arXiv subjects

Sebastian Kurtek

Publications and source records attributed to Sebastian Kurtek.

At least 19 recordsLinked to original sources

arXiv2025

Second-order spatial analysis of shapes of tumor cell nuclei

Intra-tumor heterogeneity driving disease progression is characterized by distinct growth and spatial proliferation patterns of cells and their nuclei within tumor and non-tumor tissues. A widely accepted hypothesis is that these spatial patterns are correlated with morphology of the cells and their nuclei. Nevertheless, tools to quantify the correlation, with uncertainty, are scarce, and the state-of-the-art is based on low-dimensional numerical summaries of the shapes that are inadequate to fully encode shape information. To this end, we propose a marked point process framework to assess spatial correlation among shapes of planar closed curves, which represent cell or nuclei outlines. With shapes of curves as marks, the framework is based on a mark-weighted $K$ function, a second-order spatial statistic that accounts for the marks' variation by using test functions that capture only the shapes of cells and their nuclei. We then develop local and global hypothesis tests for spatial dependence between the marks using the $K$ function. The framework is brought to bear on the cell nuclei extracted from histopathology images of breast cancer, where we uncover distinct correlation patterns that are consistent with clinical expectations.

stat.AP↗

arXiv2025

Joint Registration and Conformal Prediction for Partially Observed Functional Data

Predicting missing segments in partially observed functions is challenging due to infinite-dimensionality, complex dependence within and across observations, and irregular noise. These challenges are further exacerbated by the existence of two distinct sources of variation in functional data, termed amplitude (variation along the $y$-axis) and phase (variation along the $x$-axis). While registration can disentangle them from complete functional data, the process is more difficult for partial observations. Thus, existing methods for functional data prediction often ignore phase variation. Furthermore, they rely on strong parametric assumptions, and require either precise model specifications or computationally intensive techniques, such as bootstrapping, to construct prediction intervals. To tackle this problem, we propose a unified registration and prediction approach for partially observed functions under the conformal prediction framework, which separately focuses on the amplitude and phase components. By leveraging split conformal methods, our approach integrates registration and prediction while ensuring exchangeability through carefully constructed predictor-response pairs. Using a neighborhood smoothing algorithm, the framework produces pointwise prediction bands with finite-sample marginal coverage guarantees under weak assumptions. The method is easy to implement, computationally efficient, and suitable for parallelization. Numerical studies and real-world data examples clearly demonstrate the effectiveness and practical utility of the proposed approach.

stat.ME↗

arXiv2024

Probabilistic size-and-shape functional mixed models

The reliable recovery and uncertainty quantification of a fixed effect function $\mu$ in a functional mixed model, for modelling population- and object-level variability in noisily observed functional data, is a notoriously challenging task: variations along the $x$ and $y$ axes are confounded with additive measurement error, and cannot in general be disentangled. The question then as to what properties of $\mu$ may be reliably recovered becomes important. We demonstrate that it is possible to recover the size-and-shape of a square-integrable $\mu$ under a Bayesian functional mixed model. The size-and-shape of $\mu$ is a geometric property invariant to a family of space-time unitary transformations, viewed as rotations of the Hilbert space, that jointly transform the $x$ and $y$ axes. A random object-level unitary transformation then captures size-and-shape \emph{preserving} deviations of $\mu$ from an individual function, while a random linear term and measurement error capture size-and-shape \emph{altering} deviations. The model is regularized by appropriate priors on the unitary transformations, posterior summaries of which may then be suitably interpreted as optimal data-driven rotations of a fixed orthonormal basis for the Hilbert space. Our numerical experiments demonstrate utility of the proposed model, and superiority over the current state-of-the-art.

