More Like this

1. Semiparametric mixed‐scale models using shared Bayesian forests

   https://doi.org/10.1111/biom.13107  

   Linero, Antonio R. ; Sinha, Debajyoti ; Lipsitz, Stuart R. ( November 2019 , Biometrics)

   This paper demonstrates the advantages of sharing information about unknown features of covariates across multiple model components in various nonparametric regression problems including multivariate, heteroscedastic, and semicontinuous responses. In this paper, we present a methodology which allows for information to be shared nonparametrically across various model components using Bayesian sum‐of‐tree models. Our simulation results demonstrate that sharing of information across related model components is often very beneficial, particularly in sparse high‐dimensional problems in which variable selection must be conducted. We illustrate our methodology by analyzing medical expenditure data from the Medical Expenditure Panel Survey (MEPS). To facilitate the Bayesian nonparametric regression analysis, we develop two novel models for analyzing the MEPS data using Bayesian additive regression trees—a heteroskedastic log‐normal hurdle model with a “shrink‐toward‐homoskedasticity” prior and a gamma hurdle model.

    

   more » « less
2. Prior and posterior checking of implicit causal assumptions

   https://doi.org/10.1111/biom.13886  

   Linero, Antonio R. ( June 2023 , Biometrics)

   Causal inference practitioners have increasingly adopted machine learning techniques with the aim of producing principled uncertainty quantification for causal effects while minimizing the risk of model misspecification. Bayesian nonparametric approaches have attracted attention as well, both for their flexibility and their promise of providing natural uncertainty quantification. Priors on high‐dimensional or nonparametric spaces, however, can often unintentionally encode prior information that is at odds with substantive knowledge in causal inference—specifically, the regularization required for high‐dimensional Bayesian models to work can indirectly imply that the magnitude of the confounding is negligible. In this paper, we explain this problem and provide tools for (i) verifying that the prior distribution does not encode an inductive bias away from confounded models and (ii) verifying that the posterior distribution contains sufficient information to overcome this issue if it exists. We provide a proof‐of‐concept on simulated data from a high‐dimensional probit‐ridge regression model, and illustrate on a Bayesian nonparametric decision tree ensemble applied to a large medical expenditure survey.

    

   more » « less
3. Identifying Diffuse Spatial Structures in High-energy Photon Lists

   https://doi.org/10.3847/1538-3881/aca478  

   Fan, Minjie ; Wang, Jue ; Kashyap, Vinay L. ; Lee, Thomas C. M. ; van Dyk, David A. ; Zezas, Andreas ( January 2023 , The Astronomical Journal)

   Data from high-energy observations are usually obtained as lists of photon events. A common analysis task for such data is to identify whether diffuse emission exists, and to estimate its surface brightness, even in the presence of point sources that may be superposed. We have developed a novel nonparametric event list segmentation algorithm to divide up the field of view into distinct emission components. We use photon location data directly, without binning them into an image. We first construct a graph from the Voronoi tessellation of the observed photon locations and then grow segments using a new adaptation of seeded region growing that we callSeeded Region Growing on Graph, after which the overall method is namedSRGonG. Starting with a set of seed locations, this results in an oversegmented data set, whichSRGonGthen coalesces using a greedy algorithm where adjacent segments are merged to minimize a model comparison statistic; we use the Bayesian Information Criterion. UsingSRGonGwe are able to identify point-like and diffuse extended sources in the data with equal facility. We validateSRGonGusing simulations, demonstrating that it is capable of discerning irregularly shaped low-surface-brightness emission structures as well as point-like sources with strengths comparable to that seen in typical X-ray data. We demonstrateSRGonG’s use on the Chandra data of the Antennae galaxies and show that it segments the complex structures appropriately.

    

   more » « less
4. Semiparametric analysis of clustered interval‐censored survival data using soft Bayesian additive regression trees (SBART)

   https://doi.org/10.1111/biom.13478  

   Basak, Piyali ; Linero, Antonio ; Sinha, Debajyoti ; Lipsitz, Stuart ( April 2021 , Biometrics)

   Popular parametric and semiparametric hazards regression models for clustered survival data are inappropriate and inadequate when the unknown effects of different covariates and clustering are complex. This calls for a flexible modeling framework to yield efficient survival prediction. Moreover, for some survival studies involving time to occurrence of some asymptomatic events, survival times are typically interval censored between consecutive clinical inspections. In this article, we propose a robust semiparametric model for clustered interval‐censored survival data under a paradigm of Bayesian ensemble learning, called soft Bayesian additive regression trees or SBART (Linero and Yang, 2018), which combines multiple sparse (soft) decision trees to attain excellent predictive accuracy. We develop a novel semiparametric hazards regression model by modeling the hazard function as a product of a parametric baseline hazard function and a nonparametric component that uses SBART to incorporate clustering, unknown functional forms of the main effects, and interaction effects of various covariates. In addition to being applicable for left‐censored, right‐censored, and interval‐censored survival data, our methodology is implemented using a data augmentation scheme which allows for existing Bayesian backfitting algorithms to be used. We illustrate the practical implementation and advantages of our method via simulation studies and an analysis of a prostate cancer surgery study where dependence on the experience and skill level of the physicians leads to clustering of survival times. We conclude by discussing our method's applicability in studies involving high‐dimensional data with complex underlying associations.

    

   more » « less
5. Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime

   https://doi.org/10.1093/bioinformatics/btac423  

   Cui, Elvis Han ; Song, Dongyuan ; Wong, Weng Kee ; Li, Jingyi Jessica ; Mathelier, ed., Anthony ( June 2022 , Bioinformatics)

   Modeling single-cell gene expression trends along cell pseudotime is a crucial analysis for exploring biological processes. Most existing methods rely on nonparametric regression models for their flexibility; however, nonparametric models often provide trends too complex to interpret. Other existing methods use interpretable but restrictive models. Since model interpretability and flexibility are both indispensable for understanding biological processes, the single-cell field needs a model that improves the interpretability and largely maintains the flexibility of nonparametric regression models.

   Here, we propose the single-cell generalized trend model (scGTM) for capturing a gene’s expression trend, which may be monotone, hill-shaped or valley-shaped, along cell pseudotime. The scGTM has three advantages: (i) it can capture non-monotonic trends that are easy to interpret, (ii) its parameters are biologically interpretable and trend informative, and (iii) it can flexibly accommodate common distributions for modeling gene expression counts. To tackle the complex optimization problems, we use the particle swarm optimization algorithm to find the constrained maximum likelihood estimates for the scGTM parameters. As an application, we analyze several single-cell gene expression datasets using the scGTM and show that scGTM can capture interpretable gene expression trends along cell pseudotime and reveal molecular insights underlying biological processes.

   The Python package scGTM is open-access and available at https://github.com/ElvisCuiHan/scGTM.

   Supplementary data are available at Bioinformatics online.

    

   more » « less