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Register a new userPositive-Unlabelled Survival Data Analysis
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Added by
Takahiro Hoshino
Publication date
2020
fields
Mathematical Statistics
and research's language is
English
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In this paper, we consider a novel framework of positive-unlabeled data in which as positive data survival times are observed for subjects who have events during the observation time as positive data and as unlabeled data censoring times are observed but whether the event occurs or not are unknown for some subjects. We consider two cases: (1) when censoring time is observed in positive data, and (2) when it is not observed. For both cases, we developed parametric models, nonparametric models, and machine learning models and the estimation strategies for these models. Simulation studies show that under this data setup, traditional survival analysis may yield severely biased results, while the proposed estimation method can provide valid results.
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The scarcity of class-labeled data is a ubiquitous bottleneck in a wide range of machine learning problems. While abundant unlabeled data normally exist and provide a potential solution, it is extremely challenging to exploit them. In this paper, we address this problem by leveraging Positive-Unlabeled~(PU) classification and conditional generation with extra unlabeled data emph{simultaneously}, both of which aim to make full use of agnostic unlabeled data to improve classification and generation performances. In particular, we present a novel training framework to jointly target both PU classification and conditional generation when exposing to extra data, especially out-of-distribution unlabeled data, by exploring the interplay between them: 1) enhancing the performance of PU classifiers with the assistance of a novel Conditional Generative Adversarial Network~(CGAN) that is robust to noisy labels, 2) leveraging extra data with predicted labels from a PU classifier to help the generation. Our key contribution is a Classifier-Noise-Invariant Conditional GAN~(CNI-CGAN) that can learn the clean data distribution from noisy labels predicted by a PU classifier. Theoretically, we proved the optimal condition of CNI-CGAN and experimentally, we conducted extensive evaluations on diverse datasets, verifying the simultaneous improvements on both classification and generation.
This paper introduces a general framework for survival analysis based on ordinary differential equations (ODE). Specifically, this framework unifies many existing survival models, including proportional hazards models, linear transformation models, accelerated failure time models, and time-varying coefficient models as special cases. Such a unified framework provides a novel perspective on modeling censored data and offers opportunities for designing new and more flexible survival model structures. Further, the aforementioned existing survival models are traditionally estimated by procedures that suffer from lack of scalability, statistical inefficiency, or implementation difficulty. Based on well-established numerical solvers and sensitivity analysis tools for ODEs, we propose a novel, scalable, and easy-to-implement general estimation procedure that is applicable to a wide range of models. In particular, we develop a sieve maximum likelihood estimator for a general semi-parametric class of ODE models as an illustrative example. We also establish a general sieve M-theorem for bundled parameters and show that the proposed sieve estimator is consistent and asymptotically normal, and achieves the semi-parametric efficiency bound. The finite sample performance of the proposed estimator is examined in simulation studies and a real-world data example.
Survival analysis is a hotspot in statistical research for modeling time-to-event information with data censorship handling, which has been widely used in many applications such as clinical research, information system and other fields with survivorship bias. Many works have been proposed for survival analysis ranging from traditional statistic methods to machine learning models. However, the existing methodologies either utilize counting-based statistics on the segmented data, or have a pre-assumption on the event probability distribution w.r.t. time. Moreover, few works consider sequential patterns within the feature space. In this paper, we propose a Deep Recurrent Survival Analysis model which combines deep learning for conditional probability prediction at fine-grained level of the data, and survival analysis for tackling the censorship. By capturing the time dependency through modeling the conditional probability of the event for each sample, our method predicts the likelihood of the true event occurrence and estimates the survival rate over time, i.e., the probability of the non-occurrence of the event, for the censored data. Meanwhile, without assuming any specific form of the event probability distribution, our model shows great advantages over the previous works on fitting various sophisticated data distributions. In the experiments on the three real-world tasks from different fields, our model significantly outperforms the state-of-the-art solutions under various metrics.
Canonical correlation analysis (CCA) is a classical and important multivariate technique for exploring the relationship between two sets of continuous variables. CCA has applications in many fields, such as genomics and neuroimaging. It can extract meaningful features as well as use these features for subsequent analysis. Although some sparse CCA methods have been developed to deal with high-dimensional problems, they are designed specifically for continuous data and do not consider the integer-valued data from next-generation sequencing platforms that exhibit very low counts for some important features. We propose a model-based probabilistic approach for correlation and canonical correlation estimation for two sparse count data sets (PSCCA). PSCCA demonstrates that correlations and canonical correlations estimated at the natural parameter level are more appropriate than traditional estimation methods applied to the raw data. We demonstrate through simulation studies that PSCCA outperforms other standard correlation approaches and sparse CCA approaches in estimating the true correlations and canonical correlations at the natural parameter level. We further apply the PSCCA method to study the association of miRNA and mRNA expression data sets from a squamous cell lung cancer study, finding that PSCCA can uncover a large number of strongly correlated pairs than standard correlation and other sparse CCA approaches.
Survival analysis in the presence of multiple possible adverse events, i.e., competing risks, is a pervasive problem in many industries (healthcare, finance, etc.). Since only one event is typically observed, the incidence of an event of interest is often obscured by other related competing events. This nonidentifiability, or inability to estimate true cause-specific survival curves from empirical data, further complicates competing risk survival analysis. We introduce Siamese Survival Prognosis Network (SSPN), a novel deep learning architecture for estimating personalized risk scores in the presence of competing risks. SSPN circumvents the nonidentifiability problem by avoiding the estimation of cause-specific survival curves and instead determines pairwise concordant time-dependent risks, where longer event times are assigned lower risks. Furthermore, SSPN is able to directly optimize an approximation to the C-discrimination index, rather than relying on well-known metrics which are unable to capture the unique requirements of survival analysis with competing risks.
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