arXiv subjects

Anuj Srivastava

Publications and source records attributed to Anuj Srivastava.

At least 19 recordsLinked to original sources

arXiv2026

Smooth Reparameterizations of Functions on Simplicial Product Spaces: Applications to Probabilistic Tensor Decomposition and Functional Data Registration

We consider optimization problems defined on product spaces of simplices. Examples of this class of problems include learning low-rank discrete multivariate probability distributions via simplex constrained tensor decomposition and performing functional data registration under the Square Root Velocity Function (SRVF) representation. In this work, we demonstrate the feasibility of replacing the product simplex with a smooth, elementwise strictly convex reparameterization, resulting in an unconstrained optimization problem on a manifold. We show that performing such a reparameterization results in the second order Karush-Kuhn-Tucker (KKT) points on the smooth manifold being mapped to the weak second order KKT points on the product simplex. This leads to a Riemannian Gradient Descent (RGD) algorithm for solving the reparameterized problem, which outperforms Projected Gradient Descent (PGD), and provides a more faithful representation of the original function shapes while performing curve registration.

cs.LG↗

arXiv2026

TreeSRNF: Square-Root Normal Fields for Generative Modelling of the Geometric and Structural Variability in Tree-like 3D Objects

We introduce a novel mathematical framework for analyzing and generating complex tree-shaped 3D objects, such as botanical trees and plants, which deform both in their 3D geometry and branching structure. Unlike previous works, which either consider only the skeletal structure of tree-like objects or approximate their 3D geometry using branch thickness, the proposed framework accurately models both the 3D geometry of the tree branches and the way they are interconnected. In this paper, we first generalize the Square Root Normal Fields (SRNF) representation, originally proposed for the statistical analysis of genus-0 surfaces, to tree-shaped 3D objects. We then treat tree-shaped 3D objects as points on a novel Riemannian tree-shape space equipped with a novel Riemannian metric that measures the amount of surface bending and stretching, and structural changes one needs to apply to one 3D tree-shape to align it with another. This way, deformations become trajectories in this novel tree-shape space. We analyze the theoretical properties of this novel tree-shape space and the corresponding metric and develop algorithms for computing point-wise and branch-wise correspondences and geodesic paths between complex 3D trees. We finally show how to use these building blocks for (1) computing statistical summaries, \ie means and modes of variation, of collections of tree-shaped 3D objects, and (2) synthesizing novel tree-shaped 3D objects by sampling from probability distributions fitted to a population of tree-shaped 3D objects. We demonstrate the performance and utility of the proposed framework on real and synthetic plants and botanical trees and show that it significantly outperforms the state-of-the-art.

cs.CV↗

arXiv2026

Bayesian In Vivo Tracking of Synapses using Joint Poisson Deconvolution and Diffeomorphic Registration

Synapses are densely packed submicron structures that dynamically reorganize during learning and memory formation. Longitudinal \textit{in vivo} imaging of fluorescently tagged synaptic receptors offers a promising opportunity to study large-scale synaptic dynamics and how these processes are disrupted in neurological disease. However, in vivo imaging with 2-photon microscopy uses low laser power and therefore suffers from low signal-to-noise ratio (SNR) and high shot noise, nonlinear tissue motion between days, nonstationary fluctuations in synaptic fluorescence, and significant blur induced by the microscope point spread function (PSF). Together, these factors make it challenging to detect and track synapses, especially in regions with high synaptic density. This paper presents a novel template-based framework for modeling synapses as varying luminance point sources that move under a nonlinear tissue deformation. Taking a unified Bayesian approach, we apply this model to microscopy data by deriving a posterior that incorporates a diffeomorphic mapping for domain warping, a Gaussian point spread function for the imaging process, and a Poisson observation model for raw photon counts. The Bayesian solution simultaneously: (1) Constructs a probabilistic template of synapse locations, (2) denoises and deconvolves the image data, (3) infers fluorescence intensities, (4) performs diffeomorphic image registration to correct for tissue motion, and (5) provides confidence regions for these parameter estimates. We demonstrate the framework on both a 2D+t simulated dataset and a 3D+t longitudinal \textit{in vivo} microscopy dataset of fluorescent synapses imaged in a mouse over two weeks.

