arXiv subjects

Joshua C. Chang

Publications and source records attributed to Joshua C. Chang.

16 recordsLinked to original sources

arXiv2026

A renormalization-group inspired lattice-based framework for piecewise generalized linear models

We formally introduce a class of models inspired by renormalization group (RG) theory, built on additive hierarchical expansions analogous to those appearing in functional ANOVA and mixed-effects models. Like ReLU convolutional neural networks, they are almost everywhere locally linear; unlike ReLU networks, their partition structure is explicit, interpretable, and easy to modify or constrain. In these models, one defines a multidimensional lattice partition of the input space and uses it to scaffold variations in regression parameters. Each dimension of the lattice corresponds to an attribute by which the statistics of the problem may vary. The parameters are themselves expressed in the form of an expansion, where each term captures variations relative to a lower (coarser) interaction scale. These models admit multiple equivalent interpretations: as piecewise GLMs, as hierarchical mixed-effects regressions, or as regression trees with structured parameter sharing. Since RG motivates the design of these models, we use techniques from statistical physics -- specifically replica analysis -- to study their generalization properties. Specifically, we analyze the behavior of the Watanabe-Akaike Information Criterion (WAIC) as a proxy for generalization loss. This analysis yields two practical results: (i) guidance on the lattice design as a function of dataset size and predictor dimensionality; and (ii) a principled scaling law for the regularization prior when adding higher-order terms to the expansion so that one can increase model complexity without an expected increase in generalization loss. We evaluate the methodology on public datasets and find performance competitive against both blackbox methods and other intrinsically interpretable approaches.

stat.ME↗

arXiv2026

Bayesian model-averaging stochastic item selection for adaptive testing

Computer Adaptive Testing (CAT) aims to accurately estimate an individual's ability using only a subset of an Item Response Theory (IRT) instrument. Many applications also require diverse item exposure across testing sessions, preventing any single item from being over- or underutilized. In CAT, items are selected sequentially based on a running estimate of a respondent's ability. Prior methods almost universally see item selection through an optimization lens, motivating greedy item selection procedures. While efficient, these deterministic methods tend to have poor item exposure. Existing stochastic methods for item selection are ad-hoc, with item sampling weights that lack theoretical justification. We formulate stochastic CAT as a Bayesian model averaging problem. We seek item sampling probabilities, treated in the long-run frequentist sense, that perform optimal model averaging for the ability estimate in a Bayesian sense. The derivation yields an information criterion for optimal stochastic mixing: the expected entropy of the next posterior. We tested our method on seven publicly available psychometric instruments spanning personality, social attitudes, narcissism, and work preferences, in addition to the eight scales of the Work Disability Functional Assessment Battery. Across all instruments, accuracy differences between selection methods at a given test length are varied but minimal relative to the natural noise in ability estimation; however, the stochastic selector achieves full item bank exposure, resolving the longstanding tradeoff between measurement efficiency and item security at negligible accuracy cost.

stat.ME↗

arXiv2023

Interpretable (not just posthoc-explainable) heterogeneous survivor bias-corrected treatment effects for assignment of postdischarge interventions to prevent readmissions

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.

stat.ME↗

arXiv2023

Autoencoded sparse Bayesian in-IRT factorization, calibration, and amortized inference for the Work Disability Functional Assessment Battery

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.

stat.ME↗

arXiv2023

Interpretable (not just posthoc-explainable) medical claims modeling for discharge placement to prevent avoidable all-cause readmissions or death

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.

cs.CY↗

arXiv2021

Regularized Bayesian calibration and scoring of the WD-FAB IRT model improves predictive performance over marginal maximum likelihood

Item response theory (IRT) is the statistical paradigm underlying a dominant family of generative probabilistic models for test responses, used to quantify traits in individuals relative to target populations. The graded response model (GRM) is a particular IRT model that is used for ordered polytomous test responses. Both the development and the application of the GRM and other IRT models require statistical decisions. For formulating these models (calibration), one needs to decide on methodologies for item selection, inference, and regularization. For applying these models (test scoring), one needs to make similar decisions, often prioritizing computational tractability and/or interpretability. In many applications, such as in the Work Disability Functional Assessment Battery (WD-FAB), tractability implies approximating an individual's score distribution using estimates of mean and variance, and obtaining that score conditional on only point estimates of the calibrated model. In this manuscript, we evaluate the calibration and scoring of models under this common use-case using Bayesian cross-validation. Applied to the WD-FAB responses collected for the National Institutes of Health, we assess the predictive power of implementations of the GRM based on their ability to yield, on validation sets of respondents, ability estimates that are most predictive of patterns of item responses. Our main finding indicates that regularized Bayesian calibration of the GRM outperforms the regularization-free empirical Bayesian procedure of marginal maximum likelihood. We also motivate the use of compactly supported priors in test scoring.

