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Determining causal effects of interventions onto outcomes from real-world, observational (non-randomized) data, e.g., treatment repurposing using electronic health records, is challenging due to underlying bias. Causal deep learning has improved over traditional techniques for estimating individualized treatment effects (ITE). We present the Doubly Robust Variational Information-theoretic Deep Adversarial Learning (DR-VIDAL), a novel generative framework that combines two joint models of treatment and outcome, ensuring an unbiased ITE estimation even when one of the two is misspecified. DR-VIDAL integrates: (i) a variational autoencoder (VAE) to factorize confounders into latent variables according to causal assumptions; (ii) an information-theoretic generative adversarial network (Info-GAN) to generate counterfactuals; (iii) a doubly robust block incorporating treatment propensities for outcome predictions. On synthetic and real-world datasets (Infant Health and Development Program, Twin Birth Registry, and National Supported Work Program), DR-VIDAL achieves better performance than other non-generative and generative methods. In conclusion, DR-VIDAL uniquely fuses causal assumptions, VAE, Info-GAN, and doubly robustness into a comprehensive, performant framework. Code is available at: //github.com/Shantanu48114860/DR-VIDAL-AMIA-22 under MIT license.

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Interpreting the inner function of neural networks is crucial for the trustworthy development and deployment of these black-box models. Prior interpretability methods focus on correlation-based measures to attribute model decisions to individual examples. However, these measures are susceptible to noise and spurious correlations encoded in the model during the training phase (e.g., biased inputs, model overfitting, or misspecification). Moreover, this process has proven to result in noisy and unstable attributions that prevent any transparent understanding of the model's behavior. In this paper, we develop a robust interventional-based method grounded by causal analysis to capture cause-effect mechanisms in pre-trained neural networks and their relation to the prediction. Our novel approach relies on path interventions to infer the causal mechanisms within hidden layers and isolate relevant and necessary information (to model prediction), avoiding noisy ones. The result is task-specific causal explanatory graphs that can audit model behavior and express the actual causes underlying its performance. We apply our method to vision models trained on classification tasks. On image classification tasks, we provide extensive quantitative experiments to show that our approach can capture more stable and faithful explanations than standard attribution-based methods. Furthermore, the underlying causal graphs reveal the neural interactions in the model, making it a valuable tool in other applications (e.g., model repair).

With the rise in popularity of digital Atlases to communicate spatial variation, there is an increasing need for robust small-area estimates. However, current small-area estimation methods suffer from various modelling problems when data are very sparse or when estimates are required for areas with very small populations. These issues are particularly heightened when modelling proportions. Additionally, recent work has shown significant benefits in modelling at both the individual and area levels. We propose a two-stage Bayesian hierarchical small area estimation model for proportions that can: account for survey design; use both individual-level survey-only covariates and area-level census covariates; reduce direct estimate instability; and generate prevalence estimates for small areas with no survey data. Using a simulation study we show that, compared with existing Bayesian small area estimation methods, our model can provide optimal predictive performance (Bayesian mean relative root mean squared error, mean absolute relative bias and coverage) of proportions under a variety of data conditions, including very sparse and unstable data. To assess the model in practice, we compare modeled estimates of current smoking prevalence for 1,630 small areas in Australia using the 2017-2018 National Health Survey data combined with 2016 census data.

Motivated by the Acute Respiratory Distress Syndrome Network (ARDSNetwork) ARDS respiratory management (ARMA) trial, we developed a flexible Bayesian machine learning approach to estimate the average causal effect and heterogeneous causal effects among the always-survivors stratum when clinical outcomes are subject to truncation. We adopted Bayesian additive regression trees (BART) to flexibly specify separate models for the potential outcomes and latent strata membership. In the analysis of the ARMA trial, we found that the low tidal volume treatment had an overall benefit for participants sustaining acute lung injuries on the outcome of time to returning home, but substantial heterogeneity in treatment effects among the always-survivors, driven most strongly by sex and the alveolar-arterial oxygen gradient at baseline (a physiologic measure of lung function and source of hypoxemia). These findings illustrate how the proposed methodology could guide the prognostic enrichment of future trials in the field. We also demonstrated through a simulation study that our proposed Bayesian machine learning approach outperforms other parametric methods in reducing the estimation bias in both the average causal effect and heterogeneous causal effects for always-survivors.

