arXiv subjects

Nivetha Jayakumar

Publications and source records attributed to Nivetha Jayakumar.

10 recordsLinked to original sources

arXiv2026

Geodesic-informed Generative Diffusion Model For Topology-preserved Image Video Generation

Generative diffusion models have emerged as a class of powerful techniques for various imaging applications, including but not limited to synthesis, reconstruction, and segmentation. Despite their success, current generative models pose two key limitations. First, they primarily rely on image intensity and texture information, with limited attention to underlying object geometry. As a result, they do not guarantee geometric or topological consistency during the generation process, which is a crucial requirement for high-stakes domains such as computational anatomy, biology, and robotics, where preserving object structure is critical. Second, existing models fail to explicitly learn or represent shape changes in the generative process. Such deformation dynamics remain occluded within network parameters; hence leaving the transformation process uninterpretable and physically uninformed. To address these challenges, we introduce IGG (Image Generation informed by Geodesic dynamics), a novel framework that integrates topology-preserving geodesic principles into the diffusion-based generative process. In contrast to conventional methods that operate in image intensity space, IGG learns and synthesizes diverse samples within geodesic deformation spaces, where geometric object changes are learned as smooth and invertible smooth mappings from a given template/source image. Our code is publicly available at https://github.com/nellie689/IGG.

cs.LG↗

arXiv2026

CalcSeg: Confidence-aware 3D Latent Context Curriculum Learning For Myocardial Scar Segmentation From Single-Stack LGE-CMRs

Myocardial scar segmentation from single-stack late gadolinium-enhanced cardiac magnetic resonance (LGE-CMR) imaging has been a longstanding and clinically important challenge, particularly in the presence of low tissue contrast, diffuse, and small scar regions. These challenges are further intensified by the limited availability of 3D spatial context. This paper presents CalcSeg, a Confidence-aware latent context curriculum learning framework that leverages fused 3D feature representations from single-stack 2D LGE-CMR images for robust scar segmentation. Specifically, we introduce a dynamic semi-supervised curriculum learning strategy that progressively expands training from easier to more challenging scar cases using a learned confidence-aware scoring function. Such a function integrates errors in the predicted scar maps with quantified epistemic uncertainty and scar burden estimation to automatically assess sample difficulty without requiring manual labels. To compensate for the limited spatial context in single-stack acquisitions, we then develop a latent slice-wise self-attention to capture inter-slice dependencies and infer 3D spatial representations from sparse 2D inputs. We evaluate CalcSeg on multi-center clinical LGE-CMR datasets and benchmark against existing scar segmentation networks. Experimental results show that CalcSeg consistently outperforms all competing methods, particularly with substantial improvements on clinically challenging cases. Our code is released on Github.

cs.CV↗

arXiv2026

4DLoG: Generative Modeling of Neurodegenerative Brain Anatomy with 4D Longitudinal Diffusion Model

Modeling and predicting neurodegenerative disease progression from medical images remains a major challenge in medical AI, with significant implications for early diagnosis, disease monitoring, and treatment planning. However, most longitudinal neuroimaging datasets are temporally sparse, with substantial gaps and missing follow-up scans for individual subjects. This makes it difficult to learn and accurately capture the continuous anatomical changes associated with disease progression at the level of individual subjects. To address this problem, we propose a novel model named 4DLoG, a full 4D (3DxT) Longitudinal Generative framework that effectively models and synthesizes follow-up brain anatomy over time, conditioned on available clinical and demographic variables. In contrast to previous approaches, our 4DLoG features two main contributions. First, it introduces a full 4D generative diffusion framework that jointly models spatial and temporal dependencies across complete longitudinal sequences through dedicated spatiotemporal attention, with robust spatial patch extraction and temporal alignment. Second, it explicitly learns the distribution of topology-preserving spatiotemporal deformations, which captures realistic geometric changes in brain structures over time. These new components enable a better generation of anatomically plausible future states from an imaging scan at any time point, providing greater flexibility for modeling individual longitudinal brain trajectories. We validate our model through both synthetic sequence generation and downstream longitudinal disease classification, as well as brain segmentation. Experiments on two large-scale longitudinal neuroimage datasets demonstrate that our method outperforms state-of-the-art baselines in generating anatomically accurate, temporally consistent, and clinically meaningful brain trajectories. Our code is available on Github

cs.CV↗

arXiv2026

Curriculum-Guided Myocardial Scar Segmentation for Ischemic and Non-ischemic Cardiomyopathy