stat.AP↗

arXiv2020

Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization

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.

cs.LG↗

arXiv2019

Probabilistically-autoencoded horseshoe-disentangled multidomain item-response theory models

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.

cs.LG↗

arXiv2019

Predictive Bayesian selection of multistep Markov chains, applied to the detection of the hot hand and other statistical dependencies in free throws

Consider the problem of modeling memory effects in discrete-state random walks using higher-order Markov chains. This paper explores cross validation and information criteria as proxies for a model's predictive accuracy. Our objective is to select, from data, the number of prior states of recent history upon which a trajectory is statistically dependent. Through simulations, I evaluate these criteria in the case where data are drawn from systems with fixed orders of history, noting trends in the relative performance of the criteria. As a real-world illustrative example of these methods, this manuscript evaluates the problem of detecting statistical dependencies in shot outcomes in free throw shooting. Over three NBA seasons analyzed, several players exhibited statistical dependencies in free throw hitting probability of various types - hot handedness, cold handedness, and error correction. For the 2013-2014 through 2015-2016 NBA seasons, I detected statistical dependencies in 23% of all player-seasons. Focusing on a single player, in two of these three seasons, LeBron James shot a better percentage after an immediate miss than otherwise. In those seasons, conditioning on the previous outcome makes for a more predictive model than treating free throw makes as independent. When extended to data from the 2016-2017 NBA season specifically for LeBron James, a model depending on the previous shot (single-step Markovian) does not clearly beat a model with independent outcomes. An error-correcting variable length model of two parameters, where James shoots a higher percentage after a missed free throw than otherwise, is more predictive than either model.

stat.ME↗

arXiv2018

Asymptotic convergence in distribution of the area bounded by prevalence-weighted Kaplan-Meier curves using empirical process modeling

The Kaplan-Meier product-limit estimator is a simple and powerful tool in time to event analysis. An extension exists for populations stratified into cohorts where a population survival curve is generated by weighted averaging of cohort-level survival curves. For making population-level comparisons using this statistic, we analyze the statistics of the area between two such weighted survival curves. We derive the large sample behavior of this statistic based on an empirical process of product-limit estimators. This estimator was used by an interdisciplinary NIH-SSA team in the identification of medical conditions to prioritize for adjudication in disability benefits processing.

stat.ME↗

arXiv2018

Determination of hysteresis in finite-state random walks using Bayesian cross validation

Consider the problem of modeling hysteresis for finite-state random walks using higher-order Markov chains. This Letter introduces a Bayesian framework to determine, from data, the number of prior states of recent history upon which a trajectory is statistically dependent. The general recommendation is to use leave-one-out cross validation, using an easily-computable formula that is provided in closed form. Importantly, Bayes factors using flat model priors are biased in favor of too-complex a model (more hysteresis) when a large amount of data is present and the Akaike information criterion (AIC) is biased in favor of too-sparse a model (less hysteresis) when few data are present.

stat.ME↗

arXiv2017

High-resolution reconstruction of cellular traction-force distributions: the role of physically motivated constraints and compressive regularization

We develop a method to reconstruct, from measured displacements of an underlying elastic substrate, the spatially dependent forces that cells or tissues impart on it. Given newly available high-resolution images of substrate displacements, it is desirable to be able to reconstruct small scale, compactly supported focal adhesions which are often localized and exist only within the footprint of a cell. In addition to the standard quadratic data mismatch terms that define least-squares fitting, we motivate a regularization term in the objective function that penalizes vectorial invariants of the reconstructed surface stress while preserving boundaries. We solve this inverse problem by providing a numerical method for setting up a discretized inverse problem that is solvable by standard convex optimization techniques. By minimizing the objective function subject to a number of important physically motivated constraints, we are able to efficiently reconstruct stress fields with localized structure from simulated and experimental substrate displacements. Our method incorporates the exact solution for the stress tensor accurate to first-order finite-differences and motivates the use of distance-based cut-offs for data inclusion and problem sparsification.

q-bio.QM↗

arXiv2016

Regulatory inhibition of biological tissue mineralization by calcium phosphate through post-nucleation shielding by Fetuin-A