cs.CV↗

arXiv2026

An Elastic Shape Variational Autoencoder for Skeleton Pose Trajectories

Deep generative models provide flexible frameworks for modeling complex, structured data such as images, videos, 3D objects, and texts. However, when applied to sequences of human skeletons, standard variational autoencoders (VAEs) often allocate substantial capacity to nuisance factors-such as camera orientation, subject scale, viewpoint, and execution speed-rather than the intrinsic geometry of shapes and their motion. We propose the Elastic Shape - Variational Autoencoder (ES-VAE), a geometry-aware generative model for skeletal trajectories that leverages the transported square-root velocity field (TSRVF) representation on Kendall's shape manifold. This representation inherently removes rigid translations, rotations, and global scaling of shapes, and temporal rate variability of sequences, isolating the underlying shape dynamics. The ES-VAE encoder maps skeletal sequences to a low-dimensional latent space incorporating the Riemannian logarithm map, while the decoder reconstructs sequences using the corresponding exponential map. We demonstrate the effectiveness of ES-VAE on two datasets. First, we analyze skeletal gait cycles to predict clinical mobility scores and classify subjects into healthy and post-stroke groups. Second, we evaluate action recognition on the NTU RGB+D dataset. Across both settings, ES-VAE consistently outperforms standard VAEs and a range of sequence modeling baselines, including temporal convolutional networks, transformers, and graph convolutional networks. More broadly, ES-VAE provides a principled framework for learning generative models of longitudinal data on pose shape manifolds, offering improved latent representation and downstream performance compared to existing deep learning approaches.

cs.CV↗

arXiv2026

Geometry Preserving Loss Functions Promote Improved Adaptation of Blackbox Generative Model

Adaptation of blackbox generative models has been widely studied recently through the exploration of several methods including generator fine-tuning, latent space searches, leveraging singular value decomposition, and so on. However, adapting large-scale generative AI tools to specific use cases continues to be challenging, as many of these industry-grade models are not made widely available. The traditional approach of fine-tuning certain layers of a generative network is not feasible due to the expense of storing and fine-tuning generative models, as well as the restricted access to weights and gradients. Recognizing these challenges, we propose a novel end-to-end pipeline aimed at domain adaptation by leveraging geometry-preserving loss functions in conjunction to pre-trained generative adversarial networks (GANs). Our method rethinks the problem of adaptation by re-contextualizing the role of GAN inversion in obtaining accurate latent space representations. Extending the ability of existing state-of-the-art inverters, we preserve pair-wise distances between tangent spaces to successfully train a latent generative model to produce samples from the target distribution. We evaluate our proposed pipeline on StyleGANs with real distribution shifts and demonstrate that the introduction of the geometry preserving loss function lends to improved adaptation of generative models compared to other traditional loss functions.

cs.LG↗

arXiv2025

A Riemannian Framework for the Elastic Analysis of the Spatiotemporal Variability in the Shape and Structure of Tree-like 4D Objects

This paper introduces a novel computational framework for modeling and analyzing the spatiotemporal shape variability of tree-like 4D structures whose shapes deform and evolve over time. Tree-like 3D objects, such as botanical trees and plants, deform and grow at different rates. In this process, they bend and stretch their branches and change their branching structure, making their spatiotemporal registration challenging. We address this problem within a Riemannian framework that represents tree-like 3D objects as points in a tree-shape space endowed with a proper elastic metric that quantifies branch bending, stretching, and topological changes. With this setting, a 4D tree-like object becomes a trajectory in the tree-shape space. Thus, the problem of modeling and analyzing the spatiotemporal variability in tree-like 4D objects reduces to the analysis of trajectories within this tree-shape space. However, performing spatiotemporal registration and subsequently computing geodesics and statistics in the nonlinear tree-shape space is inherently challenging, as these tasks rely on complex nonlinear optimizations. Our core contribution is the mapping of the tree-like 3D objects to the space of the Extended Square Root Velocity Field, where the complex elastic metric is reduced to the L2 metric. By solving spatial registration in the ESRVF space, analyzing tree-like 4D objects can be reformulated as the problem of analyzing elastic trajectories in the ESRVF space. Based on this formulation, we develop a comprehensive framework for analyzing the spatiotemporal dynamics of tree-like objects, including registration under large deformations and topological differences, geodesic computation, statistical summarization through mean trajectories and modes of variation, and the synthesis of new, random tree-like 4D shapes.

