on metastatic castrate-resistant prostate cancer (mCRPC) patients in the comparator arm of four phase III clinical trials. In total, over 2,000 mCRPC patients treated with first-line docetaxel comprised the training and testing data sets used in this challenge. In this paper we describe: (a) the sub-challenges comprising the PCDC, (b) the statistical metrics used to benchmark prediction performance, (c) our analytical approach, and finally (d) our team's overall performance in this challenge. Specifically, we discuss our curated, ad-hoc, feature selection (CAFS) strategy for identifying clinically important risk-predictors, the ensemble-based Cox proportional hazards regression framework used in our final submission, and the adaptation of our modeling framework based on the results from the intermittent leaderboard rounds. Strong predictors of patient survival were successfully identified utilizing our model building approach. Several of the identified predictors were new features created by our team via strategically merging collections of weak predictors. In each of the three intermittent leaderboard rounds, our prediction models scored among the top four models across all participating teams and our final submission ranked 9 th place overall with an integrated area under the curve (iAUC) of 0.7711 computed in an independent test set. While the prediction performance of teams placing between 2 nd- 10 th (iAUC: 0.7710-0.7789) was better than the current gold-standard prediction model for prostate cancer survival, the top-performing team, FIMM-UTU significantly outperformed all other contestants with an iAUC of 0.7915. In summary, our ensemble-based Cox regression framework with CAFS resulted in strong overall performance for predicting prostate cancer survival and represents a promising approach for future prediction problems.

Project description:IntroductionMachine learning algorithms such as elastic net regression and backward selection provide a unique and powerful approach to model building given a set of psychosocial predictors of smoking lapse measured repeatedly via ecological momentary assessment (EMA). Understanding these predictors may aid in developing interventions for smoking lapse prevention.MethodsIn a randomized-controlled smoking cessation trial, smartphone-based EMAs were collected from 92 participants following a scheduled quit date. This secondary analysis utilized elastic net-penalized cox proportional hazards regression and model approximation via backward elimination to (1) optimize a predictive model of time to first lapse and (2) simplify that model to its core constituent predictors to maximize parsimony and generalizability.ResultsElastic net proportional hazards regression selected 17 of 26 possible predictors from 2065 EMAs to model time to first lapse. The predictors with the highest magnitude regression coefficients were having consumed alcohol in the past hour, being around and interacting with a smoker, and having cigarettes easily available. This model was reduced using backward elimination, retaining five predictors and approximating to 93.9% of model fit. The retained predictors included those mentioned above as well as feeling irritable and being in areas where smoking is either discouraged or allowed (as opposed to not permitted).ConclusionsThe strongest predictors of smoking lapse were environmental in nature (e.g., being in smoking-permitted areas) as opposed to internal factors such as psychological affect. Interventions may be improved by a renewed focus of interventions on these predictors.ImplicationsThe present study demonstrated the utility of machine learning algorithms to optimize the prediction of time to smoking lapse using EMA data. The two models generated by the present analysis found that environmental factors were most strongly related to smoking lapse. The results support the use of machine learning algorithms to investigate intensive longitudinal data, and provide a foundation for the development of highly tailored, just-in-time interventions that can target on multiple antecedents of smoking lapse.

Dataset Information

High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.

Publications

High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis.

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