arXiv subjects

Satabdi Saha

Publications and source records attributed to Satabdi Saha.

5 recordsLinked to original sources

arXiv2026

Graph-Adaptive Horseshoe for Compositional Regression

Compositional predictors, such as microbiome abundances, pose unique challenges in variable selection due to their unit-sum constraint and inherent dependencies. Existing approaches often rely on fixed association graphs derived from phylogenetic or ecological distances, which may not reflect outcome-relevant relationships. We propose GRACE (GRaph-Adaptive horseshoe for Compositional rEgression), a fully Bayesian framework that enforces compositional constraints, performs variable selection, and adaptively learns an outcome-driven shrinkage graph. GRACE achieves compositionality through a novel linear reparameterization of regression coefficients, while a structured horseshoe prior induces sparsity and smooths coefficients along the learned graph. Graph learning is accomplished via scaled beta2 priors on edge weights, providing both outcome-specific adaptation and posterior uncertainty quantification. We develop an efficient Gibbs sampler incorporating elliptical slice sampling to ensure scalability in high dimensions. Through extensive simulations, GRACE demonstrates competitive predictive accuracy and improved graph recovery compared with existing methods, particularly under graph misspecification. Application to oral microbiome data from the ORIGINS study identifies taxa associated with insulin resistance and yields an outcome-driven graph summarizing how those taxa relate to the outcome, a structure that differs substantially from phylogenetic or co-occurrence networks. These findings highlight that fixed predictor graphs useful for regularization may not faithfully represent outcome-relevant feature relationships, underscoring the need for adaptive, outcome-informed approaches in compositional regression.

stat.ME↗

arXiv2026

Bayesian Sparse Regression for Microbiome-Metabolite Data Integration

Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large proportion of missing values, which may result from either low abundance or technical challenges in data processing. Moreover, given the compositionality of microbiome data, where the observed abundances can only be interpreted on a relative scale, standard variable selection methods are not applicable. In this project, we propose a novel Bayesian regression method to address these challenges in the integration of metabolite and microbiome data. Key features of our proposed model include modeling the two different mechanisms of missingness for the metabolite data and adopting a Bayesian prior designed to address the compositional characteristics of microbiome data. We demonstrate on simulated data that our proposed model can accurately impute the unobserved true metabolite values and correctly select the relevant microbiome predictors. We further illustrate our method using real data from a study focused on understanding the interplay between the microbiome and metabolome in colorectal cancer.

stat.AP↗

arXiv2024

Flexible aggregation of compositional predictors with shared effects for microbiome association analysis

Ongoing advancements in microbiome profiling have provided unprecedented insights into the molecular dynamics of microbial communities, sparking a surge of interest in uncovering the microbiome's critical role in human health. Identifying microbial features linked to clinical outcomes, however, remains challenging due to the high-dimensional, sparse, and compositional nature of microbiome data. Additionally, many microbial taxa, although classified as distinct, may share functional roles, complicating traditional variable selection methods. To overcome these obstacles, we introduce Bayesian Regression with Agglomerated Compositional Effects (BRACE), a novel approach using a spike-and-cluster prior combining Bernoulli activity indicators, an Ewens exchangeable partition prior on the finite active set, and a projection-based constrained Gaussian prior on cluster effects to perform data-adaptive clustering and variable selection. The methodological innovation of our work lies in how we combine the Ewens partition prior with a projection-based constrained Gaussian on the cluster atoms to enforce the sum-to-zero constraint. BRACE groups microbial taxa with similar effects on the outcome, yielding more interpretable models while enabling effective dimension reduction. Through comprehensive simulations and a real-world application examining the influence of oral microbiome composition on insulin resistance, we demonstrate BRACE's superior performance over existing methods, particularly in identifying key features with shared effects on outcomes.

stat.ME↗

arXiv2023

Operational requirements for localization in autonomous vehicles

Autonomous vehicles (AVs) need to determine their position and orientation accurately with respect to global coordinate system or local features under different scene geometries, traffic conditions and environmental conditions. \cite{reid2019localization} provides a comprehensive framework for the localization requirements for AVs. However, the framework is too restrictive whereby - (a) only a very small deviation from the lane is tolerated (one every $10^{8}$ hours), (b) all roadway types are considered same without any attention to restriction provided by the environment onto the localization and (c) the temporal nature of the location and orientation is not considered in the requirements. In this research, we present a more practical view of the localization requirement aimed at keeping the AV safe during an operation. We present the following novel contributions - (a) we propose a deviation penalty as a cumulative distribution function of the Weibull distribution which starts from the adjacent lane boundary, (b) we customize the parameters of the deviation penalty according to the current roadway type, particular lane boundary that the ego vehicle is against and roadway curvature and (c) we update the deviation penalty based on the available gap in the adjacent lane. We postulate that this formulation can provide a more robust and achievable view of the localization requirements than previous research while focusing on safety.

cs.RO↗

arXiv2019

Variable Selection with Random Survival Forest and Bayesian Additive Regression Tree for Survival Data

In this paper we utilize a survival analysis methodology incorporating Bayesian additive regression trees to account for nonlinear and additive covariate effects. We compare the performance of Bayesian additive regression trees, Cox proportional hazards and random survival forests models for censored survival data, using simulation studies and survival analysis for breast cancer with U.S. SEER database for the year 2005. In simulation studies, we compare the three models across varying sample sizes and censoring rates on the basis of bias and prediction accuracy. In survival analysis for breast cancer, we retrospectively analyze a subset of 1500 patients having invasive ductal carcinoma that is a common form of breast cancer mostly affecting older woman. Predictive potential of the three models are then compared using some widely used performance assessment measures in survival literature.

stat.AP↗