arXiv subjects

Mohammad Yaqub

Publications and source records attributed to Mohammad Yaqub.

At least 73 records · Page 4Linked to original sources

arXiv2025

FedSECA: Sign Election and Coordinate-wise Aggregation of Gradients for Byzantine Tolerant Federated Learning

One of the most common defense strategies against Byzantine clients in federated learning (FL) is to employ a robust aggregator mechanism that makes the training more resilient. While many existing Byzantine robust aggregators provide theoretical convergence guarantees and are empirically effective against certain categories of attacks, we observe that certain high-strength attacks can subvert the robust aggregator and collapse the training. To overcome this limitation, we propose a method called FedSECA for robust Sign Election and Coordinate-wise Aggregation of gradients in FL that is less susceptible to malicious updates by an omniscient attacker. The proposed method has two main components. The Concordance Ratio Induced Sign Election(CRISE) module determines the consensus direction (elected sign) for each individual parameter gradient through a weighted voting strategy. The client weights are assigned based on a novel metric called concordance ratio, which quantifies the degree of sign agreement between the client gradient updates. Based on the elected sign, a Robust Coordinate-wise Aggregation(RoCA) strategy is employed, where variance-reduced sparse gradients are aggregated only if they are in alignment with the corresponding elected sign. We compare our proposed FedSECA method against 10 robust aggregators under 7 Byzantine attacks on 3 datasets and architectures. The results show that existing robust aggregators fail for at least some attacks, while FedSECA exhibits better robustness. Code - https://github.com/JosephGeoBenjamin/FedSECA-ByzantineTolerance

cs.CV↗

arXiv2025

Can language-guided unsupervised adaptation improve medical image classification using unpaired images and texts?

In medical image classification, supervised learning is challenging due to the scarcity of labeled medical images. To address this, we leverage the visual-textual alignment within Vision-Language Models (VLMs) to enable unsupervised learning of a medical image classifier. In this work, we propose \underline{Med}ical \underline{Un}supervised \underline{A}daptation (\texttt{MedUnA}) of VLMs, where the LLM-generated descriptions for each class are encoded into text embeddings and matched with class labels via a cross-modal adapter. This adapter attaches to a visual encoder of \texttt{MedCLIP} and aligns the visual embeddings through unsupervised learning, driven by a contrastive entropy-based loss and prompt tuning. Thereby, improving performance in scenarios where textual information is more abundant than labeled images, particularly in the healthcare domain. Unlike traditional VLMs, \texttt{MedUnA} uses \textbf{unpaired images and text} for learning representations and enhances the potential of VLMs beyond traditional constraints. We evaluate the performance on three chest X-ray datasets and two multi-class datasets (diabetic retinopathy and skin lesions), showing significant accuracy gains over the zero-shot baseline. Our code is available at https://github.com/rumaima/meduna.

cs.CV↗

arXiv2025

RP-SAM2: Refining Point Prompts for Stable Surgical Instrument Segmentation

Accurate surgical instrument segmentation is essential in cataract surgery for tasks such as skill assessment and workflow optimization. However, limited annotated data makes it difficult to develop fully automatic models. Prompt-based methods like SAM2 offer flexibility yet remain highly sensitive to the point prompt placement, often leading to inconsistent segmentations. We address this issue by introducing RP-SAM2, which incorporates a novel shift block and a compound loss function to stabilize point prompts. Our approach reduces annotator reliance on precise point positioning while maintaining robust segmentation capabilities. Experiments on the Cataract1k dataset demonstrate that RP-SAM2 improves segmentation accuracy, with a 2% mDSC gain, a 21.36% reduction in mHD95, and decreased variance across random single-point prompt results compared to SAM2. Additionally, on the CaDIS dataset, pseudo masks generated by RP-SAM2 for fine-tuning SAM2's mask decoder outperformed those generated by SAM2. These results highlight RP-SAM2 as a practical, stable and reliable solution for semi-automatic instrument segmentation in data-constrained medical settings. The code is available at https://github.com/BioMedIA-MBZUAI/RP-SAM2.

