There is an increasing number of potential biomarkers that could allow for early assessment of treatment response or disease progression. However, measurements of quantitative biomarkers are subject to random variability. Hence, differences of a biomarker in longitudinal measurements do not necessarily represent real change but might be caused by this random measurement variability. Before utilizing a quantitative biomarker in longitudinal studies, it is therefore essential to assess the measurement repeatability. Measurement repeatability obtained from test-retest studies can be quantified by the repeatability coefficient (RC), which is then used in the subsequent longitudinal study to determine if a measured difference represents real change or is within the range of expected random measurement variability. The quality of the point estimate of RC therefore directly governs the assessment quality of the longitudinal study. RC estimation accuracy depends on the case number in the test-retest study, but despite its pivotal role, no comprehensive framework for sample size calculation of test-retest studies exists. To address this issue, we have established such a framework, which allows for flexible sample size calculation of test-retest studies, based upon newly introduced criteria concerning assessment quality in the longitudinal study. This also permits retrospective assessment of prior test-retest studies.
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The presence of measurement error is a widespread issue which, when ignored, can render the results of an analysis unreliable. Numerous corrections for the effects of measurement error have been proposed and studied, often under the assumption of a normally distributed, additive measurement error model. One such method is simulation extrapolation, or SIMEX. In many situations observed data are non-symmetric, heavy-tailed, or otherwise highly non-normal. In these settings, correction techniques relying on the assumption of normality are undesirable. We propose an extension to the simulation extrapolation method which is nonparametric in the sense that no specific distributional assumptions are required on the error terms. The technique is implemented when either validation data or replicate measurements are available, and is designed to be immediately accessible for those familiar with simulation extrapolation.
This paper studies a house allocation problem in a networked housing market, where agents can invite others to join the system in order to enrich their options. Top Trading Cycle is a well-known matching mechanism that achieves a set of desirable properties in a market without invitations. However, under a tree-structured networked market, existing agents have to strategically propagate the barter market as their invitees may compete in the same house with them. Our impossibility result shows that TTC cannot work properly in a networked housing market. Hence, we characterize the possible competitions between inviters and invitees, which lead agents to fail to refer others truthfully (strategy-proof). We then present a novel mechanism based on TTC, avoiding the aforementioned competition to ensure all agents report preference and propagate the barter market truthfully. Unlike the existing mechanisms, the agents' preferences are less restricted under our mechanism. Furthermore, we show by simulations that our mechanism outperforms the existing matching mechanisms in terms of the number of swaps and agents' satisfaction.
Negative control is a common technique in scientific investigations and broadly refers to the situation where a null effect (''negative result'') is expected. Motivated by a real proteomic dataset, we will present three promising and closely connected methods of using negative controls to assist simultaneous hypothesis testing. The first method uses negative controls to construct a permutation p-value for every hypothesis under investigation, and we give several sufficient conditions for such p-values to be valid and positive regression dependent on the set (PRDS) of true nulls. The second method uses negative controls to construct an estimate of the false discovery rate (FDR), and we give a sufficient condition under which the step-up procedure based on this estimate controls the FDR. The third method, derived from an existing ad hoc algorithm for proteomic analysis, uses negative controls to construct a nonparametric estimator of the local false discovery rate. We conclude with some practical suggestions and connections to some closely related methods that are propsed recently.
The use of expectiles in risk management has recently gathered remarkable momentum due to their excellent axiomatic and probabilistic properties. In particular, the class of elicitable law-invariant coherent risk measures only consists of expectiles. While the theory of expectile estimation at central levels is substantial, tail estimation at extreme levels has so far only been considered when the tail of the underlying distribution is heavy. This article is the first work to handle the short-tailed setting where the loss (e.g. negative log-returns) distribution of interest is bounded to the right and the corresponding extreme value index is negative. We derive an asymptotic expansion of tail expectiles in this challenging context under a general second-order extreme value condition, which allows to come up with two semiparametric estimators of extreme expectiles, and with their asymptotic properties in a general model of strictly stationary but weakly dependent observations. A simulation study and a real data analysis from a forecasting perspective are performed to verify and compare the proposed competing estimation procedures.
Tabular question answering (TQA) presents a challenging setting for neural systems by requiring joint reasoning of natural language with large amounts of semi-structured data. Unlike humans who use programmatic tools like filters to transform data before processing, language models in TQA process tables directly, resulting in information loss as table size increases. In this paper we propose ToolWriter to generate query specific programs and detect when to apply them to transform tables and align them with the TQA model's capabilities. Focusing ToolWriter to generate row-filtering tools improves the state-of-the-art for WikiTableQuestions and WikiSQL with the most performance gained on long tables. By investigating headroom, our work highlights the broader potential for programmatic tools combined with neural components to manipulate large amounts of structured data.
