arXiv subjects

Shadab Ahamed

Publications and source records attributed to Shadab Ahamed.

17 recordsLinked to original sources

arXiv2026

Preconditioned Flow Matching

Flow matching (FM) learns vector fields by regressing stochastic velocity targets along intermediate distributions $p_t$. We identify a geometric optimization bottleneck in this regression problem: when the covariance $\Sigma_t$ of $p_t$ is ill-conditioned, gradient-based training rapidly fits high-variance directions while making slow progress along low-variance ones. In an exactly solvable Gaussian setting, we prove that the excess risk is weighted by $\Sigma_t$, and that both gradient descent and stochastic gradient descent inherit condition-number-dependent convergence. We then extend the analysis to Gaussian mixtures, showing that multimodality does not average away this effect; instead, the slowest and worst-conditioned component can control optimization. Motivated by this analysis, we propose \emph{preconditioned flow matching}, a precondition-then-match framework that transforms the target distribution into a more isotropic representation, trains the main flow in the transformed space, and maps generated samples back through the inverse transformation. We show theoretically that preconditioning reshapes the intermediate FM path and improves its conditioning. Across controlled Gaussian and Gaussian-mixture experiments, latent MNIST and other high resolution image datasets up to $512{\times}512$ resolution, preconditioning improves path-conditioning diagnostics, low-eigenvalue recovery, FID, MMD, precision, and recall. Compute-matched baselines and preconditioner-quality ablations further show that the gains are not explained merely by additional preconditioner parameters, but by improved geometry of the downstream flow matching problem.

cs.LG↗

arXiv2025

Comprehensive Evaluation of Quantitative Measurements from Automated Deep Segmentations of PSMA PET/CT Images

This study performs a comprehensive evaluation of quantitative measurements as extracted from automated deep-learning-based segmentation methods, beyond traditional Dice Similarity Coefficient assessments, focusing on six quantitative metrics, namely SUVmax, SUVmean, total lesion activity (TLA), tumor volume (TMTV), lesion count, and lesion spread. We analyzed 380 prostate-specific membrane antigen (PSMA) targeted [18F]DCFPyL PET/CT scans of patients with biochemical recurrence of prostate cancer, training deep neural networks, U-Net, Attention U-Net and SegResNet with four loss functions: Dice Loss, Dice Cross Entropy, Dice Focal Loss, and our proposed L1 weighted Dice Focal Loss (L1DFL). Evaluations indicated that Attention U-Net paired with L1DFL achieved the strongest correlation with the ground truth (concordance correlation = 0.90-0.99 for SUVmax and TLA), whereas models employing the Dice Loss and the other two compound losses, particularly with SegResNet, underperformed. Equivalence testing (TOST, alpha = 0.05, Delta = 20%) confirmed high performance for SUV metrics, lesion count and TLA, with L1DFL yielding the best performance. By contrast, tumor volume and lesion spread exhibited greater variability. Bland-Altman, Coverage Probability, and Total Deviation Index analyses further highlighted that our proposed L1DFL minimizes variability in quantification of the ground truth clinical measures. The code is publicly available at: https://github.com/ObedDzik/pca\_segment.git.

eess.IV↗

arXiv2025

Iterative Flow Matching: Path Correction and Gradual Refinement for Enhanced Generative Modeling

Generative models for image generation are now commonly used for a wide variety of applications, ranging from guided image generation for entertainment to solving inverse problems. Nonetheless, training a generator is a non-trivial feat that requires fine-tuning and can lead to so-called hallucinations, that is, the generation of images that are unrealistic. In this work, we explore image generation using flow matching. We explain and demonstrate why flow matching can generate hallucinations, and propose an iterative process to improve the generation process. Our iterative process can be integrated into virtually any generative modeling technique, thereby enhancing the performance and robustness of image synthesis systems.

