CIMTx provides efficient and unified functions to implement modern methods for causal inferences with multiple treatments using observational data with a focus on binary outcomes. The methods include regression adjustment, inverse probability of treatment weighting, Bayesian additive regression trees, regression adjustment with multivariate spline of the generalized propensity score, vector matching and targeted maximum likelihood estimation. In addition, CIMTx illustrates ways in which users can simulate data adhering to the complex data structures in the multiple treatment setting. Furthermore, the CIMTx package offers a unique set of features to address the key causal assumptions: positivity and ignorability. For the positivity assumption, CIMTx demonstrates techniques to identify the common support region for retaining inferential units. To handle the ignorability assumption, CIMTx provides a flexible Monte Carlo sensitivity analysis approach to evaluate how causal conclusions would be altered in response to different magnitude of departure from ignorable treatment assignment.
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Continuous-time (CT) models have shown an improved sample efficiency during learning and enable ODE analysis methods for enhanced interpretability compared to discrete-time (DT) models. Even with numerous recent developments, the multifaceted CT state-space model identification problem remains to be solved in full, considering common experimental aspects such as the presence of external inputs, measurement noise, and latent states. This paper presents a novel estimation method that includes these aspects and that is able to obtain state-of-the-art results on multiple benchmarks where a small fully connected neural network describes the CT dynamics. The novel estimation method called the subspace encoder approach ascertains these results by altering the well-known simulation loss to include short subsections instead, by using an encoder function and a state-derivative normalization term to obtain a computationally feasible and stable optimization problem. This encoder function estimates the initial states of each considered subsection. We prove that the existence of the encoder function has the necessary condition of a Lipschitz continuous state-derivative utilizing established properties of ODEs.
The variational autoencoder (VAE) is a popular deep latent variable model used to analyse high-dimensional datasets by learning a low-dimensional latent representation of the data. It simultaneously learns a generative model and an inference network to perform approximate posterior inference. Recently proposed extensions to VAEs that can handle temporal and longitudinal data have applications in healthcare, behavioural modelling, and predictive maintenance. However, these extensions do not account for heterogeneous data (i.e., data comprising of continuous and discrete attributes), which is common in many real-life applications. In this work, we propose the heterogeneous longitudinal VAE (HL-VAE) that extends the existing temporal and longitudinal VAEs to heterogeneous data. HL-VAE provides efficient inference for high-dimensional datasets and includes likelihood models for continuous, count, categorical, and ordinal data while accounting for missing observations. We demonstrate our model's efficacy through simulated as well as clinical datasets, and show that our proposed model achieves competitive performance in missing value imputation and predictive accuracy.
This paper considers the problem of inference in cluster randomized experiments when cluster sizes are non-ignorable. Here, by a cluster randomized experiment, we mean one in which treatment is assigned at the level of the cluster; by non-ignorable cluster sizes we mean that "large" clusters and "small" clusters may be heterogeneous, and, in particular, the effects of the treatment may vary across clusters of differing sizes. In order to permit this sort of flexibility, we consider a sampling framework in which cluster sizes themselves are random. In this way, our analysis departs from earlier analyses of cluster randomized experiments in which cluster sizes are treated as non-random. We distinguish between two different parameters of interest: the equally-weighted cluster-level average treatment effect, and the size-weighted cluster-level average treatment effect. For each parameter, we provide methods for inference in an asymptotic framework where the number of clusters tends to infinity and treatment is assigned using simple random sampling. We additionally permit the experimenter to sample only a subset of the units within each cluster rather than the entire cluster and demonstrate the implications of such sampling for some commonly used estimators. A small simulation study shows the practical relevance of our theoretical results.