Autoencoders have demonstrated remarkable success in learning low-dimensional latent features of high-dimensional data across various applications. Assuming that data are sampled near a low-dimensional manifold, we employ chart autoencoders, which encode data into low-dimensional latent features on a collection of charts, preserving the topology and geometry of the data manifold. Our paper establishes statistical guarantees on the generalization error of chart autoencoders, and we demonstrate their denoising capabilities by considering $n$ noisy training samples, along with their noise-free counterparts, on a $d$-dimensional manifold. By training autoencoders, we show that chart autoencoders can effectively denoise the input data with normal noise. We prove that, under proper network architectures, chart autoencoders achieve a squared generalization error in the order of $\displaystyle n^{-\frac{2}{d+2}}\log^4 n$, which depends on the intrinsic dimension of the manifold and only weakly depends on the ambient dimension and noise level. We further extend our theory on data with noise containing both normal and tangential components, where chart autoencoders still exhibit a denoising effect for the normal component. As a special case, our theory also applies to classical autoencoders, as long as the data manifold has a global parametrization. Our results provide a solid theoretical foundation for the effectiveness of autoencoders, which is further validated through several numerical experiments.
Selection of covariates is crucial in the estimation of average treatment effects given observational data with high or even ultra-high dimensional pretreatment variables. Existing methods for this problem typically assume sparse linear models for both outcome and univariate treatment, and cannot handle situations with ultra-high dimensional covariates. In this paper, we propose a new covariate selection strategy called double screening prior adaptive lasso (DSPAL) to select confounders and predictors of the outcome for multivariate treatments, which combines the adaptive lasso method with the marginal conditional (in)dependence prior information to select target covariates, in order to eliminate confounding bias and improve statistical efficiency. The distinctive features of our proposal are that it can be applied to high-dimensional or even ultra-high dimensional covariates for multivariate treatments, and can deal with the cases of both parametric and nonparametric outcome models, which makes it more robust compared to other methods. Our theoretical analyses show that the proposed procedure enjoys the sure screening property, the ranking consistency property and the variable selection consistency. Through a simulation study, we demonstrate that the proposed approach selects all confounders and predictors consistently and estimates the multivariate treatment effects with smaller bias and mean squared error compared to several alternatives under various scenarios. In real data analysis, the method is applied to estimate the causal effect of a three-dimensional continuous environmental treatment on cholesterol level and enlightening results are obtained.
Conditional normalizing flows can generate diverse image samples for solving inverse problems. Most normalizing flows for inverse problems in imaging employ the conditional affine coupling layer that can generate diverse images quickly. However, unintended severe artifacts are occasionally observed in the output of them. In this work, we address this critical issue by investigating the origins of these artifacts and proposing the conditions to avoid them. First of all, we empirically and theoretically reveal that these problems are caused by "exploding inverse" in the conditional affine coupling layer for certain out-of-distribution (OOD) conditional inputs. Then, we further validated that the probability of causing erroneous artifacts in pixels is highly correlated with a Mahalanobis distance-based OOD score for inverse problems in imaging. Lastly, based on our investigations, we propose a remark to avoid exploding inverse and then based on it, we suggest a simple remedy that substitutes the affine coupling layers with the modified rational quadratic spline coupling layers in normalizing flows, to encourage the robustness of generated image samples. Our experimental results demonstrated that our suggested methods effectively suppressed critical artifacts occurring in normalizing flows for super-resolution space generation and low-light image enhancement.
Using generated data to improve the performance of downstream discriminative models has recently gained popularity due to the great development of pre-trained language models. In most previous studies, generative models and discriminative models are trained separately and thus could not adapt to any changes in each other. As a result, the generated samples can easily deviate from the real data distribution, while the improvement of the discriminative model quickly reaches saturation. Generative adversarial networks (GANs) train generative models via an adversarial process with discriminative models to achieve joint training. However, the training of standard GANs is notoriously unstable and often falls short of convergence. In this paper, to address these issues, we propose a $\textit{self-consistent learning}$ framework, in which a discriminator and a generator are cooperatively trained in a closed-loop form. The discriminator and the generator enhance each other during multiple rounds of alternating training until a scoring consensus is reached. This framework proves to be easy to train and free from instabilities such as mode collapse and non-convergence. Extensive experiments on sentence semantic matching demonstrate the effectiveness of the proposed framework: the discriminator achieves 10+ AP of improvement on the zero-shot setting and new state-of-the-art performance on the full-data setting.
Gaussian graphical models typically assume a homogeneous structure across all subjects, which is often restrictive in applications. In this article, we propose a weighted pseudo-likelihood approach for graphical modeling which allows different subjects to have different graphical structures depending on extraneous covariates. The pseudo-likelihood approach replaces the joint distribution by a product of the conditional distributions of each variable. We cast the conditional distribution as a heteroscedastic regression problem, with covariate-dependent variance terms, to enable information borrowing directly from the data instead of a hierarchical framework. This allows independent graphical modeling for each subject, while retaining the benefits of a hierarchical Bayes model and being computationally tractable. An efficient embarrassingly parallel variational algorithm is developed to approximate the posterior and obtain estimates of the graphs. Using a fractional variational framework, we derive asymptotic risk bounds for the estimate in terms of a novel variant of the $\alpha$-R\'{e}nyi divergence. We theoretically demonstrate the advantages of information borrowing across covariates over independent modeling. We show the practical advantages of the approach through simulation studies and illustrate the dependence structure in protein expression levels on breast cancer patients using CNV information as covariates.
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