stat.ME↗

arXiv2022

Elastic Metrics on Spaces of Euclidean Curves: Theory and Algorithms

A main goal in the field of statistical shape analysis is to define computable and informative metrics on spaces of immersed manifolds, such as the space of curves in a Euclidean space. The approach taken in the elastic shape analysis framework is to define such a metric by starting with a reparameterization-invariant Riemannian metric on the space of parameterized shapes and inducing a metric on the quotient by the group of diffeomorphisms. This quotient metric is computed, in practice, by finding a registration of two shapes over the diffeomorphism group. For spaces of Euclidean curves, the initial Riemannian metric is frequently chosen from a two-parameter family of Sobolev metrics, called elastic metrics. Elastic metrics are especially convenient because, for several parameter choices, they are known to be locally isometric to Riemannian metrics for which one is able to solve the geodesic boundary problem explictly -- well-known examples of these local isometries include the complex square root transform of Younes, Michor, Mumford and Shah and square root velocity (SRV) transform of Srivastava, Klassen, Joshi and Jermyn. In this paper, we show that the SRV transform extends to elastic metrics for all choices of parameters, for curves in any dimension, thereby fully generalizing the work of many authors over the past two decades. We give a unified treatment of the elastic metrics: we extend results of Trouv\'{e} and Younes, Bruveris as well as Lahiri, Robinson and Klassen on the existence of solutions to the registration problem, we develop algorithms for computing distances and geodesics, and we apply these algorithms to metric learning problems, where we learn optimal elastic metric parameters for statistical shape analysis tasks.

math.DG↗

arXiv2022

Spatially Penalised Registration of Multivariate Functional Data

Registration of multivariate functional data involves handling of both cross-component and cross-observation phase variations. Allowing for the two phase variations to be modelled as general diffeomorphic time warpings, in this work we focus on the hitherto unconsidered setting where phase variation of the component functions are spatially correlated. We propose an algorithm to optimize a metric-based objective function for registration with a novel penalty term that incorporates the spatial correlation between the component phase variations through a kriging estimate of an appropriate phase random field. The penalty term encourages the overall phase at a particular location to be similar to the spatially weighted average phase in its neighbourhood, and thus engenders a regularization that prevents over-alignment. Utility of the registration method, and its superior performance compared to methods that fail to account for the spatial correlation, is demonstrated through performance on simulated examples and two multivariate functional datasets pertaining to EEG signals and ozone concentrations. The generality of the framework opens up the possibility for extension to settings involving different forms of correlation between the component functions and their phases.

stat.ME↗

arXiv2021

Topo-Geometric Analysis of Variability in Point Clouds using Persistence Landscapes

Topological data analysis provides a set of tools to uncover low-dimensional structure in noisy point clouds. Prominent amongst the tools is persistence homology, which summarizes birth-death times of homological features using data objects known as persistence diagrams. To better aid statistical analysis, a functional representation of the diagrams, known as persistence landscapes, enable use of functional data analysis and machine learning tools. Topological and geometric variabilities inherent in point clouds are confounded in both persistence diagrams and landscapes, and it is important to distinguish topological signal from noise to draw reliable conclusions on the structure of the point clouds when using persistence homology. We develop a framework for decomposing variability in persistence diagrams into topological signal and topological noise through alignment of persistence landscapes using an elastic Riemannian metric. Aligned landscapes (amplitude) isolate the topological signal. Reparameterizations used for landscape alignment (phase) are linked to a resolution parameter used to generate persistence diagrams, and capture topological noise in the form of geometric, global scaling and sampling variabilities. We illustrate the importance of decoupling topological signal and topological noise in persistence diagrams (landscapes) using several simulated examples. We also demonstrate that our approach provides novel insights in two real data studies.

stat.ME↗

arXiv2021

Tumor Radiogenomics with Bayesian Layered Variable Selection

We propose a statistical framework to integrate radiological magnetic resonance imaging (MRI) and genomic data to identify the underlying radiogenomic associations in lower grade gliomas (LGG). We devise a novel imaging phenotype by dividing the tumor region into concentric spherical layers that mimics the tumor evolution process. MRI data within each layer is represented by voxel--intensity-based probability density functions which capture the complete information about tumor heterogeneity. Under a Riemannian-geometric framework these densities are mapped to a vector of principal component scores which act as imaging phenotypes. Subsequently, we build Bayesian variable selection models for each layer with the imaging phenotypes as the response and the genomic markers as predictors. Our novel hierarchical prior formulation incorporates the interior-to-exterior structure of the layers, and the correlation between the genomic markers. We employ a computationally-efficient Expectation--Maximization-based strategy for estimation. Simulation studies demonstrate the superior performance of our approach compared to other approaches. With a focus on the cancer driver genes in LGG, we discuss some biologically relevant findings. Genes implicated with survival and oncogenesis are identified as being associated with the spherical layers, which could potentially serve as early-stage diagnostic markers for disease monitoring, prior to routine invasive approaches.