Identification and quantification of myocardial scar is important for diagnosis and prognosis of cardiovascular diseases. However, reliable scar segmentation from Late Gadolinium Enhancement Cardiac Magnetic Resonance (LGE-CMR) images remains a challenge due to variations in contrast enhancement across patients, suboptimal imaging conditions such as post contrast washout, and inconsistencies in ground truth annotations on diffuse scars caused by inter observer variability. In this work, we propose a curriculum learning-based framework designed to improve segmentation performance under these challenging conditions. The method introduces a progressive training strategy that guides the model from high-confidence, clearly defined scar regions to low confidence or visually ambiguous samples with limited scar burden. By structuring the learning process in this manner, the network develops robustness to uncertain labels and subtle scar appearances that are often underrepresented in conventional training pipelines. Experimental results show that the proposed approach enhances segmentation accuracy and consistency, particularly for cases with minimal or diffuse scar, outperforming standard training baselines. This strategy provides a principled way to leverage imperfect data for improved myocardial scar quantification in clinical applications. Our code is publicly available on GitHub.

cs.CV↗

arXiv2025

IGG: Image Generation Informed by Geodesic Dynamics in Deformation Spaces

Generative models have recently gained increasing attention in image generation and editing tasks. However, they often lack a direct connection to object geometry, which is crucial in sensitive domains such as computational anatomy, biology, and robotics. This paper presents a novel framework for Image Generation informed by Geodesic dynamics (IGG) in deformation spaces. Our IGG model comprises two key components: (i) an efficient autoencoder that explicitly learns the geodesic path of image transformations in the latent space; and (ii) a latent geodesic diffusion model that captures the distribution of latent representations of geodesic deformations conditioned on text instructions. By leveraging geodesic paths, our method ensures smooth, topology-preserving, and interpretable deformations, capturing complex variations in image structures while maintaining geometric consistency. We validate the proposed IGG on plant growth data and brain magnetic resonance imaging (MRI). Experimental results show that IGG outperforms the state-of-the-art image generation/editing models with superior performance in generating realistic, high-quality images with preserved object topology and reduced artifacts. Our code is publicly available at https://github.com/nellie689/IGG.

cs.GR↗

arXiv2024

TPIE: Topology-Preserved Image Editing With Text Instructions

Preserving topological structures is important in real-world applications, particularly in sensitive domains such as healthcare and medicine, where the correctness of human anatomy is critical. However, most existing image editing models focus on manipulating intensity and texture features, often overlooking object geometry within images. To address this issue, this paper introduces a novel method, Topology-Preserved Image Editing with text instructions (TPIE), that for the first time ensures the topology and geometry remaining intact in edited images through text-guided generative diffusion models. More specifically, our method treats newly generated samples as deformable variations of a given input template, allowing for controllable and structure-preserving edits. Our proposed TPIE framework consists of two key modules: (i) an autoencoder-based registration network that learns latent representations of object transformations, parameterized by velocity fields, from pairwise training images; and (ii) a novel latent conditional geometric diffusion (LCDG) model efficiently capturing the data distribution of learned transformation features conditioned on custom-defined text instructions. We validate TPIE on a diverse set of 2D and 3D images and compare them with state-of-the-art image editing approaches. Experimental results show that our method outperforms other baselines in generating more realistic images with well-preserved topology. Our code will be made publicly available on Github.

cs.CV↗

arXiv2024

LaMoD: Latent Motion Diffusion Model For Myocardial Strain Generation

Motion and deformation analysis of cardiac magnetic resonance (CMR) imaging videos is crucial for assessing myocardial strain of patients with abnormal heart functions. Recent advances in deep learning-based image registration algorithms have shown promising results in predicting motion fields from routinely acquired CMR sequences. However, their accuracy often diminishes in regions with subtle appearance changes, with errors propagating over time. Advanced imaging techniques, such as displacement encoding with stimulated echoes (DENSE) CMR, offer highly accurate and reproducible motion data but require additional image acquisition, which poses challenges in busy clinical flows. In this paper, we introduce a novel Latent Motion Diffusion model (LaMoD) to predict highly accurate DENSE motions from standard CMR videos. More specifically, our method first employs an encoder from a pre-trained registration network that learns latent motion features (also considered as deformation-based shape features) from image sequences. Supervised by the ground-truth motion provided by DENSE, LaMoD then leverages a probabilistic latent diffusion model to reconstruct accurate motion from these extracted features. Experimental results demonstrate that our proposed method, LaMoD, significantly improves the accuracy of motion analysis in standard CMR images; hence improving myocardial strain analysis in clinical settings for cardiac patients. Our code is publicly available at https://github.com/jr-xing/LaMoD.

