Residuals in normal regression are used to assess a model's goodness-of-fit (GOF) and discover directions for improving the model. However, there is a lack of residuals with a characterized reference distribution for censored regression. In this paper, we propose to diagnose censored regression with normalized randomized survival probabilities (RSP). The key idea of RSP is to replace the survival probability of a censored failure time with a uniform random number between 0 and the survival probability of the censored time. We prove that RSPs always have the uniform distribution on $(0,1)$ under the true model with the true generating parameters. Therefore, we can transform RSPs into normally-distributed residuals with the normal quantile function. We call such residuals by normalized RSP (NRSP residuals). We conduct simulation studies to investigate the sizes and powers of statistical tests based on NRSP residuals in detecting the incorrect choice of distribution family and non-linear effect in covariates. Our simulation studies show that, although the GOF tests with NRSP residuals are not as powerful as a traditional GOF test method, a non-linear test based on NRSP residuals has significantly higher power in detecting non-linearity. We also compared these model diagnostics methods with a breast-cancer recurrent-free time dataset. The results show that the NRSP residual diagnostics successfully captures a subtle non-linear relationship in the dataset, which is not detected by the graphical diagnostics with CS residuals and existing GOF tests.
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Existing survival analysis techniques heavily rely on strong modelling assumptions and are, therefore, prone to model misspecification errors. In this paper, we develop an inferential method based on ideas from conformal prediction, which can wrap around any survival prediction algorithm to produce calibrated, covariate-dependent lower predictive bounds on survival times. In the Type I right-censoring setting, when the censoring times are completely exogenous, the lower predictive bounds have guaranteed coverage in finite samples without any assumptions other than that of operating on independent and identically distributed data points. Under a more general conditionally independent censoring assumption, the bounds satisfy a doubly robust property which states the following: marginal coverage is approximately guaranteed if either the censoring mechanism or the conditional survival function is estimated well. Further, we demonstrate that the lower predictive bounds remain valid and informative for other types of censoring. The validity and efficiency of our procedure are demonstrated on synthetic data and real COVID-19 data from the UK Biobank.
The Bayesian information criterion (BIC), defined as the observed data log likelihood minus a penalty term based on the sample size $N$, is a popular model selection criterion for factor analysis with complete data. This definition has also been suggested for incomplete data. However, the penalty term based on the `complete' sample size $N$ is the same no matter whether in a complete or incomplete data case. For incomplete data, there are often only $N_i<N$ observations for variable $i$, which means that using the `complete' sample size $N$ implausibly ignores the amounts of missing information inherent in incomplete data. Given this observation, a novel criterion called hierarchical BIC (HBIC) for factor analysis with incomplete data is proposed. The novelty is that it only uses the actual amounts of observed information, namely $N_i$'s, in the penalty term. Theoretically, it is shown that HBIC is a large sample approximation of variational Bayesian (VB) lower bound, and BIC is a further approximation of HBIC, which means that HBIC shares the theoretical consistency of BIC. Experiments on synthetic and real data sets are conducted to access the finite sample performance of HBIC, BIC, and related criteria with various missing rates. The results show that HBIC and BIC perform similarly when the missing rate is small, but HBIC is more accurate when the missing rate is not small.
We consider the question of adaptive data analysis within the framework of convex optimization. We ask how many samples are needed in order to compute $\epsilon$-accurate estimates of $O(1/\epsilon^2)$ gradients queried by gradient descent, and we provide two intermediate answers to this question. First, we show that for a general analyst (not necessarily gradient descent) $\Omega(1/\epsilon^3)$ samples are required. This rules out the possibility of a foolproof mechanism. Our construction builds upon a new lower bound (that may be of interest of its own right) for an analyst that may ask several non adaptive questions in a batch of fixed and known $T$ rounds of adaptivity and requires a fraction of true discoveries. We show that for such an analyst $\Omega (\sqrt{T}/\epsilon^2)$ samples are necessary. Second, we show that, under certain assumptions on the oracle, in an interaction with gradient descent $\tilde \Omega(1/\epsilon^{2.5})$ samples are necessary. Our assumptions are that the oracle has only \emph{first order access} and is \emph{post-hoc generalizing}. First order access means that it can only compute the gradients of the sampled function at points queried by the algorithm. Our assumption of \emph{post-hoc generalization} follows from existing lower bounds for statistical queries. More generally then, we provide a generic reduction from the standard setting of statistical queries to the problem of estimating gradients queried by gradient descent. These results are in contrast with classical bounds that show that with $O(1/\epsilon^2)$ samples one can optimize the population risk to accuracy of $O(\epsilon)$ but, as it turns out, with spurious gradients.
The emerging public awareness and government regulations of data privacy motivate new paradigms of collecting and analyzing data that are transparent and acceptable to data owners. We present a new concept of privacy and corresponding data formats, mechanisms, and theories for privatizing data during data collection. The privacy, named Interval Privacy, enforces the raw data conditional distribution on the privatized data to be the same as its unconditional distribution over a nontrivial support set. Correspondingly, the proposed privacy mechanism will record each data value as a random interval (or, more generally, a range) containing it. The proposed interval privacy mechanisms can be easily deployed through survey-based data collection interfaces, e.g., by asking a respondent whether its data value is within a randomly generated range. Another unique feature of interval mechanisms is that they obfuscate the truth but do not perturb it. Using narrowed range to convey information is complementary to the popular paradigm of perturbing data. Also, the interval mechanisms can generate progressively refined information at the discretion of individuals, naturally leading to privacy-adaptive data collection. We develop different aspects of theory such as composition, robustness, distribution estimation, and regression learning from interval-valued data. Interval privacy provides a new perspective of human-centric data privacy where individuals have a perceptible, transparent, and simple way of sharing sensitive data.
