Recently it has become common for applied works to combine commonly used survival analysis modeling methods, such as the multivariable Cox model, and propensity score weighting with the intention of forming a doubly robust estimator that is unbiased in large samples when either the Cox model or the propensity score model is correctly specified. This combination does not, in general, produce a doubly robust estimator, even after regression standardization, when there is truly a causal effect. We demonstrate via simulation this lack of double robustness for the semiparametric Cox model, the Weibull proportional hazards model, and a simple proportional hazards flexible parametric model, with both the latter models fit via maximum likelihood. We provide a novel proof that the combination of propensity score weighting and a proportional hazards survival model, fit either via full or partial likelihood, is consistent under the null of no causal effect of the exposure on the outcome under particular censoring mechanisms if either the propensity score or the outcome model is correctly specified and contains all confounders. Given our results suggesting that double robustness only exists under the null, we outline two simple alternative estimators that are doubly robust for the survival difference at a given time point (in the above sense), provided the censoring mechanism can be correctly modeled, and one doubly robust method of estimation for the full survival curve. We provide R code to use these estimators for estimation and inference in the supplementary materials.
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This work is concerned with solving high-dimensional Fokker-Planck equations with the novel perspective that solving the PDE can be reduced to independent instances of density estimation tasks based on the trajectories sampled from its associated particle dynamics. With this approach, one sidesteps error accumulation occurring from integrating the PDE dynamics on a parameterized function class. This approach significantly simplifies deployment, as one is free of the challenges of implementing loss terms based on the differential equation. In particular, we introduce a novel class of high-dimensional functions called the functional hierarchical tensor (FHT). The FHT ansatz leverages a hierarchical low-rank structure, offering the advantage of linearly scalable runtime and memory complexity relative to the dimension count. We introduce a sketching-based technique that performs density estimation over particles simulated from the particle dynamics associated with the equation, thereby obtaining a representation of the Fokker-Planck solution in terms of our ansatz. We apply the proposed approach successfully to three challenging time-dependent Ginzburg-Landau models with hundreds of variables.
Permutation tests are widely recognized as robust alternatives to tests based on normal theory. Random permutation tests have been frequently employed to assess the significance of variables in linear models. Despite their widespread use, existing random permutation tests lack finite-sample and assumption-free guarantees for controlling type I error in partial correlation tests. To address this ongoing challenge, we have developed a conformal test through permutation-augmented regressions, which we refer to as PALMRT. PALMRT not only achieves power competitive with conventional methods but also provides reliable control of type I errors at no more than $2\alpha$, given any targeted level $\alpha$, for arbitrary fixed designs and error distributions. We have confirmed this through extensive simulations. Compared to the cyclic permutation test (CPT) and residual permutation test (RPT), which also offer theoretical guarantees, PALMRT does not compromise as much on power or set stringent requirements on the sample size, making it suitable for diverse biomedical applications. We further illustrate the differences in a long-Covid study where PALMRT validated key findings previously identified using the t-test after multiple corrections, while both CPT and RPT suffered from a drastic loss of power and failed to identify any discoveries. We endorse PALMRT as a robust and practical hypothesis test in scientific research for its superior error control, power preservation, and simplicity. An R package for PALMRT is available at \url{//github.com/LeyingGuan/PairedRegression}.
In survival analysis, complex machine learning algorithms have been increasingly used for predictive modeling. Given a collection of features available for inclusion in a predictive model, it may be of interest to quantify the relative importance of a subset of features for the prediction task at hand. In particular, in HIV vaccine trials, participant baseline characteristics are used to predict the probability of infection over the intended follow-up period, and investigators may wish to understand how much certain types of predictors, such as behavioral factors, contribute toward overall predictiveness. Time-to-event outcomes such as time to infection are often subject to right censoring, and existing methods for assessing variable importance are typically not intended to be used in this setting. We describe a broad class of algorithm-agnostic variable importance measures for prediction in the context of survival data. We propose a nonparametric efficient estimation procedure that incorporates flexible learning of nuisance parameters, yields asymptotically valid inference, and enjoys double-robustness. We assess the performance of our proposed procedure via numerical simulations and analyze data from the HVTN 702 study to inform enrollment strategies for future HIV vaccine trials.
Differential privacy is often studied under two different models of neighboring datasets: the add-remove model and the swap model. While the swap model is used extensively in the academic literature, many practical libraries use the more conservative add-remove model. However, analysis under the add-remove model can be cumbersome, and obtaining results with tight constants requires some additional work. Here, we study the problem of one-dimensional mean estimation under the add-remove model of differential privacy. We propose a new algorithm and show that it is min-max optimal, that it has the correct constant in the leading term of the mean squared error, and that this constant is the same as the optimal algorithm in the swap model. Our results show that, for mean estimation, the add-remove and swap model give nearly identical error even though the add-remove model cannot treat the size of the dataset as public information. In addition, we demonstrate empirically that our proposed algorithm yields a factor of two improvement in mean squared error over algorithms often used in practice.