cs.CG↗

arXiv2025

Graph Network Modeling Techniques for Visualizing Human Mobility Patterns

Human mobility analysis at urban-scale requires models to represent the complex nature of human movements, which in turn are affected by accessibility to nearby points of interest, underlying socioeconomic factors of a place, and local transport choices for people living in a geographic region. In this work, we represent human mobility and the associated flow of movements as a grapyh. Graph-based approaches for mobility analysis are still in their early stages of adoption and are actively being researched. The challenges of graph-based mobility analysis are multifaceted - the lack of sufficiently high-quality data to represent flows at high spatial and teporal resolution whereas, limited computational resources to translate large voluments of mobility data into a network structure, and scaling issues inherent in graph models etc. The current study develops a methodology by embedding graphs into a continuous space, which alleviates issues related to fast graph matching, graph time-series modeling, and visualization of mobility dynamics. Through experiments, we demonstrate how mobility data collected from taxicab trajectories could be transformed into network structures and patterns of mobility flow changes, and can be used for downstream tasks reporting approx 40% decrease in error on average in matched graphs vs unmatched ones.

cs.SI↗

arXiv2025

Alignment of Continuous Brain Connectivity

Brain networks are typically represented by adjacency matrices, where each node corresponds to a brain region. In traditional brain network analysis, nodes are assumed to be matched across individuals, but the methods used for node matching often overlook the underlying connectivity information. This oversight can result in inaccurate node alignment, leading to inflated edge variability and reduced statistical power in downstream connectivity analyses. To overcome this challenge, we propose a novel framework for registering high resolution continuous connectivity (ConCon), defined as a continuous function on a product manifold space specifically, the cortical surface capturing structural connectivity between all pairs of cortical points. Leveraging ConCon, we formulate an optimal diffeomorphism problem to align both connectivity profiles and cortical surfaces simultaneously. We introduce an efficient algorithm to solve this problem and validate our approach using data from the Human Connectome Project (HCP). Results demonstrate that our method substantially improves the accuracy and robustness of connectome-based analyses compared to existing techniques.

stat.ME↗

arXiv2025

Investigating Image Manifolds of 3D Objects: Learning, Shape Analysis, and Comparisons

Despite high-dimensionality of images, the sets of images of 3D objects have long been hypothesized to form low-dimensional manifolds. What is the nature of such manifolds? How do they differ across objects and object classes? Answering these questions can provide key insights in explaining and advancing success of machine learning algorithms in computer vision. This paper investigates dual tasks -- learning and analyzing shapes of image manifolds -- by revisiting a classical problem of manifold learning but from a novel geometrical perspective. It uses geometry-preserving transformations to map the pose image manifolds, sets of images formed by rotating 3D objects, to low-dimensional latent spaces. The pose manifolds of different objects in latent spaces are found to be nonlinear, smooth manifolds. The paper then compares shapes of these manifolds for different objects using Kendall's shape analysis, modulo rigid motions and global scaling, and clusters objects according to these shape metrics. Interestingly, pose manifolds for objects from the same classes are frequently clustered together. The geometries of image manifolds can be exploited to simplify vision and image processing tasks, to predict performances, and to provide insights into learning methods.

cs.CV↗

arXiv2025

Dynamic Neural Surfaces for Elastic 4D Shape Representation and Analysis

We propose a novel framework for the statistical analysis of genus-zero 4D surfaces, i.e., 3D surfaces that deform and evolve over time. This problem is particularly challenging due to the arbitrary parameterizations of these surfaces and their varying deformation speeds, necessitating effective spatiotemporal registration. Traditionally, 4D surfaces are discretized, in space and time, before computing their spatiotemporal registrations, geodesics, and statistics. However, this approach may result in suboptimal solutions and, as we demonstrate in this paper, is not necessary. In contrast, we treat 4D surfaces as continuous functions in both space and time. We introduce Dynamic Spherical Neural Surfaces (D-SNS), an efficient smooth and continuous spatiotemporal representation for genus-0 4D surfaces. We then demonstrate how to perform core 4D shape analysis tasks such as spatiotemporal registration, geodesics computation, and mean 4D shape estimation, directly on these continuous representations without upfront discretization and meshing. By integrating neural representations with classical Riemannian geometry and statistical shape analysis techniques, we provide the building blocks for enabling full functional shape analysis. We demonstrate the efficiency of the framework on 4D human and face datasets. The source code and additional results are available at https://4d-dsns.github.io/DSNS/.

cs.CV↗

arXiv2025

A Shape-Based Functional Index for Objective Assessment of Pediatric Motor Function

