Shadab Ahamed

Shadab Ahamed, Arman Rahmim

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.

Shadab Ahamed, Yixi Xu, Sara Kurkowska et al.

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.

Maziar Sabouri, Shadab Ahamed, Azin Asadzadeh et al.

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.

Shadab Ahamed

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.

Shadab Ahamed, Eshed Gal, Simon Ghyselincks et al.

Flow matching and score-based diffusion train vector fields under intermediate distributions $p_t$, whose geometry can strongly affect their optimization. We show that the covariance $Σ_t$ of $p_t$ governs optimization bias: when $Σ_t$ is ill-conditioned, and gradient-based training rapidly fits high-variance directions while systematically under-optimizing low-variance modes, leading to learning that plateaus at suboptimal weights. We formalize this effect in analytically tractable settings and propose reversible, label-conditional \emph{preconditioning} maps that reshape the geometry of $p_t$ by improving the conditioning of $Σ_t$ without altering the underlying generative model. Rather than accelerating early convergence, preconditioning primarily mitigates optimization stagnation by enabling continued progress along previously suppressed directions. Across MNIST latent flow matching, and additional high-resolution datasets, we empirically track conditioning diagnostics and distributional metrics and show that preconditioning consistently yields better-trained models by avoiding suboptimal plateaus.

Obed Korshie Dzikunu, Shadab Ahamed, Amirhossein Toosi et al.

This study proposes a new loss function for deep neural networks, L1-weighted Dice Focal Loss (L1DFL), that leverages L1 norms for adaptive weighting of voxels based on their classification difficulty, towards automated detection and segmentation of metastatic prostate cancer lesions in PET/CT scans. We obtained 380 PSMA [18-F] DCFPyL PET/CT scans of patients diagnosed with biochemical recurrence metastatic prostate cancer. We trained two 3D convolutional neural networks, Attention U-Net and SegResNet, and concatenated the PET and CT volumes channel-wise as input. The performance of our custom loss function was evaluated against the Dice and Dice Focal Loss functions. For clinical significance, we considered a detected region of interest (ROI) as a true positive if at least the voxel with the maximum standardized uptake value falls within the ROI. We assessed the models' performance based on the number of lesions in an image, tumour volume, activity, and extent of spread. The L1DFL outperformed the comparative loss functions by at least 13% on the test set. In addition, the F1 scores of the Dice Loss and the Dice Focal Loss were lower than that of L1DFL by at least 6% and 34%, respectively. The Dice Focal Loss yielded more false positives, whereas the Dice Loss was more sensitive to smaller volumes and struggled to segment larger lesions accurately. They also exhibited network-specific variations and yielded declines in segmentation accuracy with increased tumour spread. Our results demonstrate the potential of L1DFL to yield robust segmentation of metastatic prostate cancer lesions in PSMA PET/CT images. The results further highlight potential complexities arising from the variations in lesion characteristics that may influence automated prostate cancer tumour detection and segmentation. The code is publicly available at: https://github.com/ObedDzik/pca_segment.git.

Obed Korshie Dzikunu, Amirhossein Toosi, Shadab Ahamed et al.

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.

Shadab Ahamed, Simon Ghyselincks, Pablo Chang Huang Arias et al.

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.

Shadab Ahamed, Arman Rahmim

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.

Shadab Ahamed, Natalia Dubljevic, Ingrid Bloise et al.

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.

Shadab Ahamed, Niloufar Zakariaei, Eldad Haber et al.

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 4-16$\times$ 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.

Shadab Ahamed, Yixi Xu, Ingrid Bloise et al.

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.

Eldad Haber, Shadab Ahamed, Md. Shahriar Rahim Siddiqui et al.

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 $\textit{any}$ generative modeling technique, thereby enhancing the performance and robustness of image synthesis systems.

Shadab Ahamed, Eldad Haber

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 pre-trained 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.