arXiv subjects

Maxime Turgeon

Publications and source records attributed to Maxime Turgeon.

5 recordsLinked to original sources

arXiv2026

Enhanced Forest Inventories for Habitat Mapping: A Case Study in the Sierra Nevada Mountains of California

Traditional forest inventory systems, originally designed to quantify merchantable timber volume, often lack the spatial resolution and structural detail required for modern multi-resource ecosystem management. In this manuscript, we present an Enhanced Forest Inventory (EFI) and demonstrate its utility for high-resolution wildlife habitat mapping. The project area covers 270,000 acres of the Eldorado National Forest in California's Sierra Nevada. By integrating 118 ground-truth Forest Inventory and Analysis (FIA) plots with multi-modal remote sensing data (LiDAR, aerial photography, and Sentinel-2 satellite imagery), we developed predictive models for key forest attributes. Our methodology employed a two-tier segmentation approach, partitioning the landscape into approximately 575,000 reporting units with an average size of 0.5 acre to capture forest heterogeneity. We utilized an Elastic-Net Regression framework and automated feature selection to relate remote sensing metrics to ground-measured variables such as basal area, stems per acre, and canopy cover. These physical metrics were translated into functional habitat attributes to evaluate suitability for two focal species: the California Spotted Owl (Strix occidentalis occidentalis) and the Pacific Fisher (Pekania pennanti). Our analysis identified 25,630 acres of nesting and 26,622 acres of foraging habitat for the owl, and 25,636 acres of likely habitat for the fisher based on structural requirements like large-diameter trees and high canopy closure. The results demonstrate that EFIs provide a critical bridge between forestry and conservation ecology, offering forest managers a spatially explicit tool to monitor ecosystem health and manage vulnerable species in complex environments.

stat.AP↗

arXiv2024

A Bayesian factor analysis model for high-dimensional microbiome count data

Dimension reduction techniques are among the most essential analytical tools in the analysis of high-dimensional data. Generalized principal component analysis (PCA) is an extension to standard PCA that has been widely used to identify low-dimensional features in high-dimensional discrete data, such as binary, multi-category and count data. For microbiome count data in particular, the multinomial PCA is a natural counterpart of the standard PCA. However, this technique fails to account for the excessive number of zero values, which is frequently observed in microbiome count data. To allow for sparsity, zero-inflated multivariate distributions can be used. We propose a zero-inflated probabilistic PCA model for latent factor analysis. The proposed model is a fully Bayesian factor analysis technique that is appropriate for microbiome count data analysis. In addition, we use the mean-field-type variational family to approximate the marginal likelihood and develop a classification variational approximation algorithm to fit the model. We demonstrate the efficiency of our procedure for predictions based on the latent factors and the model parameters through simulation experiments, showcasing its superiority over competing methods. This efficiency is further illustrated with two real microbiome count datasets. The method is implemented in R.

stat.ME↗

arXiv2023

Case-Base Neural Networks: survival analysis with time-varying, higher-order interactions

In the context of survival analysis, data-driven neural network-based methods have been developed to model complex covariate effects. While these methods may provide better predictive performance than regression-based approaches, not all can model time-varying interactions and complex baseline hazards. To address this, we propose Case-Base Neural Networks (CBNNs) as a new approach that combines the case-base sampling framework with flexible neural network architectures. Using a novel sampling scheme and data augmentation to naturally account for censoring, we construct a feed-forward neural network that includes time as an input. CBNNs predict the probability of an event occurring at a given moment to estimate the full hazard function. We compare the performance of CBNNs to regression and neural network-based survival methods in a simulation and three case studies using two time-dependent metrics. First, we examine performance on a simulation involving a complex baseline hazard and time-varying interactions to assess all methods, with CBNN outperforming competitors. Then, we apply all methods to three real data applications, with CBNNs outperforming the competing models in two studies and showing similar performance in the third. Our results highlight the benefit of combining case-base sampling with deep learning to provide a simple and flexible framework for data-driven modeling of single event survival outcomes that estimates time-varying effects and a complex baseline hazard by design. An R package is available at https://github.com/Jesse-Islam/cbnn.

stat.ML↗

arXiv2020

casebase: An Alternative Framework For Survival Analysis and Comparison of Event Rates

In epidemiological studies of time-to-event data, a quantity of interest to the clinician and the patient is the risk of an event given a covariate profile. However, methods relying on time matching or risk-set sampling (including Cox regression) eliminate the baseline hazard from the likelihood expression or the estimating function. The baseline hazard then needs to be estimated separately using a non-parametric approach. This leads to step-wise estimates of the cumulative incidence that are difficult to interpret. Using case-base sampling, Hanley & Miettinen (2009) explained how the parametric hazard functions can be estimated using logistic regression. Their approach naturally leads to estimates of the cumulative incidence that are smooth-in-time. In this paper, we present the casebase R package, a comprehensive and flexible toolkit for parametric survival analysis. We describe how the case-base framework can also be used in more complex settings: competing risks, time-varying exposure, and variable selection. Our package also includes an extensive array of visualization tools to complement the analysis of time-to-event data. We illustrate all these features through four different case studies. *SRB and MT contributed equally to this work.

stat.ME↗

arXiv2018

A Tracy-Widom Empirical Estimator For Valid P-values With High-Dimensional Datasets

Recent technological advances in many domains including both genomics and brain imaging have led to an abundance of high-dimensional and correlated data being routinely collected. Classical multivariate approaches like Multivariate Analysis of Variance (MANOVA) and Canonical Correlation Analysis (CCA) can be used to study relationships between such multivariate datasets. Yet, special care is required with high-dimensional data, as the test statistics may be ill-defined and classical inference procedures break down. In this work, we explain how valid p-values can be derived for these multivariate methods even in high dimensional datasets. Our main contribution is an empirical estimator for the largest root distribution of a singular double Wishart problem; this general framework underlies many common multivariate analysis approaches. From a small number of permutations of the data, we estimate the location and scale parameters of a parametric Tracy-Widom family that provides a good approximation of this distribution. Through simulations, we show that this estimated distribution also leads to valid p-values that can be used for high-dimensional inference. We then apply our approach to a pathway-based analysis of the association between DNA methylation and disease type in patients with systemic auto-immune rheumatic diseases.

stat.ME↗