In vertebrates, insufficient availability of calcium and phosphate ions in extracellular fluids leads to loss of bone density and neuronal hyper-excitability. To counteract this problem, calcium ions are present at high concentrations throughout body fluids -- at concentrations exceeding the saturation point. This condition leads to the opposite situation where unwanted mineral sedimentation may occur. Remarkably, ectopic or out-of-place sedimentation into soft tissues is rare, in spite of the thermodynamic driving factors. This fortunate fact is due to the presence of auto-regulatory proteins that are found in abundance in bodily fluids. Yet, many important inflammatory disorders such as atherosclerosis and osteoarthritis are associated with this undesired calcification. Hence, it is important to gain an understanding of the regulatory process and the conditions under which it can go awry. In this manuscript, we adapt mean-field classical nucleation theory to the case of surface-shielding in order to study the regulation of sedimentation of calcium phosphate salts in biological tissues through the mechanism of post-nuclear shielding of nascent mineral particles by binding proteins. We develop a mathematical description of this phenomenon using a countable system of hyperbolic partial differential equations. A critical concentration of regulatory protein is identified as a function of the physical parameters that describe the system.

cond-mat.soft↗

arXiv2015

Bayesian field theoretic reconstruction of bond potential and bond mobility in single molecule force spectroscopy

Quantifying the forces between and within macromolecules is a necessary first step in understanding the mechanics of molecular structure, protein folding, and enzyme function and performance. In such macromolecular settings, dynamic single-molecule force spectroscopy (DFS) has been used to distort bonds. The resulting responses, in the form of rupture forces, work applied, and trajectories of displacements, have been used to reconstruct bond potentials. Such approaches often rely on simple parameterizations of one-dimensional bond potentials, assumptions on equilibrium starting states, and/or large amounts of trajectory data. Parametric approaches typically fail at inferring complex-shaped bond potentials with multiple minima, while piecewise estimation may not guarantee smooth results with the appropriate behavior at large distances. Existing techniques, particularly those based on work theorems, also do not address spatial variations in the diffusivity that may arise from spatially inhomogeneous coupling to other degrees of freedom in the macromolecule, thereby presenting an incomplete picture of the overall bond dynamics. To solve these challenges, we have developed a comprehensive empirical Bayesian approach that incorporates data and regularization terms directly into a path integral. All experiemental and statistical parameters in our method are estimated empirically directly from the data. Upon testing our method on simulated data, our regularized approach requires fewer data and allows simultaneous inference of both complex bond potentials and diffusivity profiles.

physics.data-an↗

arXiv2013

A mathematical model of the metabolic and perfusion effects on cortical spreading depression

Cortical spreading depression (CSD) is a slow-moving ionic and metabolic disturbance that propagates in cortical brain tissue. In addition to massive cellular depolarization, CSD also involves significant changes in perfusion and metabolism -- aspects of CSD that had not been modeled and are important to traumatic brain injury, subarachnoid hemorrhage, stroke, and migraine. In this study, we develop a mathematical model for CSD where we focus on modeling the features essential to understanding the implications of neurovascular coupling during CSD. In our model, the sodium-potassium--ATPase, mainly responsible for ionic homeostasis and active during CSD, operates at a rate that is dependent on the supply of oxygen. The supply of oxygen is determined by modeling blood flow through a lumped vascular tree with an effective local vessel radius that is controlled by the extracellular potassium concentration. We show that during CSD, the metabolic demands of the cortex exceed the physiological limits placed on oxygen delivery, regardless of vascular constriction or dilation. However, vasoconstriction and vasodilation play important roles in the propagation of CSD and its recovery. Our model replicates the qualitative and quantitative behavior of CSD -- vasoconstriction, oxygen depletion, extracellular potassium elevation, prolonged depolarization -- found in experimental studies. We predict faster, longer duration CSD in vivo than in vitro due to the contribution of the vasculature. Our results also help explain some of the variability of CSD between species and even within the same animal. These results have clinical and translational implications, as they allow for more precise in vitro, in vivo, and in silico exploration of a phenomenon broadly relevant to neurological disease.

q-bio.NC↗

arXiv2013

Iterative graph cuts for image segmentation with a nonlinear statistical shape prior

Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object. When a collection of possible shapes is available, the specification of a shape prior using kernel density estimation is a natural technique. Unfortunately, energy functionals arising from kernel density estimation are of a form that makes them impossible to directly minimize using efficient optimization algorithms such as graph cuts. Our main contribution is to show how one may recast the energy functional into a form that is minimizable iteratively and efficiently using graph cuts.

cs.CV↗