Clinical assessments for neuromuscular disorders, such as Spinal Muscular Atrophy (SMA) and Duchenne Muscular Dystrophy (DMD), continue to rely on subjective measures to monitor treatment response and disease progression. We introduce a novel method using wearable sensors to objectively assess motor function during daily activities in 19 patients with DMD, 9 with SMA, and 13 age-matched controls. Pediatric movement data is complex due to confounding factors such as limb length variations in growing children and variability in movement speed. Our approach uses Shape-based Principal Component Analysis to align movement trajectories and identify distinct kinematic patterns, including variations in motion speed and asymmetry. Both DMD and SMA cohorts have individuals with motor function on par with healthy controls. Notably, patients with SMA showed greater activation of the motion asymmetry pattern. We further combined projections on these principal components with partial least squares (PLS) to identify a covariation mode with a canonical correlation of r = 0.78 (95% CI: [0.34, 0.94]) with muscle fat infiltration, the Brooke score (a motor function score), and age-related degenerative changes, proposing a novel motor function index. This data-driven method can be deployed in home settings, enabling better longitudinal tracking of treatment efficacy for children with neuromuscular disorders.

stat.AP↗

arXiv2024

Statistical Emulations of Human Operational Motions in Industrial Environments

This paper tackles the challenging problem of developing emulators for human operational motions in industrial workplaces. We represent human motion as time-indexed sequences of body shapes and formulate a statistical generative model for these shape sequences. The sequences are modeled as continuous-time stochastic processes on a Riemannian shape manifold. Key challenges include the manifold's nonlinearity, variability in motion execution rates, the infinite-dimensional nature of the processes, and population-level variability across action classes. Deep learning methods are ineffective due to the small training samples typically available in this domain. To address these issues, we integrate a number of tools: temporal alignment via time warping, Riemannian geometry for handling nonlinearities, and shape- and functional-PCA for dimensionality reduction. A Gaussian model is then imposed on the reduced Euclidean spaces to emulate random motion sequences, which are then evaluated in representative industrial scenarios. We utilize a number of metrics to validate randomly generated shape sequences.

stat.AP↗

arXiv2024

Scalar-on-Shape Regression Models for Functional Data Analysis

Functional data contains two components: shape (or amplitude) and phase. This paper focuses on a branch of functional data analysis (FDA), namely Shape-Based FDA, that isolates and focuses on shapes of functions. Specifically, this paper focuses on Scalar-on-Shape (ScoSh) regression models that incorporate the shapes of predictor functions and discard their phases. This aspect sets ScoSh models apart from the traditional Scalar-on-Function (ScoF) regression models that incorporate full predictor functions. ScoSh is motivated by object data analysis, {\it, e.g.}, for neuro-anatomical objects, where object morphologies are relevant and their parameterizations are arbitrary. ScoSh also differs from methods that arbitrarily pre-register data and uses it in subsequent analysis. In contrast, ScoSh models perform registration during regression, using the (non-parametric) Fisher-Rao inner product and nonlinear index functions to capture complex predictor-response relationships. This formulation results in novel concepts of {\it regression phase} and {\it regression mean} of functions. Regression phases are time-warpings of predictor functions that optimize prediction errors, and regression means are optimal regression coefficients. We demonstrate practical applications of the ScoSh model using extensive simulated and real-data examples, including predicting COVID outcomes when daily rate curves are predictors.

stat.ME↗

arXiv2024

Fused Gromov-Wasserstein Variance Decomposition with Linear Optimal Transport

Wasserstein distances form a family of metrics on spaces of probability measures that have recently seen many applications. However, statistical analysis in these spaces is complex due to the nonlinearity of Wasserstein spaces. One potential solution to this problem is Linear Optimal Transport (LOT). This method allows one to find a Euclidean embedding, called LOT embedding, of measures in some Wasserstein spaces, but some information is lost in this embedding. So, to understand whether statistical analysis relying on LOT embeddings can make valid inferences about original data, it is helpful to quantify how well these embeddings describe that data. To answer this question, we present a decomposition of the Fréchet variance of a set of measures in the 2-Wasserstein space, which allows one to compute the percentage of variance explained by LOT embeddings of those measures. We then extend this decomposition to the Fused Gromov-Wasserstein setting. We also present several experiments that explore the relationship between the dimension of the LOT embedding, the percentage of variance explained by the embedding, and the classification accuracy of machine learning classifiers built on the embedded data. We use the MNIST handwritten digits dataset, IMDB-50000 dataset, and Diffusion Tensor MRI images for these experiments. Our results illustrate the effectiveness of low dimensional LOT embeddings in terms of the percentage of variance explained and the classification accuracy of models built on the embedded data.