cs.LG↗

arXiv2025

Inversion of Magnetic Data using Learned Dictionaries and Scale Space

Magnetic data inversion is an important tool in geophysics, used to infer subsurface magnetic susceptibility distributions from surface magnetic field measurements. This inverse problem is inherently ill-posed, characterized by non-unique solutions, depth ambiguity, and sensitivity to noise. Traditional inversion approaches rely on predefined regularization techniques to stabilize solutions, limiting their adaptability to complex or diverse geological scenarios. In this study, we propose an approach that integrates variable dictionary learning and scale-space methods to address these challenges. Our method employs learned dictionaries, allowing for adaptive representation of complex subsurface features that are difficult to capture with predefined bases. Additionally, we extend classical variational inversion by incorporating multi-scale representations through a scale-space framework, enabling the progressive introduction of structural detail while mitigating overfitting. We implement both fixed and dynamic dictionary learning techniques, with the latter introducing iteration-dependent dictionaries for enhanced flexibility. Using a synthetic dataset to simulate geological scenarios, we demonstrate significant improvements in reconstruction accuracy and robustness compared to conventional variational and dictionary-based methods. Our results highlight the potential of learned dictionaries, especially when coupled with scale-space dynamics, to improve model recovery and noise handling. These findings underscore the promise of our data-driven approach for advance magnetic data inversion and its applications in geophysical exploration, environmental assessment, and mineral prospecting. The code is publicly available at: https://github.com/ahxmeds/magnetic-inversion-dictionary.git.

physics.geo-ph↗

arXiv2025

Adaptive Voxel-Weighted Loss Using L1 Norms in Deep Neural Networks for Detection and Segmentation of Prostate Cancer Lesions in PET/CT Images

Accurate automated detection of recurrent prostate cancer in PSMA PET/CT scans is challenging due to heterogeneous lesion size, activity, anatomical location, and intra- and inter-class imbalances. Conventional deep learning loss functions often produce suboptimal optimization, as gradients are dominated by easy background voxels or extreme outliers. To address this, we propose L1-weighted Dice Focal Loss (L1DFL), which harmonizes gradient magnitudes across voxels using L1 norms to adaptively weight samples based on classification difficulty, resulting in well-calibrated predictions with a bimodal separation between correct and incorrect predictions. We trained three 3D convolutional networks (Attention U-Net, SegResNet, U-Net) and a transformer-based UNETR model on 380 PSMA PET/CT scans. PET and CT volumes were concatenated as input to the models. We also fine-tuned SAM-Med3D foundation model with the different loss functions and evaluated their performance. Across architectures, L1DFL consistently outperformed Dice Loss (DL) and Dice Focal Loss (DFL), achieving at least a 4% improvement in Dice Similarity Coefficient. F1 scores were higher by 6% and 26% compared to DL and DFL, respectively. While DFL produced more false positives and DL struggled with larger lesions, L1DFL achieved balanced detection, minimizing false detections while maintaining high true positive rates. The gradient harmonization mechanism ensured robustness across varying lesion sizes, volumes, and spread. The code is publicly available at: https://github.com/ObedDzik/pca_segment.git.

eess.IV↗

arXiv2025

Multiscale Training of Convolutional Neural Networks

Training convolutional neural networks (CNNs) on high-resolution images is often bottlenecked by the cost of evaluating gradients of the loss on the finest spatial mesh. To address this, we propose Multiscale Gradient Estimation (MGE), a Multilevel Monte Carlo-inspired estimator that expresses the expected gradient on the finest mesh as a telescopic sum of gradients computed on progressively coarser meshes. By assigning larger batches to the cheaper coarse levels, MGE achieves the same variance as single-scale stochastic gradient estimation while reducing the number of fine mesh convolutions by a factor of 4 with each downsampling. We further embed MGE within a Full-Multiscale training algorithm that solves the learning problem on coarse meshes first and "hot-starts" the next finer level, cutting the required fine mesh iterations by an additional order of magnitude. Extensive experiments on image denoising, deblurring, inpainting and super-resolution tasks using UNet, ResNet and ESPCN backbones confirm the practical benefits: Full-Multiscale reduces the computation costs by 4-16x with no significant loss in performance. Together, MGE and Full-Multiscale offer a principled, architecture-agnostic route to accelerate CNN training on high-resolution data without sacrificing accuracy, and they can be combined with other variance-reduction or learning-rate schedules to further enhance scalability.

