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Register a new userA Simplified Stochastic EM Algorithm for Cure Rate Model with Negative Binomial Competing Risks: An Application to Breast Cancer Data
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Suvra Pal
Publication date
2020
fields
Mathematical Statistics
and research's language is
English
Authors
Suvra Pal
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In this paper, a long-term survival model under competing risks is considered. The unobserved number of competing risks is assumed to follow a negative binomial distribution that can capture both over- and under-dispersion. Considering the latent competing risks as missing data, a variation of the well-known expectation maximization (EM) algorithm, called the stochastic EM algorithm (SEM), is developed. It is shown that the SEM algorithm avoids calculation of complicated expectations, which is a major advantage of the SEM algorithm over the EM algorithm. The proposed procedure also allows the objective function to be split into two simpler functions, one corresponding to the parameters associated with the cure rate and the other corresponding to the parameters associated with the progression times. The advantage of this approach is that each simple function, with lower parameter dimension, can be maximized independently. An extensive Monte Carlo simulation study is carried out to compare the performances of the SEM and EM algorithms. Finally, a breast cancer survival data is analyzed and it is shown that the SEM algorithm performs better than the EM algorithm.
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Handling missing values plays an important role in the analysis of survival data, especially, the ones marked by cure fraction. In this paper, we discuss the properties and implementation of stochastic approximations to the expectation-maximization (EM) algorithm to obtain maximum likelihood (ML) type estimates in situations where missing data arise naturally due to right censoring and a proportion of individuals are immune to the event of interest. A flexible family of three parameter exponentiated-Weibull (EW) distributions is assumed to characterize lifetimes of the non-immune individuals as it accommodates both monotone (increasing and decreasing) and non-monotone (unimodal and bathtub) hazard functions. To evaluate the performance of the SEM algorithm, an extensive simulation study is carried out under various parameter settings. Using likelihood ratio test we also carry out model discrimination within the EW family of distributions. Furthermore, we study the robustness of the SEM algorithm with respect to outliers and algorithm starting values. Few scenarios where stochastic EM (SEM) algorithm outperforms the well-studied EM algorithm are also examined in the given context. For further demonstration, a real survival data on cutaneous melanoma is analyzed using the proposed cure rate model with EW lifetime distribution and the proposed estimation technique. Through this data, we illustrate the applicability of the likelihood ratio test towards rejecting several well-known lifetime distributions that are nested within the wider class of EW distributions.
In this paper, we propose a new estimation methodology based on a projected non-linear conjugate gradient (PNCG) algorithm with an efficient line search technique. We develop a general PNCG algorithm for a survival model incorporating a proportion cure under a competing risks setup, where the initial number of competing risks are exposed to elimination after an initial treatment (known as destruction). In the literature, expectation maximization (EM) algorithm has been widely used for such a model to estimate the model parameters. Through an extensive Monte Carlo simulation study, we compare the performance of our proposed PNCG with that of the EM algorithm and show the advantages of our proposed method. Through simulation, we also show the advantages of our proposed methodology over other optimization algorithms (including other conjugate gradient type methods) readily available as R software packages. To show these we assume the initial number of competing risks to follow a negative binomial distribution although our general algorithm allows one to work with any competing risks distribution. Finally, we apply our proposed algorithm to analyze a well-known melanoma data.
The mixture cure rate model is the most commonly used cure rate model in the literature. In the context of mixture cure rate model, the standard approach to model the effect of covariates on the cured or uncured probability is to use a logistic function. This readily implies that the boundary classifying the cured and uncured subjects is linear. In this paper, we propose a new mixture cure rate model based on interval censored data that uses the support vector machine (SVM) to model the effect of covariates on the uncured or the cured probability (i.e., on the incidence part of the model). Our proposed model inherits the features of the SVM and provides flexibility to capture classification boundaries that are non-linear and more complex. Furthermore, the new model can be used to model the effect of covariates on the incidence part when the dimension of covariates is high. The latency part is modeled by a proportional hazards structure. We develop an estimation procedure based on the expectation maximization (EM) algorithm to estimate the cured/uncured probability and the latency model parameters. Our simulation study results show that the proposed model performs better in capturing complex classification boundaries when compared to the existing logistic regression based mixture cure rate model. We also show that our models ability to capture complex classification boundaries improve the estimation results corresponding to the latency parameters. For illustrative purpose, we present our analysis by applying the proposed methodology to an interval censored data on smoking cessation.
In this paper, we develop a new estimation procedure based on the non-linear conjugate gradient (NCG) algorithm for the Box-Cox transformation cure rate model. We compare the performance of the NCG algorithm with the well-known expectation maximization (EM) algorithm through a simulation study and show the advantages of the NCG algorithm over the EM algorithm. In particular, we show that the NCG algorithm allows simultaneous maximization of all model parameters when the likelihood surface is flat with respect to a Box-Cox model parameter. This is a big advantage over the EM algorithm, where a profile likelihood approach has been proposed in the literature that may not provide satisfactory results. We finally use the NCG algorithm to analyze a well-known melanoma data and show that it results in a better fit.
A new robust stochastic volatility (SV) model having Student-t marginals is proposed. Our process is defined through a linear normal regression model driven by a latent gamma process that controls temporal dependence. This gamma process is strategically chosen to enable us to find an explicit expression for the pairwise joint density function of the Student-t response process. With this at hand, we propose a composite likelihood (CL) based inference for our model, which can be straightforwardly implemented with a low computational cost. This is a remarkable feature of our Student-t SV process over existing SV models in the literature that involve computationally heavy algorithms for estimating parameters. Aiming at a precise estimation of the parameters related to the latent process, we propose a CL Expectation-Maximization algorithm and discuss a bootstrap approach to obtain standard errors. The finite-sample performance of our composite likelihood methods is assessed through Monte Carlo simulations. The methodology is motivated by an empirical application in the financial market. We analyze the relationship, across multiple time periods, between various US sector Exchange-Traded Funds returns and individual companies stock price returns based on our novel Student-t model. This relationship is further utilized in selecting optimal financial portfolios.
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