Hidden Imputations and the Kaplan-Meier Estimator.
Ontology highlight
ABSTRACT:
SUBMITTER: Cole SR
PROVIDER: S-EPMC7731992 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:This study presents a novel methodology to investigate the nonparametric estimation of a survival probability under random censoring time using the ranked observations from a Partially Rank-Ordered Set (PROS) sampling design and employs it in a hematological disorder study. The PROS sampling design has numerous applications in medicine, social sciences and ecology where the exact measurement of the sampling units is costly; however, sampling units can be ordered by using judgment ranking or available concomitant information. The general estimation methods are not directly applicable to the case where samples are from rank-based sampling designs, because the sampling units do not meet the identically distributed assumption. We derive asymptotic distribution of a Kaplan-Meier (KM) estimator under PROS sampling design. Finally, we compare the performance of the suggested estimators via several simulation studies and apply the proposed methods to a real data set. The results show that the proposed estimator under rank-based sampling designs outperforms its counterpart in a simple random sample (SRS).
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Project description:BackgroundPatient data is considered particularly sensitive personal data. Privacy regulations strictly govern the use of patient data and restrict their exchange. However, medical research can benefit from multicentric studies in which patient data from different institutions are pooled and evaluated together. Thus, the goals of data utilization and data protection are in conflict. Secure multiparty computation (SMPC) solves this conflict because it allows direct computation on distributed proprietary data-held by different data owners-in a secure way without exchanging private data.ObjectiveThe objective of this work was to provide a proof-of-principle of secure and privacy-preserving multicentric computation by SMPC with real-patient data over the free internet. A privacy-preserving log-rank test for the Kaplan-Meier estimator was implemented and tested in both an experimental setting and a real-world setting between two university hospitals.MethodsThe domain of survival analysis is particularly relevant in clinical research. For the Kaplan-Meier estimator, we provided a secure version of the log-rank test. It was based on the SMPC realization SPDZ and implemented via the FRESCO framework in Java. The complexity of the algorithm was explored both for synthetic data and for real-patient data in a proof-of-principle over the internet between two clinical institutions located in Munich and Berlin, Germany.ResultsWe obtained a functional realization of an SMPC-based log-rank evaluation. This implementation was assessed with respect to performance and scaling behavior. We showed that network latency strongly influences execution time of our solution. Furthermore, we identified a lower bound of 2 Mbit/s for the transmission rate that has to be fulfilled for unimpeded communication. In contrast, performance of the participating parties have comparatively low influence on execution speed, since the peer-side processing is parallelized and the computational time only constitutes 30% to 50% even with optimal network settings. In the real-world setting, our computation between three parties over the internet, processing 100 items each, took approximately 20 minutes.ConclusionsWe showed that SMPC is applicable in the medical domain. A secure version of commonly used evaluation methods for clinical studies is possible with current implementations of SMPC. Furthermore, we infer that its application is practically feasible in terms of execution time.
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Project description:In case of heavy and even moderate censoring, a common problem with the Greenwood and Peto variance estimators of the Kaplan-Meier survival function is that they can underestimate the true variance in the left and right tails of the survival distribution. Here, we introduce a variance estimator for the Kaplan-Meier survival function by assigning weight greater than zero to the censored observation. On the basis of this weight, a modification of the Kaplan-Meier survival function and its variance is proposed. An advantage of this approach is that it gives non-parametric estimates at each point whether the event occurred or not. The performance of the variance of this new method is compared with the Greenwood, Peto, regular, and adjusted hybrid variance estimators. Several combinations of these methods with the new method are examined and compared on three datasets, such as leukemia clinical trial data, thalassaemia data as well as cancer data. Thalassaemia is an inherited blood disease, very common in Pakistan, where our data are derived from.
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Project description:For time-to-event outcomes, the Kaplan-Meier estimator is commonly used to estimate survival functions of treatment groups and to compute marginal treatment effects, such as the difference in survival rates between treatments at a landmark time. The derived estimates of the marginal treatment effect are uniformly consistent under general conditions when data are from randomized clinical trials. For data from observational studies, however, these statistical quantities are often biased due to treatment-selection bias. Propensity score-based methods estimate the survival function by adjusting for the disparity of propensity scores between treatment groups. Unfortunately, misspecification of the regression model can lead to biased estimates. Using an empirical likelihood (EL) method in which the moments of the covariate distribution of treatment groups are constrained to equality, we obtain consistent estimates of the survival functions and the marginal treatment effect. Equating moments of the covariate distribution between treatment groups simulate the covariate distribution that would have been obtained if the patients had been randomized to these treatment groups. We establish the consistency and the asymptotic limiting distribution of the proposed EL estimators. We demonstrate that the proposed estimator is robust to model misspecification. Simulation is used to study the finite sample properties of the proposed estimator. The proposed estimator is applied to a lung cancer observational study to compare two surgical procedures in treating early-stage lung cancer patients.
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Project description:In studies of survival and its association with treatment and other prognostic variables, elapsed time alone will often show itself to be among the strongest, if not the strongest, of the predictor variables. Kaplan-Meier curves will show the overall survival of each group and the general differences between groups due to treatment. However, the time-dependent nature of treatment effects is not always immediately transparent from these curves. More sophisticated tools are needed to spotlight the treatment effects. An important tool in this context is the treatment effect process. This tool can be potent in revealing the complex myriad of ways in which treatment can affect survival time. We look at a recently published study in which the outcome was relapse-free survival, and we illustrate how the use of the treatment effect process can provide a much deeper understanding of the relationship between time and treatment in this trial.
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Project description:BACKGROUND:Analysis of clinical studies often necessitates multiple graphical representations of the results. Many professional software packages are available for this purpose. Most packages are either only commercially available or hard to use especially if one aims to generate or customize a huge number of similar graphical outputs. We developed a new, freely available software tool called KMWin (Kaplan-Meier for Windows) facilitating Kaplan-Meier survival time analysis. KMWin is based on the statistical software environment R and provides an easy to use graphical interface. Survival time data can be supplied as SPSS (sav), SAS export (xpt) or text file (dat), which is also a common export format of other applications such as Excel. Figures can directly be exported in any graphical file format supported by R. RESULTS:On the basis of a working example, we demonstrate how to use KMWin and present its main functions. We show how to control the interface, customize the graphical output, and analyse survival time data. A number of comparisons are performed between KMWin and SPSS regarding graphical output, statistical output, data management and development. Although the general functionality of SPSS is larger, KMWin comprises a number of features useful for survival time analysis in clinical trials and other applications. These are for example number of cases and number of cases under risk within the figure or provision of a queue system for repetitive analyses of updated data sets. Moreover, major adjustments of graphical settings can be performed easily on a single window. CONCLUSIONS:We conclude that our tool is well suited and convenient for repetitive analyses of survival time data. It can be used by non-statisticians and provides often used functions as well as functions which are not supplied by standard software packages. The software is routinely applied in several clinical study groups.
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