cs.LG↗

arXiv2024

DAWN-FM: Data-Aware and Noise-Informed Flow Matching for Solving Inverse Problems

Inverse problems, which involve estimating parameters from incomplete or noisy observations, arise in various fields such as medical imaging, geophysics, and signal processing. These problems are often ill-posed, requiring regularization techniques to stabilize the solution. In this work, we employ Flow Matching (FM), a generative framework that integrates a deterministic processes to map a simple reference distribution, such as a Gaussian, to the target distribution. Our method DAWN-FM: Data-AWare and Noise-Informed Flow Matching incorporates data and noise embedding, allowing the model to access representations about the measured data explicitly and also account for noise in the observations, making it particularly robust in scenarios where data is noisy or incomplete. By learning a time-dependent velocity field, FM not only provides accurate solutions but also enables uncertainty quantification by generating multiple plausible outcomes. Unlike pretrained diffusion models, which may struggle in highly ill-posed settings, our approach is trained specifically for each inverse problem and adapts to varying noise levels. We validate the effectiveness and robustness of our method through extensive numerical experiments on tasks such as image deblurring and tomography. The code is available at: https://github.com/ahxmeds/DAWN-FM.git.

eess.IV↗

arXiv2024

AutoPET Challenge III: Testing the Robustness of Generalized Dice Focal Loss trained 3D Residual UNet for FDG and PSMA Lesion Segmentation from Whole-Body PET/CT Images

Automated segmentation of cancerous lesions in PET/CT scans is a crucial first step in quantitative image analysis. However, training deep learning models for segmentation with high accuracy is particularly challenging due to the variations in lesion size, shape, and radiotracer uptake. These lesions can appear in different parts of the body, often near healthy organs that also exhibit considerable uptake, making the task even more complex. As a result, creating an effective segmentation model for routine PET/CT image analysis is challenging. In this study, we utilized a 3D Residual UNet model and employed the Generalized Dice Focal Loss function to train the model on the AutoPET Challenge 2024 dataset. We conducted a 5-fold cross-validation and used an average ensembling technique using the models from the five folds. In the preliminary test phase for Task-1, the average ensemble achieved a mean Dice Similarity Coefficient (DSC) of 0.6687, mean false negative volume (FNV) of 10.9522 ml and mean false positive volume (FPV) 2.9684 ml. More details about the algorithm can be found on our GitHub repository: https://github.com/ahxmeds/autosegnet2024.git. The training code has been shared via the repository: https://github.com/ahxmeds/autopet2024.git.

cs.CV↗

arXiv2024

Thyroidiomics: An Automated Pipeline for Segmentation and Classification of Thyroid Pathologies from Scintigraphy Images