We provide a decision theoretic analysis of bandit experiments. The setting corresponds to a dynamic programming problem, but solving this directly is typically infeasible. Working within the framework of diffusion asymptotics, we define suitable notions of asymptotic Bayes and minimax risk for bandit experiments. For normally distributed rewards, the minimal Bayes risk can be characterized as the solution to a nonlinear second-order partial differential equation (PDE). Using a limit of experiments approach, we show that this PDE characterization also holds asymptotically under both parametric and non-parametric distribution of the rewards. The approach further describes the state variables it is asymptotically sufficient to restrict attention to, and therefore suggests a practical strategy for dimension reduction. The upshot is that we can approximate the dynamic programming problem defining the bandit experiment with a PDE which can be efficiently solved using sparse matrix routines. We derive the optimal Bayes and minimax policies from the numerical solutions to these equations. The proposed policies substantially dominate existing methods such as Thompson sampling. The framework also allows for substantial generalizations to the bandit problem such as time discounting and pure exploration motives.
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper, we present an alternative approach: a variational framework for Bayesian phylogenetic analysis. We propose combining subsplit Bayesian networks, an expressive graphical model for tree topology distributions, and a structured amortization of the branch lengths over tree topologies for a suitable variational family of distributions. We train the variational approximation via stochastic gradient ascent and adopt gradient estimators for continuous and discrete variational parameters separately to deal with the composite latent space of phylogenetic models. We show that our variational approach provides competitive performance to MCMC, while requiring much less computation due to a more efficient exploration mechanism enabled by variational inference. Experiments on a benchmark of challenging real data Bayesian phylogenetic inference problems demonstrate the effectiveness and efficiency of our methods.
Dynamic Linear Models (DLMs) are commonly employed for time series analysis due to their versatile structure, simple recursive updating, ability to handle missing data, and probabilistic forecasting. However, the options for count time series are limited: Gaussian DLMs require continuous data, while Poisson-based alternatives often lack sufficient modeling flexibility. We introduce a novel semiparametric methodology for count time series by warping a Gaussian DLM. The warping function has two components: a (nonparametric) transformation operator that provides distributional flexibility and a rounding operator that ensures the correct support for the discrete data-generating process. We develop conjugate inference for the warped DLM, which enables analytic and recursive updates for the state space filtering and smoothing distributions. We leverage these results to produce customized and efficient algorithms for inference and forecasting, including Monte Carlo simulation for offline analysis and an optimal particle filter for online inference. This framework unifies and extends a variety of discrete time series models and is valid for natural counts, rounded values, and multivariate observations. Simulation studies illustrate the excellent forecasting capabilities of the warped DLM. The proposed approach is applied to a multivariate time series of daily overdose counts and demonstrates both modeling and computational successes.
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.
Models for dependent data are distinguished by their targets of inference. Marginal models are useful when interest lies in quantifying associations averaged across a population of clusters. When the functional form of a covariate-outcome association is unknown, flexible regression methods are needed to allow for potentially non-linear relationships. We propose a novel marginal additive model (MAM) for modelling cluster-correlated data with non-linear population-averaged associations. The proposed MAM is a unified framework for estimation and uncertainty quantification of a marginal mean model, combined with inference for between-cluster variability and cluster-specific prediction. We propose a fitting algorithm that enables efficient computation of standard errors and corrects for estimation of penalty terms. We demonstrate the proposed methods in simulations and in application to (i) a longitudinal study of beaver foraging behaviour, and (ii) a spatial analysis of Loaloa infection in West Africa. R code for implementing the proposed methodology is available at //github.com/awstringer1/mam.
This paper focuses on the expected difference in borrower's repayment when there is a change in the lender's credit decisions. Classical estimators overlook the confounding effects and hence the estimation error can be magnificent. As such, we propose another approach to construct the estimators such that the error can be greatly reduced. The proposed estimators are shown to be unbiased, consistent, and robust through a combination of theoretical analysis and numerical testing. Moreover, we compare the power of estimating the causal quantities between the classical estimators and the proposed estimators. The comparison is tested across a wide range of models, including linear regression models, tree-based models, and neural network-based models, under different simulated datasets that exhibit different levels of causality, different degrees of nonlinearity, and different distributional properties. Most importantly, we apply our approaches to a large observational dataset provided by a global technology firm that operates in both the e-commerce and the lending business. We find that the relative reduction of estimation error is strikingly substantial if the causal effects are accounted for correctly.
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