We investigate the feature compression of high-dimensional ridge regression using the optimal subsampling technique. Specifically, based on the basic framework of random sampling algorithm on feature for ridge regression and the A-optimal design criterion, we first obtain a set of optimal subsampling probabilities. Considering that the obtained probabilities are uneconomical, we then propose the nearly optimal ones. With these probabilities, a two step iterative algorithm is established which has lower computational cost and higher accuracy. We provide theoretical analysis and numerical experiments to support the proposed methods. Numerical results demonstrate the decent performance of our methods.
The instrumental variable method is widely used in the health and social sciences for identification and estimation of causal effects in the presence of potentially unmeasured confounding. In order to improve efficiency, multiple instruments are routinely used, leading to concerns about bias due to possible violation of the instrumental variable assumptions. To address this concern, we introduce a new class of g-estimators that are guaranteed to remain consistent and asymptotically normal for the causal effect of interest provided that a set of at least $\gamma$ out of $K$ candidate instruments are valid, for $\gamma\leq K$ set by the analyst ex ante, without necessarily knowing the identities of the valid and invalid instruments. We provide formal semiparametric efficiency theory supporting our results. Both simulation studies and applications to the UK Biobank data demonstrate the superior empirical performance of our estimators compared to competing methods.
The inverse probability (IPW) and doubly robust (DR) estimators are often used to estimate the average causal effect (ATE), but are vulnerable to outliers. The IPW/DR median can be used for outlier-resistant estimation of the ATE, but the outlier resistance of the median is limited and it is not resistant enough for heavy contamination. We propose extensions of the IPW/DR estimators with density power weighting, which can eliminate the influence of outliers almost completely. The outlier resistance of the proposed estimators is evaluated through the unbiasedness of the estimating equations. Unlike the median-based methods, our estimators are resistant to outliers even under heavy contamination. Interestingly, the naive extension of the DR estimator requires bias correction to keep the double robustness even under the most tractable form of contamination. In addition, the proposed estimators are found to be highly resistant to outliers in more difficult settings where the contamination ratio depends on the covariates. The outlier resistance of our estimators from the viewpoint of the influence function is also favorable. Our theoretical results are verified via Monte Carlo simulations and real data analysis. The proposed methods were found to have more outlier resistance than the median-based methods and estimated the potential mean with a smaller error than the median-based methods.
Applications of machine learning in healthcare often require working with time-to-event prediction tasks including prognostication of an adverse event, re-hospitalization or death. Such outcomes are typically subject to censoring due to loss of follow up. Standard machine learning methods cannot be applied in a straightforward manner to datasets with censored outcomes. In this paper, we present auton-survival, an open-source repository of tools to streamline working with censored time-to-event or survival data. auton-survival includes tools for survival regression, adjustment in the presence of domain shift, counterfactual estimation, phenotyping for risk stratification, evaluation, as well as estimation of treatment effects. Through real world case studies employing a large subset of the SEER oncology incidence data, we demonstrate the ability of auton-survival to rapidly support data scientists in answering complex health and epidemiological questions.
Estimating counterfactual outcomes over time from observational data is relevant for many applications (e.g., personalized medicine). Yet, state-of-the-art methods build upon simple long short-term memory (LSTM) networks, thus rendering inferences for complex, long-range dependencies challenging. In this paper, we develop a novel Causal Transformer for estimating counterfactual outcomes over time. Our model is specifically designed to capture complex, long-range dependencies among time-varying confounders. For this, we combine three transformer subnetworks with separate inputs for time-varying covariates, previous treatments, and previous outcomes into a joint network with in-between cross-attentions. We further develop a custom, end-to-end training procedure for our Causal Transformer. Specifically, we propose a novel counterfactual domain confusion loss to address confounding bias: it aims to learn adversarial balanced representations, so that they are predictive of the next outcome but non-predictive of the current treatment assignment. We evaluate our Causal Transformer based on synthetic and real-world datasets, where it achieves superior performance over current baselines. To the best of our knowledge, this is the first work proposing transformer-based architecture for estimating counterfactual outcomes from longitudinal data.
We propose a simple yet powerful extension of Bayesian Additive Regression Trees which we name Hierarchical Embedded BART (HE-BART). The model allows for random effects to be included at the terminal node level of a set of regression trees, making HE-BART a non-parametric alternative to mixed effects models which avoids the need for the user to specify the structure of the random effects in the model, whilst maintaining the prediction and uncertainty calibration properties of standard BART. Using simulated and real-world examples, we demonstrate that this new extension yields superior predictions for many of the standard mixed effects models' example data sets, and yet still provides consistent estimates of the random effect variances. In a future version of this paper, we outline its use in larger, more advanced data sets and structures.
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