The objective of this study was to develop an automated pipeline that enhances thyroid disease classification using thyroid scintigraphy images, aiming to decrease assessment time and increase diagnostic accuracy. Anterior thyroid scintigraphy images from 2,643 patients were collected and categorized into diffuse goiter (DG), multinodal goiter (MNG), and thyroiditis (TH) based on clinical reports, and then segmented by an expert. A ResUNet model was trained to perform auto-segmentation. Radiomic features were extracted from both physician (scenario 1) and ResUNet segmentations (scenario 2), followed by omitting highly correlated features using Spearman's correlation, and feature selection using Recursive Feature Elimination (RFE) with XGBoost as the core. All models were trained under leave-one-center-out cross-validation (LOCOCV) scheme, where nine instances of algorithms were iteratively trained and validated on data from eight centers and tested on the ninth for both scenarios separately. Segmentation performance was assessed using the Dice similarity coefficient (DSC), while classification performance was assessed using metrics, such as precision, recall, F1-score, accuracy, area under the Receiver Operating Characteristic (ROC AUC), and area under the precision-recall curve (PRC AUC). ResUNet achieved DSC values of 0.84$\pm$0.03, 0.71$\pm$0.06, and 0.86$\pm$0.02 for MNG, TH, and DG, respectively. Classification in scenario 1 achieved an accuracy of 0.76$\pm$0.04 and a ROC AUC of 0.92$\pm$0.02 while in scenario 2, classification yielded an accuracy of 0.74$\pm$0.05 and a ROC AUC of 0.90$\pm$0.02. The automated pipeline demonstrated comparable performance to physician segmentations on several classification metrics across different classes, effectively reducing assessment time while maintaining high diagnostic accuracy. Code available at: https://github.com/ahxmeds/thyroidiomics.git.

eess.IV↗

arXiv2024

IgCONDA-PET: Weakly-Supervised PET Anomaly Detection using Implicitly-Guided Attention-Conditional Counterfactual Diffusion Modeling -- a Multi-Center, Multi-Cancer, and Multi-Tracer Study

Minimizing the need for pixel-level annotated data to train PET lesion detection and segmentation networks is highly desired and can be transformative, given time and cost constraints associated with expert annotations. Current unsupervised or weakly-supervised anomaly detection methods rely on autoencoder or generative adversarial networks (GANs) trained only on healthy data. While these approaches reduce annotation dependency, GAN-based methods are notably more challenging to train than non-GAN alternatives (such as autoencoders) due to issues such as the simultaneous optimization of two competing networks, mode collapse, and training instability. In this paper, we present the weakly-supervised $\textbf{I}$mplicitly-$\textbf{g}$uided $\textbf{CO}$u$\textbf{N}$terfactual diffusion model for $\textbf{D}$etecting $\textbf{A}$nomalies in $\textbf{PET}$ images (IgCONDA-PET). The solution is developed and validated using PET scans from six retrospective cohorts consisting of a total of 2652 cases (multi-cancer, multi-tracer) containing both local and public datasets (spanning multiple centers). The training is conditioned on image class labels (healthy vs. unhealthy) via attention modules, and we employ implicit diffusion guidance. We perform counterfactual generation which facilitates "unhealthy-to-healthy" domain translation by generating a synthetic, healthy version of an unhealthy input image, enabling the detection of anomalies through the calculated differences. The performance of our method was compared against several other deep learning based weakly-supervised or unsupervised methods as well as traditional methods like 41% SUV$_\text{max}$ thresholding. We also highlight the importance of incorporating attention modules in our network for the detection of small anomalies. The code is publicly available at: https://github.com/ahxmeds/IgCONDA-PET.git.

eess.IV↗

arXiv2024

A cascaded deep network for automated tumor detection and segmentation in clinical PET imaging of diffuse large B-cell lymphoma

Accurate detection and segmentation of diffuse large B-cell lymphoma (DLBCL) from PET images has important implications for estimation of total metabolic tumor volume, radiomics analysis, surgical intervention and radiotherapy. Manual segmentation of tumors in whole-body PET images is time-consuming, labor-intensive and operator-dependent. In this work, we develop and validate a fast and efficient three-step cascaded deep learning model for automated detection and segmentation of DLBCL tumors from PET images. As compared to a single end-to-end network for segmentation of tumors in whole-body PET images, our three-step model is more effective (improves 3D Dice score from 58.9% to 78.1%) since each of its specialized modules, namely the slice classifier, the tumor detector and the tumor segmentor, can be trained independently to a high degree of skill to carry out a specific task, rather than a single network with suboptimal performance on overall segmentation.