stat.ME↗

arXiv2021

RADIOHEAD: Radiogenomic Analysis Incorporating Tumor Heterogeneity in Imaging Through Densities

Recent technological advancements have enabled detailed investigation of associations between the molecular architecture and tumor heterogeneity, through multi-source integration of radiological imaging and genomic (radiogenomic) data. In this paper, we integrate and harness radiogenomic data in patients with lower grade gliomas (LGG), a type of brain cancer, in order to develop a regression framework called RADIOHEAD (RADIOgenomic analysis incorporating tumor HEterogeneity in imAging through Densities) to identify radiogenomic associations. Imaging data is represented through voxel intensity probability density functions of tumor sub-regions obtained from multimodal magnetic resonance imaging, and genomic data through molecular signatures in the form of pathway enrichment scores corresponding to their gene expression profiles. Employing a Riemannian-geometric framework for principal component analysis on the set of probability densities functions, we map each probability density to a vector of principal component scores, which are then included as predictors in a Bayesian regression model with the pathway enrichment scores as the response. Variable selection compatible with the grouping structure amongst the predictors induced through the tumor sub-regions is carried out under a group spike-and-slab prior. A Bayesian false discovery rate mechanism is then used to infer significant associations based on the posterior distribution of the regression coefficients. Our analyses reveal several pathways relevant to LGG etiology (such as synaptic transmission, nerve impulse and neurotransmitter pathways), to have significant associations with the corresponding imaging-based predictors.

stat.ME↗

arXiv2021

Tangent functional canonical correlation analysis for densities and shapes, with applications to multimodal imaging data

It is quite common for functional data arising from imaging data to assume values in infinite-dimensional manifolds. Uncovering associations between two or more such nonlinear functional data extracted from the same object across medical imaging modalities can assist development of personalized treatment strategies. We propose a method for canonical correlation analysis between paired probability densities or shapes of closed planar curves, routinely used in biomedical studies, which combines a convenient linearization and dimension reduction of the data using tangent space coordinates. Leveraging the fact that the corresponding manifolds are submanifolds of unit Hilbert spheres, we describe how finite-dimensional representations of the functional data objects can be easily computed, which then facilitates use of standard multivariate canonical correlation analysis methods. We further construct and visualize canonical variate directions directly on the space of densities or shapes. Utility of the method is demonstrated through numerical simulations and performance on a magnetic resonance imaging dataset of Glioblastoma Multiforme brain tumors.

stat.ME↗

arXiv2021

4D Atlas: Statistical Analysis of the Spatiotemporal Variability in Longitudinal 3D Shape Data

We propose a novel framework to learn the spatiotemporal variability in longitudinal 3D shape data sets, which contain observations of objects that evolve and deform over time. This problem is challenging since surfaces come with arbitrary parameterizations and thus, they need to be spatially registered. Also, different deforming objects, also called 4D surfaces, evolve at different speeds and thus they need to be temporally aligned. We solve this spatiotemporal registration problem using a Riemannian approach. We treat a 3D surface as a point in a shape space equipped with an elastic Riemannian metric that measures the amount of bending and stretching that the surfaces undergo. A 4D surface can then be seen as a trajectory in this space. With this formulation, the statistical analysis of 4D surfaces can be cast as the problem of analyzing trajectories embedded in a nonlinear Riemannian manifold. However, performing the spatiotemporal registration, and subsequently computing statistics, on such nonlinear spaces is not straightforward as they rely on complex nonlinear optimizations. Our core contribution is the mapping of the surfaces to the space of Square-Root Normal Fields where the L2 metric is equivalent to the partial elastic metric in the space of surfaces. Thus, by solving the spatial registration in the SRNF space, the problem of analyzing 4D surfaces becomes the problem of analyzing trajectories embedded in the SRNF space, which has a Euclidean structure. In this paper, we develop the building blocks that enable such analysis. These include: (1) the spatiotemporal registration of arbitrarily parameterized 4D surfaces in the presence of large elastic deformations and large variations in their execution rates; (2) the computation of geodesics between 4D surfaces; (3) the computation of statistical summaries; and (4) the synthesis of random 4D surfaces.