q-bio.TO↗

arXiv2025

Segmentation-Guided CT Synthesis with Pixel-Wise Conformal Uncertainty Bounds

Accurate dose calculations in proton therapy rely on high-quality CT images. While planning CTs (pCTs) serve as a reference for dosimetric planning, Cone Beam CT (CBCT) is used throughout Adaptive Radiotherapy (ART) to generate sCTs for improved dose calculations. Despite its lower cost and reduced radiation exposure advantages, CBCT suffers from severe artefacts and poor image quality, making it unsuitable for precise dosimetry. Deep learning-based CBCT-to-CT translation has emerged as a promising approach. Still, existing methods often introduce anatomical inconsistencies and lack reliable uncertainty estimates, limiting their clinical adoption. To bridge this gap, we propose STF-RUE, a novel framework integrating two key components. First, STF, a segmentation-guided CBCT-to-CT translation method that enhances anatomical consistency by leveraging segmentation priors extracted from pCTs. Second, RUE, a conformal prediction method that augments predicted CTs with pixel-wise conformal prediction intervals, providing clinicians with robust reliability indicator. Comprehensive experiments using UNet++ and Fast-DDPM on two benchmark datasets demonstrate that STF-RUE significantly improves translation accuracy, as measured by a novel soft-tissue-focused metric designed for precise dose computation. Additionally, STF-RUE provides better-calibrated uncertainty sets for synthetic CT, reinforcing trust in synthetic CTs. By addressing both anatomical fidelity and uncertainty quantification, STF-RUE marks a crucial step toward safer and more effective adaptive proton therapy. Code is available at https://anonymous.4open.science/r/cbct2ct_translation-B2D9/.

cs.CV↗

arXiv2025

Automatic Quality Assessment of First Trimester Crown-Rump-Length Ultrasound Images

Fetal gestational age (GA) is vital clinical information that is estimated during pregnancy in order to assess fetal growth. This is usually performed by measuring the crown-rump-length (CRL) on an ultrasound image in the Dating scan which is then correlated with fetal age and growth trajectory. A major issue when performing the CRL measurement is ensuring that the image is acquired at the correct view, otherwise it could be misleading. Although clinical guidelines specify the criteria for the correct CRL view, sonographers may not regularly adhere to such rules. In this paper, we propose a new deep learning-based solution that is able to verify the adherence of a CRL image to clinical guidelines in order to assess image quality and facilitate accurate estimation of GA. We first segment out important fetal structures then use the localized structures to perform a clinically-guided mapping that verifies the adherence of criteria. The segmentation method combines the benefits of Convolutional Neural Network (CNN) and the Vision Transformer (ViT) to segment fetal structures in ultrasound images and localize important fetal landmarks. For segmentation purposes, we compare our proposed work with UNet and show that our CNN/ViT-based method outperforms an optimized version of UNet. Furthermore, we compare the output of the mapping with classification CNNs when assessing the clinical criteria and the overall acceptability of CRL images. We show that the proposed mapping is not only explainable but also more accurate than the best performing classification CNNs.

cs.CV↗

arXiv2025

Breaking Down the Hierarchy: A New Approach to Leukemia Classification

The complexities inherent to leukemia, multifaceted cancer affecting white blood cells, pose considerable diagnostic and treatment challenges, primarily due to reliance on laborious morphological analyses and expert judgment that are susceptible to errors. Addressing these challenges, this study presents a refined, comprehensive strategy leveraging advanced deep-learning techniques for the classification of leukemia subtypes. We commence by developing a hierarchical label taxonomy, paving the way for differentiating between various subtypes of leukemia. The research further introduces a novel hierarchical approach inspired by clinical procedures capable of accurately classifying diverse types of leukemia alongside reactive and healthy cells. An integral part of this study involves a meticulous examination of the performance of Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) as classifiers. The proposed method exhibits an impressive success rate, achieving approximately 90\% accuracy across all leukemia subtypes, as substantiated by our experimental results. A visual representation of the experimental findings is provided to enhance the model's explainability and aid in understanding the classification process.

cs.CV↗

arXiv2025

Learning Confident Classifiers in the Presence of Label Noise

The success of Deep Neural Network (DNN) models significantly depends on the quality of provided annotations. In medical image segmentation, for example, having multiple expert annotations for each data point is common to minimize subjective annotation bias. Then, the goal of estimation is to filter out the label noise and recover the ground-truth masks, which are not explicitly given. This paper proposes a probabilistic model for noisy observations that allows us to build a confident classification and segmentation models. To accomplish it, we explicitly model label noise and introduce a new information-based regularization that pushes the network to recover the ground-truth labels. In addition, for segmentation task we adjust the loss function by prioritizing learning in high-confidence regions where all the annotators agree on labeling. We evaluate the proposed method on a series of classification tasks such as noisy versions of MNIST, CIFAR-10, Fashion-MNIST datasets as well as CIFAR-10N, which is real-world dataset with noisy human annotations. Additionally, for segmentation task, we consider several medical imaging datasets, such as, LIDC and RIGA that reflect real-world inter-variability among multiple annotators. Our experiments show that our algorithm outperforms state-of-the-art solutions for the considered classification and segmentation problems.