cs.CV↗

arXiv2024

An end-to-end deep learning pipeline to derive blood input with partial volume corrections for automated parametric brain PET mapping

Dynamic 2-[18F] fluoro-2-deoxy-D-glucose positron emission tomography (dFDG-PET) for human brain imaging has considerable clinical potential, yet its utilization remains limited. A key challenge in the quantitative analysis of dFDG-PET is characterizing a patient-specific blood input function, traditionally reliant on invasive arterial blood sampling. This research introduces a novel approach employing non-invasive deep learning model-based computations from the internal carotid arteries (ICA) with partial volume (PV) corrections, thereby eliminating the need for invasive arterial sampling. We present an end-to-end pipeline incorporating a 3D U-Net based ICA-net for ICA segmentation, alongside a Recurrent Neural Network (RNN) based MCIF-net for the derivation of a model-corrected blood input function (MCIF) with PV corrections. The developed 3D U-Net and RNN was trained and validated using a 5-fold cross-validation approach on 50 human brain FDG PET datasets. The ICA-net achieved an average Dice score of 82.18% and an Intersection over Union of 68.54% across all tested scans. Furthermore, the MCIF-net exhibited a minimal root mean squared error of 0.0052. The application of this pipeline to ground truth data for dFDG-PET brain scans resulted in the precise localization of seizure onset regions, which contributed to a successful clinical outcome, with the patient achieving a seizure-free state after treatment. These results underscore the efficacy of the ICA-net and MCIF-net deep learning pipeline in learning the ICA structure's distribution and automating MCIF computation with PV corrections. This advancement marks a significant leap in non-invasive neuroimaging.

eess.IV↗

arXiv2023

SADIR: Shape-Aware Diffusion Models for 3D Image Reconstruction

3D image reconstruction from a limited number of 2D images has been a long-standing challenge in computer vision and image analysis. While deep learning-based approaches have achieved impressive performance in this area, existing deep networks often fail to effectively utilize the shape structures of objects presented in images. As a result, the topology of reconstructed objects may not be well preserved, leading to the presence of artifacts such as discontinuities, holes, or mismatched connections between different parts. In this paper, we propose a shape-aware network based on diffusion models for 3D image reconstruction, named SADIR, to address these issues. In contrast to previous methods that primarily rely on spatial correlations of image intensities for 3D reconstruction, our model leverages shape priors learned from the training data to guide the reconstruction process. To achieve this, we develop a joint learning network that simultaneously learns a mean shape under deformation models. Each reconstructed image is then considered as a deformed variant of the mean shape. We validate our model, SADIR, on both brain and cardiac magnetic resonance images (MRIs). Experimental results show that our method outperforms the baselines with lower reconstruction error and better preservation of the shape structure of objects within the images.

cs.CV↗

arXiv2023

Multimodal Deep Learning to Differentiate Tumor Recurrence from Treatment Effect in Human Glioblastoma

Differentiating tumor progression (TP) from treatment-related necrosis (TN) is critical for clinical management decisions in glioblastoma (GBM). Dynamic FDG PET (dPET), an advance from traditional static FDG PET, may prove advantageous in clinical staging. dPET includes novel methods of a model-corrected blood input function that accounts for partial volume averaging to compute parametric maps that reveal kinetic information. In a preliminary study, a convolution neural network (CNN) was trained to predict classification accuracy between TP and TN for $35$ brain tumors from $26$ subjects in the PET-MR image space. 3D parametric PET Ki (from dPET), traditional static PET standardized uptake values (SUV), and also the brain tumor MR voxels formed the input for the CNN. The average test accuracy across all leave-one-out cross-validation iterations adjusting for class weights was $0.56$ using only the MR, $0.65$ using only the SUV, and $0.71$ using only the Ki voxels. Combining SUV and MR voxels increased the test accuracy to $0.62$. On the other hand, MR and Ki voxels increased the test accuracy to $0.74$. Thus, dPET features alone or with MR features in deep learning models would enhance prediction accuracy in differentiating TP vs TN in GBM.

eess.IV↗