cs.CV↗

arXiv2020

KShapeNet: Riemannian network on Kendall shape space for Skeleton based Action Recognition

Deep Learning architectures, albeit successful in most computer vision tasks, were designed for data with an underlying Euclidean structure, which is not usually fulfilled since pre-processed data may lie on a non-linear space. In this paper, we propose a geometry aware deep learning approach for skeleton-based action recognition. Skeleton sequences are first modeled as trajectories on Kendall's shape space and then mapped to the linear tangent space. The resulting structured data are then fed to a deep learning architecture, which includes a layer that optimizes over rigid and non rigid transformations of the 3D skeletons, followed by a CNN-LSTM network. The assessment on two large scale skeleton datasets, namely NTU-RGB+D and NTU-RGB+D 120, has proven that proposed approach outperforms existing geometric deep learning methods and is competitive with respect to recently published approaches.

cs.CV↗

arXiv2020

Elastic $k$-means clustering of functional data for posterior exploration, with an application to inference on acute respiratory infection dynamics

We propose a new method for clustering of functional data using a $k$-means framework. We work within the elastic functional data analysis framework, which allows for decomposition of the overall variation in functional data into amplitude and phase components. We use the amplitude component to partition functions into shape clusters using an automated approach. To select an appropriate number of clusters, we additionally propose a novel Bayesian Information Criterion defined using a mixture model on principal components estimated using functional Principal Component Analysis. The proposed method is motivated by the problem of posterior exploration, wherein samples obtained from Markov chain Monte Carlo algorithms are naturally represented as functions. We evaluate our approach using a simulated dataset, and apply it to a study of acute respiratory infection dynamics in San Luis Potosí, Mexico.

stat.ME↗

arXiv2020

Variograms for spatial functional data with phase variation

Spatial, amplitude and phase variations in spatial functional data are confounded. Conclusions from the popular functional trace variogram, which quantifies spatial variation, can be misleading when analysing misaligned functional data with phase variation. To remedy this, we describe a framework that extends amplitude-phase separation methods in functional data to the spatial setting, with a view towards performing clustering and spatial prediction. We propose a decomposition of the trace variogram into amplitude and phase components and quantify how spatial correlations between functional observations manifest in their respective amplitude and phase components. This enables us to generate separate amplitude and phase clustering methods for spatial functional data, and develop a novel spatial functional interpolant at unobserved locations based on combining separate amplitude and phase predictions. Through simulations and real data analyses, we found that the proposed methods result in more accurate predictions and more interpretable clustering results.

stat.ME↗

arXiv2020

The Weighted Euler Curve Transform for Shape and Image Analysis

The Euler Curve Transform (ECT) of Turner et al.\ is a complete invariant of an embedded simplicial complex, which is amenable to statistical analysis. We generalize the ECT to provide a similarly convenient representation for weighted simplicial complexes, objects which arise naturally, for example, in certain medical imaging applications. We leverage work of Ghrist et al.\ on Euler integral calculus to prove that this invariant---dubbed the Weighted Euler Curve Transform (WECT)---is also complete. We explain how to transform a segmented region of interest in a grayscale image into a weighted simplicial complex and then into a WECT representation. This WECT representation is applied to study Glioblastoma Multiforme brain tumor shape and texture data. We show that the WECT representation is effective at clustering tumors based on qualitative shape and texture features and that this clustering correlates with patient survival time.

cs.CG↗

arXiv2019

Bayesian Framework for Simultaneous Registration and Estimation of Noisy, Sparse and Fragmented Functional Data