We consider the problem of chance constrained optimization where it is sought to optimize a function and satisfy constraints, both of which are affected by uncertainties. The real world declinations of this problem are particularly challenging because of their inherent computational cost. To tackle such problems, we propose a new Bayesian optimization method. It applies to the situation where the uncertainty comes from some of the inputs, so that it becomes possible to define an acquisition criterion in the joint controlled-uncontrolled input space. The main contribution of this work is an acquisition criterion that accounts for both the average improvement in objective function and the constraint reliability. The criterion is derived following the Stepwise Uncertainty Reduction logic and its maximization provides both optimal controlled and uncontrolled parameters. Analytical expressions are given to efficiently calculate the criterion. Numerical studies on test functions are presented. It is found through experimental comparisons with alternative sampling criteria that the adequation between the sampling criterion and the problem contributes to the efficiency of the overall optimization. As a side result, an expression for the variance of the improvement is given.
Non-parametric machine learning models, such as random forests and gradient boosted trees, are frequently used to estimate house prices due to their predictive accuracy, but such methods are often limited in their ability to quantify prediction uncertainty. Conformal Prediction (CP) is a model-agnostic framework for constructing confidence sets around machine learning prediction models with minimal assumptions. However, due to the spatial dependencies observed in house prices, direct application of CP leads to confidence sets that are not calibrated everywhere, i.e., too large of confidence sets in certain geographical regions and too small in others. We survey various approaches to adjust the CP confidence set to account for this and demonstrate their performance on a data set from the housing market in Oslo, Norway. Our findings indicate that calibrating the confidence sets on a \textit{locally weighted} version of the non-conformity scores makes the coverage more consistently calibrated in different geographical regions. We also perform a simulation study on synthetically generated sale prices to empirically explore the performance of CP on housing market data under idealized conditions with known data-generating mechanisms.
Singularly perturbed boundary value problems pose a significant challenge for their numerical approximations because of the presence of sharp boundary layers. These sharp boundary layers are responsible for the stiffness of solutions, which leads to large computational errors, if not properly handled. It is well-known that the classical numerical methods as well as the Physics-Informed Neural Networks (PINNs) require some special treatments near the boundary, e.g., using extensive mesh refinements or finer collocation points, in order to obtain an accurate approximate solution especially inside of the stiff boundary layer. In this article, we modify the PINNs and construct our new semi-analytic SL-PINNs suitable for singularly perturbed boundary value problems. Performing the boundary layer analysis, we first find the corrector functions describing the singular behavior of the stiff solutions inside boundary layers. Then we obtain the SL-PINN approximations of the singularly perturbed problems by embedding the explicit correctors in the structure of PINNs or by training the correctors together with the PINN approximations. Our numerical experiments confirm that our new SL-PINN methods produce stable and accurate approximations for stiff solutions.
We establish an $L_1$-bound between the coefficients of the optimal causal filter applied to the data-generating process and its finite sample approximation. Here, we assume that the data-generating process is a second-order stationary time series with either short or long memory autocovariances. To derive the $L_1$-bound, we first provide an exact expression for the coefficients of the causal filter and their approximations in terms of the absolute convergent series of the multistep ahead infinite and finite predictor coefficients, respectively. Then, we prove a so-called uniform Baxter's inequality to obtain a bound for the difference between the infinite and finite multistep ahead predictor coefficients in both short and long memory time series. The $L_1$-approximation error bound for the causal filter coefficients can be used to evaluate the performance of the linear predictions of time series through the mean squared error criterion.
Finite-dimensional truncations are routinely used to approximate partial differential equations (PDEs), either to obtain numerical solutions or to derive reduced-order models. The resulting discretized equations are known to violate certain physical properties of the system. In particular, first integrals of the PDE may not remain invariant after discretization. Here, we use the method of reduced-order nonlinear solutions (RONS) to ensure that the conserved quantities of the PDE survive its finite-dimensional truncation. In particular, we develop two methods: Galerkin RONS and finite volume RONS. Galerkin RONS ensures the conservation of first integrals in Galerkin-type truncations, whether used for direct numerical simulations or reduced-order modeling. Similarly, finite volume RONS conserves any number of first integrals of the system, including its total energy, after finite volume discretization. Both methods are applicable to general time-dependent PDEs and can be easily incorporated in existing Galerkin-type or finite volume code. We demonstrate the efficacy of our methods on two examples: direct numerical simulations of the shallow water equation and a reduced-order model of the nonlinear Schrodinger equation. As a byproduct, we also generalize RONS to phenomena described by a system of PDEs.
Linear transformation of the state variable (linear preconditioning) is a common technique that often drastically improves the practical performance of a Markov chain Monte Carlo algorithm. Despite this, however, the benefits of linear preconditioning are not well-studied theoretically, and rigorous guidelines for choosing preconditioners are not always readily available. Mixing time bounds for various samplers have been produced in recent works for the class of strongly log-concave and Lipschitz target distributions and depend strongly on a quantity known as the condition number. We study linear preconditioning for this class of distributions, and under appropriate assumptions we provide bounds on the condition number after using a given linear preconditioner. We provide bounds on the spectral gap of RWM that are tight in their dependence on the condition number under the same assumptions. Finally we offer a review and analysis of popular preconditioners. Of particular note, we identify a surprising case in which preconditioning with the diagonal of the target covariance can actually make the condition number \emph{increase} relative to doing no preconditioning at all.
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