eess.IV↗

arXiv2024

A slice classification neural network for automated classification of axial PET/CT slices from a multi-centric lymphoma dataset

Automated slice classification is clinically relevant since it can be incorporated into medical image segmentation workflows as a preprocessing step that would flag slices with a higher probability of containing tumors, thereby directing physicians attention to the important slices. In this work, we train a ResNet-18 network to classify axial slices of lymphoma PET/CT images (collected from two institutions) depending on whether the slice intercepted a tumor (positive slice) in the 3D image or if the slice did not (negative slice). Various instances of the network were trained on 2D axial datasets created in different ways: (i) slice-level split and (ii) patient-level split; inputs of different types were used: (i) only PET slices and (ii) concatenated PET and CT slices; and different training strategies were employed: (i) center-aware (CAW) and (ii) center-agnostic (CAG). Model performances were compared using the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC), and various binary classification metrics. We observe and describe a performance overestimation in the case of slice-level split as compared to the patient-level split training. The model trained using patient-level split data with the network input containing only PET slices in the CAG training regime was the best performing/generalizing model on a majority of metrics. Our models were additionally more closely compared using the sensitivity metric on the positive slices from their respective test sets.

eess.IV↗

arXiv2023

Comprehensive framework for evaluation of deep neural networks in detection and quantification of lymphoma from PET/CT images: clinical insights, pitfalls, and observer agreement analyses

This study addresses critical gaps in automated lymphoma segmentation from PET/CT images, focusing on issues often overlooked in existing literature. While deep learning has been applied for lymphoma lesion segmentation, few studies incorporate out-of-distribution testing, raising concerns about model generalizability across diverse imaging conditions and patient populations. We highlight the need to compare model performance with expert human annotators, including intra- and inter-observer variability, to understand task difficulty better. Most approaches focus on overall segmentation accuracy but overlook lesion-specific measures important for precise lesion detection and disease quantification. To address these gaps, we propose a clinically relevant framework for evaluating deep segmentation networks. Using this lesion measure-specific evaluation, we assess the performance of four deep networks (ResUNet, SegResNet, DynUNet, and SwinUNETR) across 611 cases from multi-institutional datasets, covering various lymphoma subtypes and lesion characteristics. Beyond standard metrics like the Dice similarity coefficient, we evaluate clinical lesion measures and their prediction errors. We also introduce detection criteria for lesion localization and propose a new detection Criterion 3 based on metabolic characteristics. We show that networks perform better on large, intense lesions with higher metabolic activity. Finally, we compare network performance to physicians via intra- and inter-observer variability analyses, demonstrating that network errors closely resemble those made by experts, i.e., the small and faint lesions remain challenging for both humans and networks. This study aims to improve automated lesion segmentation's clinical relevance, supporting better treatment decisions for lymphoma patients. The code is available at: https://github.com/microsoft/lymphoma-segmentation-dnn.

cs.CV↗

arXiv2023

Generalized Dice Focal Loss trained 3D Residual UNet for Automated Lesion Segmentation in Whole-Body FDG PET/CT Images

Automated segmentation of cancerous lesions in PET/CT images is a vital initial task for quantitative analysis. However, it is often challenging to train deep learning-based segmentation methods to high degree of accuracy due to the diversity of lesions in terms of their shapes, sizes, and radiotracer uptake levels. These lesions can be found in various parts of the body, often close to healthy organs that also show significant uptake. Consequently, developing a comprehensive PET/CT lesion segmentation model is a demanding endeavor for routine quantitative image analysis. In this work, we train a 3D Residual UNet using Generalized Dice Focal Loss function on the AutoPET challenge 2023 training dataset. We develop our models in a 5-fold cross-validation setting and ensemble the five models via average and weighted-average ensembling. On the preliminary test phase, the average ensemble achieved a Dice similarity coefficient (DSC), false-positive volume (FPV) and false negative volume (FNV) of 0.5417, 0.8261 ml, and 0.2538 ml, respectively, while the weighted-average ensemble achieved 0.5417, 0.8186 ml, and 0.2538 ml, respectively. Our algorithm can be accessed via this link: https://github.com/ahxmeds/autosegnet.

