Carson C. Chow

Hongjing Xia, Joshua C. Chang, Sarah Nowak et al.

We used survival analysis to quantify the impact of postdischarge evaluation and management (E/M) services in preventing hospital readmission or death. Our approach avoids a specific pitfall of applying machine learning to this problem, which is an inflated estimate of the effect of interventions, due to survivors bias -- where the magnitude of inflation may be conditional on heterogeneous confounders in the population. This bias arises simply because in order to receive an intervention after discharge, a person must not have been readmitted in the intervening period. After deriving an expression for this phantom effect, we controlled for this and other biases within an inherently interpretable Bayesian survival framework. We identified case management services as being the most impactful for reducing readmissions overall.

Joshua C. Chang, Carson C. Chow, Julia Porcino

The Work Disability Functional Assessment Battery (WD-FAB) is a multidimensional item response theory (IRT) instrument designed for assessing work-related mental and physical function based on responses to an item bank. In prior iterations it was developed using traditional means -- linear factorization and null hypothesis statistical testing for item partitioning/selection, and finally, posthoc calibration of disjoint unidimensional IRT models. As a result, the WD-FAB, like many other IRT instruments, is a posthoc model. Its item partitioning, based on exploratory factor analysis, is blind to the final nonlinear IRT model and is not performed in a manner consistent with goodness of fit to the final model. In this manuscript, we develop a Bayesian hierarchical model for self-consistently performing the following simultaneous tasks: scale factorization, item selection, parameter identification, and response scoring. This method uses sparsity-based shrinkage to obviate the linear factorization and null hypothesis statistical tests that are usually required for developing multidimensional IRT models, so that item partitioning is consistent with the ultimate nonlinear factor model. We also analogize our multidimensional IRT model to probabilistic autoencoders, specifying an encoder function that amortizes the inference of ability parameters from item responses. The encoder function is equivalent to the "VBE" step in a stochastic variational Bayesian expectation maximization (VBEM) procedure that we use for approxiamte Bayesian inference on the entire model. We use the method on a sample of WD-FAB item responses and compare the resulting item discriminations to those obtained using the traditional posthoc method.

Joshua C. Chang, Ted L. Chang, Carson C. Chow et al.

We developed an inherently interpretable multilevel Bayesian framework for representing variation in regression coefficients that mimics the piecewise linearity of ReLU-activated deep neural networks. We used the framework to formulate a survival model for using medical claims to predict hospital readmission and death that focuses on discharge placement, adjusting for confounding in estimating causal local average treatment effects. We trained the model on a 5% sample of Medicare beneficiaries from 2008 and 2011, based on their 2009--2011 inpatient episodes, and then tested the model on 2012 episodes. The model scored an AUROC of approximately 0.76 on predicting all-cause readmissions -- defined using official Centers for Medicare and Medicaid Services (CMS) methodology -- or death within 30-days of discharge, being competitive against XGBoost and a Bayesian deep neural network, demonstrating that one need-not sacrifice interpretability for accuracy. Crucially, as a regression model, we provide what blackboxes cannot -- the exact gold-standard global interpretation of the model, identifying relative risk factors and quantifying the effect of discharge placement. We also show that the posthoc explainer SHAP fails to provide accurate explanations.

Joshua C Chang, Xiangting Li, Shixin Xu et al.

Importance sampling (IS) allows one to approximate leave one out (LOO) cross-validation for a Bayesian model, without refitting, by inverting the Bayesian update equation to subtract a given data point from a model posterior. For each data point, one computes expectations under the corresponding LOO posterior by weighted averaging over the full data posterior. This task sometimes requires weight stabilization in the form of adapting the posterior distribution via transformation. So long as one is successful in finding a suitable transformation, one avoids refitting. To this end, we motivate the use of bijective perturbative transformations of the form $T(\boldsymbolθ)=\boldsymbolθ + h Q(\boldsymbolθ),$ for $0<h\ll 1,$ and introduce two classes of such transformations: 1) partial moment matching and 2) gradient flow evolution. The former extends prior literature on moment-matching under the recognition that adaptation for LOO is a small perturbation on the full data posterior. The latter class of methods define transformations based on relaxing various statistical objectives: in our case the variance of the IS estimator and the KL divergence between the transformed distribution and the statistics of the LOO fold. Being model-specific, the gradient flow transformations require evaluating Jacobian determinants. While these quantities are generally readily available through auto-differentiation, we derive closed-form expressions in the case of logistic regression and shallow ReLU activated neural networks. We tested the methodology on an $n\ll p$ dataset that is known to produce unstable LOO IS weights.

Joshua C. Chang, Patrick Fletcher, Jungmin Han et al.

Dimensionality reduction methods for count data are critical to a wide range of applications in medical informatics and other fields where model interpretability is paramount. For such data, hierarchical Poisson matrix factorization (HPF) and other sparse probabilistic non-negative matrix factorization (NMF) methods are considered to be interpretable generative models. They consist of sparse transformations for decoding their learned representations into predictions. However, sparsity in representation decoding does not necessarily imply sparsity in the encoding of representations from the original data features. HPF is often incorrectly interpreted in the literature as if it possesses encoder sparsity. The distinction between decoder sparsity and encoder sparsity is subtle but important. Due to the lack of encoder sparsity, HPF does not possess the column-clustering property of classical NMF -- the factor loading matrix does not sufficiently define how each factor is formed from the original features. We address this deficiency by self-consistently enforcing encoder sparsity, using a generalized additive model (GAM), thereby allowing one to relate each representation coordinate to a subset of the original data features. In doing so, the method also gains the ability to perform feature selection. We demonstrate our method on simulated data and give an example of how encoder sparsity is of practical use in a concrete application of representing inpatient comorbidities in Medicare patients.

Joshua C. Chang, Shashaank Vattikuti, Carson C. Chow

Item response theory (IRT) is a non-linear generative probabilistic paradigm for using exams to identify, quantify, and compare latent traits of individuals, relative to their peers, within a population of interest. In pre-existing multidimensional IRT methods, one requires a factorization of the test items. For this task, linear exploratory factor analysis is used, making IRT a posthoc model. We propose skipping the initial factor analysis by using a sparsity-promoting horseshoe prior to perform factorization directly within the IRT model so that all training occurs in a single self-consistent step. Being a hierarchical Bayesian model, we adapt the WAIC to the problem of dimensionality selection. IRT models are analogous to probabilistic autoencoders. By binding the generative IRT model to a Bayesian neural network (forming a probabilistic autoencoder), one obtains a scoring algorithm consistent with the interpretable Bayesian model. In some IRT applications the black-box nature of a neural network scoring machine is desirable. In this manuscript, we demonstrate within-IRT factorization and comment on scoring approaches.

Christopher Kim, Carson Chow

Spiking activity of neurons engaged in learning and performing a task show complex spatiotemporal dynamics. While the output of recurrent network models can learn to perform various tasks, the possible range of recurrent dynamics that emerge after learning remains unknown. Here we show that modifying the recurrent connectivity with a recursive least squares algorithm provides sufficient flexibility for synaptic and spiking rate dynamics of spiking networks to produce a wide range of spatiotemporal activity. We apply the training method to learn arbitrary firing patterns, stabilize irregular spiking activity of a balanced network, and reproduce the heterogeneous spiking rate patterns of cortical neurons engaged in motor planning and movement. We identify sufficient conditions for successful learning, characterize two types of learning errors, and assess the network capacity. Our findings show that synaptically-coupled recurrent spiking networks possess a vast computational capability that can support the diverse activity patterns in the brain.