In many applications, smooth processes generate data that is recorded under a variety of observation regimes, such as dense, sparse or fragmented observations that are often contaminated with error. The statistical goal of registering and estimating the individual underlying functions from discrete observations has thus far been mainly approached sequentially without formal uncertainty propagation, or in an application-specific manner. We propose a unified Bayesian framework for simultaneous registration and estimation, which is flexible enough to accommodate inference on individual functions under general observation regimes. Our ability to do this relies on the specification of strongly informative prior models over the amplitude component of function variability. We provide two strategies for this critical choice: a data-driven approach that defines an empirical basis for the amplitude subspace based on training data, and a shape-restricted approach when the relative location and number of local extrema is well-understood. The proposed methods build on elastic functional data analysis, which separately models amplitude and phase variability inherent in functional data. We emphasize the importance of uncertainty quantification and visualization of these two components as they provide complementary information about the estimated functions. We validate the framework using simulations and real applications to medical imaging and biometrics.

stat.AP↗

arXiv2019

Estimation of Spatial Deformation for Nonstationary Processes via Variogram Alignment

In modeling spatial processes, a second-order stationarity assumption is often made. However, for spatial data observed on a vast domain, the covariance function often varies over space, leading to a heterogeneous spatial dependence structure, therefore requiring nonstationary modeling. Spatial deformation is one of the main methods for modeling nonstationary processes, assuming the nonstationary process has a stationary counterpart in the deformed space. The estimation of the deformation function poses severe challenges. Here, we introduce a novel approach for nonstationary geostatistical modeling, using space deformation, when a single realization of the spatial process is observed. Our method is based, at a fundamental level, on aligning regional variograms, where warping variability of the distance from each subregion explains the spatial nonstationarity. We propose to use multi-dimensional scaling to map the warped distances to spatial locations. We asses the performance of our new method using multiple simulation studies. Additionally, we illustrate our methodology on precipitation data to estimate the heterogeneous spatial dependence and to perform spatial predictions.

stat.ME↗

arXiv2019

A Geometric Approach for Computing Tolerance Bounds for Elastic Functional Data

We develop a method for constructing tolerance bounds for functional data with random warping variability. In particular, we define a generative, probabilistic model for the amplitude and phase components of such observations, which parsimoniously characterizes variability in the baseline data. Based on the proposed model, we define two different types of tolerance bounds that are able to measure both types of variability, and as a result, identify when the data has gone beyond the bounds of amplitude and/or phase. The first functional tolerance bounds are computed via a bootstrap procedure on the geometric space of amplitude and phase functions. The second functional tolerance bounds utilize functional Principal Component Analysis to construct a tolerance factor. This work is motivated by two main applications: process control and disease monitoring. The problem of statistical analysis and modeling of functional data in process control is important in determining when a production has moved beyond a baseline. Similarly, in biomedical applications, doctors use long, approximately periodic signals (such as the electrocardiogram) to diagnose and monitor diseases. In this context, it is desirable to identify abnormalities in these signals. We additionally consider a simulated example to assess our approach and compare it to two existing methods.

stat.CO↗

arXiv2019

A Geometric Variational Approach to Bayesian Inference

We propose a novel Riemannian geometric framework for variational inference in Bayesian models based on the nonparametric Fisher-Rao metric on the manifold of probability density functions. Under the square-root density representation, the manifold can be identified with the positive orthant of the unit hypersphere in L2, and the Fisher-Rao metric reduces to the standard L2 metric. Exploiting such a Riemannian structure, we formulate the task of approximating the posterior distribution as a variational problem on the hypersphere based on the alpha-divergence. This provides a tighter lower bound on the marginal distribution when compared to, and a corresponding upper bound unavailable with, approaches based on the Kullback-Leibler divergence. We propose a novel gradient-based algorithm for the variational problem based on Frechet derivative operators motivated by the geometry of the Hilbert sphere, and examine its properties. Through simulations and real-data applications, we demonstrate the utility of the proposed geometric framework and algorithm on several Bayesian models.

stat.ME↗