eess.IV↗

arXiv2023

PyTomography: A Python Library for Medical Image Reconstruction

There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent literature, such as those that employ artificial intelligence. The purpose of this research was to create and evaluate a GPU-accelerated, open-source, and user-friendly image reconstruction library, designed to serve as a central platform for the development, validation, and deployment of various tomographic reconstruction algorithms. PyTomography was developed using Python and inherits the GPU-accelerated functionality of PyTorch and parallelproj for fast computations. Its flexible and modular design decouples system matrices, likelihoods, and reconstruction algorithms, simplifying the process of integrating new imaging modalities using various python tools. Example use cases demonstrate the software capabilities in parallel hole SPECT and listmode PET imaging. Overall, we have developed and publicly share PyTomography, a highly optimized and user-friendly software for medical image reconstruction, with a class hierarchy that fosters the development of novel imaging applications.

physics.med-ph↗

arXiv2022

Convolutional neural network with a hybrid loss function for fully automated segmentation of lymphoma lesions in FDG PET images

Segmentation of lymphoma lesions is challenging due to their varied sizes and locations in whole-body PET scans. This work presents a fully-automated segmentation technique using a multi-center dataset of diffuse large B-cell lymphoma (DLBCL) with heterogeneous characteristics. We utilized a dataset of [18F]FDG-PET scans (n=194) from two different imaging centers, including cases with primary mediastinal large B-cell lymphoma (PMBCL) (n=104). Automated brain and bladder removal approaches were utilized as preprocessing steps to tackle false positives caused by normal hypermetabolic uptake in these organs. Our segmentation model is a convolutional neural network (CNN) based on a 3D U-Net architecture that includes squeeze and excitation (SE) modules. Hybrid distribution, region, and boundary-based losses (Unified Focal and Mumford-Shah (MS)) were utilized that showed the best performance compared to other combinations (p<0.05). Cross-validation between different centers, DLBCL and PMBCL cases, and three random splits were applied on train/validation data. The ensemble of these six models achieved a Dice similarity coefficient (DSC) of 0.77 +- 0.08 and Hausdorff distance (HD) of 16.5 +-12.5. Our 3D U-net model with SE modules for segmentation with hybrid loss performed significantly better (p<0.05) as compared to the 3D U-Net (without SE modules) using the same loss function (Unified Focal and MS loss) (DSC= 0.64 +-0.21 and HD= 26.3 +- 18.7). Our model can facilitate a fully automated quantification pipeline in a multi-center context that opens the possibility for routine reporting of total metabolic tumor volume (TMTV) and other metrics shown useful for the management of lymphoma.

physics.med-ph↗

arXiv2017

Why rare-earth ferromagnets are so rare: insights from the p-wave Kondo model

Magnetic exchange in Kondo lattice systems is of the Ruderman-Kittel-Kasuya-Yosida type, whose sign depends on the Fermi wave vector, $k_F$ . In the simplest setting, for small $k_F$ , the interaction is predominately ferromagnetic, whereas it turns more antiferromagnetic with growing $k_F$. It is remarkable that even though $k_F$ varies vastly among the rare-earth systems, an overwhelming majority of lanthanide magnets are in fact antiferromagnets. To address this puzzle, we investigate the effects of a p-wave form factor for the Kondo coupling pertinent to nearly all rare-earth intermetallics. We show that this leads to interference effects which for small kF are destructive, greatly reducing the size of the RKKY interaction in the cases where ferromagnetism would otherwise be strongest. By contrast, for large $k_F$, constructive interference can enhance antiferromagnetic exchange. Based on this, we propose a new route for designing ferromagnetic rare-earth magnets.

cond-mat.str-el↗