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Register a new userNonparametric generalized fiducial inference for survival functions under censoring
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Yifan Cui
Publication date
2017
fields
Mathematical Statistics
and research's language is
English
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Fiducial Inference, introduced by Fisher in the 1930s, has a long history, which at times aroused passionate disagreements. However, its application has been largely confined to relatively simple parametric problems. In this paper, we present what might be the first time fiducial inference, as generalized by Hannig et al. (2016), is systematically applied to estimation of a nonparametric survival function under right censoring. We find that the resulting fiducial distribution gives rise to surprisingly good statistical procedures applicable to both one sample and two sample problems. In particular, we use the fiducial distribution of a survival function to construct pointwise and curvewise confidence intervals for the survival function, and propose tests based on the curvewise confidence interval. We establish a functional Bernstein-von Mises theorem, and perform thorough simulation studies in scenarios with different levels of censoring. The proposed fiducial based confidence intervals maintain coverage in situations where asymptotic methods often have substantial coverage problems. Furthermore, the average length of the proposed confidence intervals is often shorter than the length of competing methods that maintain coverage. Finally, the proposed fiducial test is more powerful than various types of log-rank tests and sup log-rank tests in some scenarios. We illustrate the proposed fiducial test comparing chemotherapy against chemotherapy combined with radiotherapy using data from the treatment of locally unresectable gastric cancer.
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Due to their accuracies, methods based on ensembles of regression trees are a popular approach for making predictions. Some common examples include Bayesian additive regression trees, boosting and random forests. This paper focuses on honest random forests, which add honesty to the original form of random forests and are proved to have better statistical properties. The main contribution is a new method that quantifies the uncertainties of the estimates and predictions produced by honest random forests. The proposed method is based on the generalized fiducial methodology, and provides a fiducial density function that measures how likely each single honest tree is the true model. With such a density function, estimates and predictions, as well as their confidence/prediction intervals, can be obtained. The promising empirical properties of the proposed method are demonstrated by numerical comparisons with several state-of-the-art methods, and by applications to a few real data sets. Lastly, the proposed method is theoretically backed up by a strong asymptotic guarantee.
Fiducial inference, as generalized by Hannig et al. (2016), is applied to nonparametric g-modeling (Efron, 2016) in the discrete case. We propose a computationally efficient algorithm to sample from the fiducial distribution, and use generated samples to construct point estimates and confidence intervals. We study the theoretical properties of the fiducial distribution and perform extensive simulations in various scenarios. The proposed approach gives rise to surprisingly good statistical performance in terms of the mean squared error of point estimators and coverage of confidence intervals. Furthermore, we apply the proposed fiducial method to estimate the probability of each satellite site being malignant using gastric adenocarcinoma data with 844 patients (Efron, 2016).
Bayesian nonparametric priors based on completely random measures (CRMs) offer a flexible modeling approach when the number of latent components in a dataset is unknown. However, managing the infinite dimensionality of CRMs typically requires practitioners to derive ad-hoc algorithms, preventing the use of general-purpose inference methods and often leading to long compute times. We propose a general but explicit recipe to construct a simple finite-dimensional approximation that can replace the infinite-dimensional CRMs. Our independent finite approximation (IFA) is a generalization of important cases that are used in practice. The independence of atom weights in our approximation (i) makes the construction well-suited for parallel and distributed computation and (ii) facilitates more convenient inference schemes. We quantify the approximation error between IFAs and the target nonparametric prior. We compare IFAs with an alternative approximation scheme -- truncated finite approximations (TFAs), where the atom weights are constructed sequentially. We prove that, for worst-case choices of observation likelihoods, TFAs are a more efficient approximation than IFAs. However, in real-data experiments with image denoising and topic modeling, we find that IFAs perform very similarly to TFAs in terms of task-specific accuracy metrics.
Partially observed cured data occur in the analysis of spontaneous abortion (SAB) in observational studies in pregnancy. In contrast to the traditional cured data, such data has an observable `cured portion as women who do not abort spontaneously. The data is also subject to left truncate in addition to right-censoring because women may enter or withdraw from a study any time during their pregnancy. Left truncation in particular causes unique bias in the presence of a cured portion. In this paper, we study a cure rate model and develop a conditional nonparametric maximum likelihood approach. To tackle the computational challenge we adopt an EM algorithm making use of ghost copies of the data, and a closed form variance estimator is derived. Under suitable assumptions, we prove the consistency of the resulting estimator involving an unbounded cumulative baseline hazard function, as well as the asymptotic normality. Simulation results are carried out to evaluate the finite sample performance. We present the analysis of the motivating SAB study to illustrate the power of our model addressing both occurrence and timing of SAB, as compared to existing approaches in practice.
Classification is the task of assigning a new instance to one of a set of predefined categories based on the attributes of the instance. A classification tree is one of the most commonly used techniques in the area of classification. In this paper, we introduce a novel classification tree algorithm which we call Direct Nonparametric Predictive Inference (D-NPI) classification algorithm. The D-NPI algorithm is completely based on the Nonparametric Predictive Inference (NPI) approach, and it does not use any other assumption or information. The NPI is a statistical methodology which learns from data in the absence of prior knowledge and uses only few modelling assumptions, enabled by the use of lower and upper probabilities to quantify uncertainty. Due to the predictive nature of NPI, it is well suited for classification, as the nature of classification is explicitly predictive as well. The D-NPI algorithm uses a new split criterion called Correct Indication (CI). The CI is about the informativity that the attribute variables will indicate, hence, if the attribute is very informative, it gives high lower and upper probabilities for CI. The CI reports the strength of the evidence that the attribute variables will indicate, based on the data. The CI is completely based on the NPI, and it does not use any additional concepts such as entropy. The performance of the D-NPI classification algorithm is tested against several classification algorithms using classification accuracy, in-sample accuracy and tree size on different datasets from the UCI machine learning repository. The experimental results indicate that the D-NPI classification algorithm performs well in terms of classification accuracy and in-sample accuracy.
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