In this article we develop a feasible version of the assumption-lean tests in Liu et al. 20 that can falsify an analyst's justification for the validity of a reported nominal $(1 - \alpha)$ Wald confidence interval (CI) centered at a double machine learning (DML) estimator for any member of the class of doubly robust (DR) functionals studied by Rotnitzky et al. 21. The class of DR functionals is broad and of central importance in economics and biostatistics. It strictly includes both (i) the class of mean-square continuous functionals that can be written as an expectation of an affine functional of a conditional expectation studied by Chernozhukov et al. 22 and the class of functionals studied by Robins et al. 08. The present state-of-the-art estimators for DR functionals $\psi$ are DML estimators $\hat{\psi}_{1}$. The bias of $\hat{\psi}_{1}$ depends on the product of the rates at which two nuisance functions $b$ and $p$ are estimated. Most commonly an analyst justifies the validity of her Wald CIs by proving that, under her complexity-reducing assumptions, the Cauchy-Schwarz (CS) upper bound for the bias of $\hat{\psi}_{1}$ is $o (n^{- 1 / 2})$. Thus if the hypothesis $H_{0}$: the CS upper bound is $o (n^{- 1 / 2})$ is rejected by our test, we will have falsified the analyst's justification for the validity of her Wald CIs. In this work, we exhibit a valid assumption-lean falsification test of $H_{0}$, without relying on complexity-reducing assumptions on $b, p$, or their estimates $\hat{b}, \hat{p}$. Simulation experiments are conducted to demonstrate how the proposed assumption-lean test can be used in practice. An unavoidable limitation of our methodology is that no assumption-lean test of $H_{0}$, including ours, can be a consistent test. Thus failure of our test to reject is not meaningful evidence in favor of $H_{0}$.

We introduce variational sequential Optimal Experimental Design (vsOED), a new method for optimally designing a finite sequence of experiments under a Bayesian framework and with information-gain utilities. Specifically, we adopt a lower bound estimator for the expected utility through variational approximation to the Bayesian posteriors. The optimal design policy is solved numerically by simultaneously maximizing the variational lower bound and performing policy gradient updates. We demonstrate this general methodology for a range of OED problems targeting parameter inference, model discrimination, and goal-oriented prediction. These cases encompass explicit and implicit likelihoods, nuisance parameters, and physics-based partial differential equation models. Our vsOED results indicate substantially improved sample efficiency and reduced number of forward model simulations compared to previous sequential design algorithms.

Detection of the outliers is pivotal for any machine learning model deployed and operated in real-world. It is essential for the Deep Neural Networks that were shown to be overconfident with such inputs. Moreover, even deep generative models that allow estimation of the probability density of the input fail in achieving this task. In this work, we concentrate on the specific type of these models: Variational Autoencoders (VAEs). First, we unveil a significant theoretical flaw in the assumption of the classical VAE model. Second, we enforce an accommodating topological property to the image of the deep neural mapping to the latent space: compactness to alleviate the flaw and obtain the means to provably bound the image within the determined limits by squeezing both inliers and outliers together. We enforce compactness using two approaches: (i) Alexandroff extension and (ii) fixed Lipschitz continuity constant on the mapping of the encoder of the VAEs. Finally and most importantly, we discover that the anomalous inputs predominantly tend to land on the vacant latent holes within the compact space, enabling their successful identification. For that reason, we introduce a specifically devised score for hole detection and evaluate the solution against several baseline benchmarks achieving promising results.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics community.

Sequential recommendation as an emerging topic has attracted increasing attention due to its important practical significance. Models based on deep learning and attention mechanism have achieved good performance in sequential recommendation. Recently, the generative models based on Variational Autoencoder (VAE) have shown the unique advantage in collaborative filtering. In particular, the sequential VAE model as a recurrent version of VAE can effectively capture temporal dependencies among items in user sequence and perform sequential recommendation. However, VAE-based models suffer from a common limitation that the representational ability of the obtained approximate posterior distribution is limited, resulting in lower quality of generated samples. This is especially true for generating sequences. To solve the above problem, in this work, we propose a novel method called Adversarial and Contrastive Variational Autoencoder (ACVAE) for sequential recommendation. Specifically, we first introduce the adversarial training for sequence generation under the Adversarial Variational Bayes (AVB) framework, which enables our model to generate high-quality latent variables. Then, we employ the contrastive loss. The latent variables will be able to learn more personalized and salient characteristics by minimizing the contrastive loss. Besides, when encoding the sequence, we apply a recurrent and convolutional structure to capture global and local relationships in the sequence. Finally, we conduct extensive experiments on four real-world datasets. The experimental results show that our proposed ACVAE model outperforms other state-of-the-art methods.

Graph Neural Networks (GNNs) for representation learning of graphs broadly follow a neighborhood aggregation framework, where the representation vector of a node is computed by recursively aggregating and transforming feature vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs in capturing different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

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