stat.ME↗

arXiv2024

Reducing Shape-Graph Complexity with Application to Classification of Retinal Blood Vessels and Neurons

Shape graphs are complex geometrical structures commonly found in biological and anatomical systems. A shape graph is a collection of nodes, some connected by curvilinear edges with arbitrary shapes. Their high complexity stems from the large number of nodes and edges and the complex shapes of edges. With an eye for statistical analysis, one seeks low-complexity representations that retain as much of the global structures of the original shape graphs as possible. This paper develops a framework for reducing graph complexity using hierarchical clustering procedures that replace groups of nodes and edges with their simpler representatives. It demonstrates this framework using graphs of retinal blood vessels in two dimensions and neurons in three dimensions. The paper also presents experiments on classifications of shape graphs using progressively reduced levels of graph complexity. The accuracy of disease detection in retinal blood vessels drops quickly when the complexity is reduced, with accuracy loss particularly associated with discarding terminal edges. Accuracy in identifying neural cell types remains stable with complexity reduction.

stat.CO↗

arXiv2024

A Riemannian Approach for Spatiotemporal Analysis and Generation of 4D Tree-shaped Structures

We propose the first comprehensive approach for modeling and analyzing the spatiotemporal shape variability in tree-like 4D objects, i.e., 3D objects whose shapes bend, stretch, and change in their branching structure over time as they deform, grow, and interact with their environment. Our key contribution is the representation of tree-like 3D shapes using Square Root Velocity Function Trees (SRVFT). By solving the spatial registration in the SRVFT space, which is equipped with an L2 metric, 4D tree-shaped structures become time-parameterized trajectories in this space. This reduces the problem of modeling and analyzing 4D tree-like shapes to that of modeling and analyzing elastic trajectories in the SRVFT space, where elasticity refers to time warping. In this paper, we propose a novel mathematical representation of the shape space of such trajectories, a Riemannian metric on that space, and computational tools for fast and accurate spatiotemporal registration and geodesics computation between 4D tree-shaped structures. Leveraging these building blocks, we develop a full framework for modelling the spatiotemporal variability using statistical models and generating novel 4D tree-like structures from a set of exemplars. We demonstrate and validate the proposed framework using real 4D plant data.

cs.CV↗

arXiv2023

Rescuing referral failures during automated diagnosis of domain-shifted medical images

The success of deep learning models deployed in the real world depends critically on their ability to generalize well across diverse data domains. Here, we address a fundamental challenge with selective classification during automated diagnosis with domain-shifted medical images. In this scenario, models must learn to avoid making predictions when label confidence is low, especially when tested with samples far removed from the training set (covariate shift). Such uncertain cases are typically referred to the clinician for further analysis and evaluation. Yet, we show that even state-of-the-art domain generalization approaches fail severely during referral when tested on medical images acquired from a different demographic or using a different technology. We examine two benchmark diagnostic medical imaging datasets exhibiting strong covariate shifts: i) diabetic retinopathy prediction with retinal fundus images and ii) multilabel disease prediction with chest X-ray images. We show that predictive uncertainty estimates do not generalize well under covariate shifts leading to non-monotonic referral curves, and severe drops in performance (up to 50%) at high referral rates (>70%). We evaluate novel combinations of robust generalization and post hoc referral approaches, that rescue these failures and achieve significant performance improvements, typically >10%, over baseline methods. Our study identifies a critical challenge with referral in domain-shifted medical images and finds key applications in reliable, automated disease diagnosis.

cs.CV↗

arXiv2023

A Wasserstein-type Distance for Gaussian Mixtures on Vector Bundles with Applications to Shape Analysis

This paper uses sample data to study the problem of comparing populations on finite-dimensional parallelizable Riemannian manifolds and more general trivial vector bundles. Utilizing triviality, our framework represents populations as mixtures of Gaussians on vector bundles and estimates the population parameters using a mode-based clustering algorithm. We derive a Wasserstein-type metric between Gaussian mixtures, adapted to the manifold geometry, in order to compare estimated distributions. Our contributions include an identifiability result for Gaussian mixtures on manifold domains and a convenient characterization of optimal couplings of Gaussian mixtures under the derived metric. We demonstrate these tools on some example domains, including the pre-shape space of planar closed curves, with applications to the shape space of triangles and populations of nanoparticles. In the nanoparticle application, we consider a sequence of populations of particle shapes arising from a manufacturing process, and utilize the Wasserstein-type distance to perform change-point detection.

stat.ME↗