cs.CV↗

arXiv2025

Noise is an Efficient Learner for Zero-Shot Vision-Language Models

Recently, test-time adaptation has garnered attention as a method for tuning models without labeled data. The conventional modus operandi for adapting pre-trained vision-language models (VLMs) during test-time primarily focuses on tuning learnable prompts; however, this approach overlooks potential distribution shifts in the visual representations themselves. In this work, we address this limitation by introducing Test-Time Noise Tuning (TNT), a novel method for handling unpredictable shifts in the visual space. TNT leverages, for the first time, a noise adaptation strategy that optimizes learnable noise directly in the visual input space, enabling adaptive feature learning from a single test sample. We further introduce a novel approach for inter-view representation alignment by explicitly enforcing coherence in embedding distances, ensuring consistent feature representations across views. Combined with scaled logits and confident view selection at inference, TNT substantially enhances VLM generalization and calibration, achieving average gains of +7.38% on natural distributions benchmark and +0.80% on cross-dataset evaluations over zero-shot CLIP. These improvements lay a strong foundation for adaptive out-of-distribution handling.

cs.CV↗

arXiv2025

PulmoFusion: Advancing Pulmonary Health with Efficient Multi-Modal Fusion

Traditional remote spirometry lacks the precision required for effective pulmonary monitoring. We present a novel, non-invasive approach using multimodal predictive models that integrate RGB or thermal video data with patient metadata. Our method leverages energy-efficient Spiking Neural Networks (SNNs) for the regression of Peak Expiratory Flow (PEF) and classification of Forced Expiratory Volume (FEV1) and Forced Vital Capacity (FVC), using lightweight CNNs to overcome SNN limitations in regression tasks. Multimodal data integration is improved with a Multi-Head Attention Layer, and we employ K-Fold validation and ensemble learning to boost robustness. Using thermal data, our SNN models achieve 92% accuracy on a breathing-cycle basis and 99.5% patient-wise. PEF regression models attain Relative RMSEs of 0.11 (thermal) and 0.26 (RGB), with an MAE of 4.52% for FEV1/FVC predictions, establishing state-of-the-art performance. Code and dataset can be found on https://github.com/ahmed-sharshar/RespiroDynamics.git

eess.IV↗

arXiv2025

MedPromptX: Grounded Multimodal Prompting for Chest X-ray Diagnosis

Chest X-ray images are commonly used for predicting acute and chronic cardiopulmonary conditions, but efforts to integrate them with structured clinical data face challenges due to incomplete electronic health records (EHR). This paper introduces MedPromptX, the first clinical decision support system that integrates multimodal large language models (MLLMs), few-shot prompting (FP) and visual grounding (VG) to combine imagery with EHR data for chest X-ray diagnosis. A pre-trained MLLM is utilized to complement the missing EHR information, providing a comprehensive understanding of patients' medical history. Additionally, FP reduces the necessity for extensive training of MLLMs while effectively tackling the issue of hallucination. Nevertheless, the process of determining the optimal number of few-shot examples and selecting high-quality candidates can be burdensome, yet it profoundly influences model performance. Hence, we propose a new technique that dynamically refines few-shot data for real-time adjustment to new patient scenarios. Moreover, VG narrows the search area in X-ray images, thereby enhancing the identification of abnormalities. We also release MedPromptX-VQA, a new in-context visual question answering dataset encompassing interleaved images and EHR data derived from MIMIC-IV and MIMIC-CXR-JPG databases. Results demonstrate the SOTA performance of MedPromptX, achieving an 11% improvement in F1-score compared to the baselines. Code and data are publicly available on https://github.com/BioMedIA-MBZUAI/MedPromptX.

cs.CV↗

arXiv2024

Optimizing Brain Tumor Segmentation with MedNeXt: BraTS 2024 SSA and Pediatrics

Identifying key pathological features in brain MRIs is crucial for the long-term survival of glioma patients. However, manual segmentation is time-consuming, requiring expert intervention and is susceptible to human error. Therefore, significant research has been devoted to developing machine learning methods that can accurately segment tumors in 3D multimodal brain MRI scans. Despite their progress, state-of-the-art models are often limited by the data they are trained on, raising concerns about their reliability when applied to diverse populations that may introduce distribution shifts. Such shifts can stem from lower quality MRI technology (e.g., in sub-Saharan Africa) or variations in patient demographics (e.g., children). The BraTS-2024 challenge provides a platform to address these issues. This study presents our methodology for segmenting tumors in the BraTS-2024 SSA and Pediatric Tumors tasks using MedNeXt, comprehensive model ensembling, and thorough postprocessing. Our approach demonstrated strong performance on the unseen validation set, achieving an average Dice Similarity Coefficient (DSC) of 0.896 on the BraTS-2024 SSA dataset and an average DSC of 0.830 on the BraTS Pediatric Tumor dataset. Additionally, our method achieved an average Hausdorff Distance (HD95) of 14.682 on the BraTS-2024 SSA dataset and an average HD95 of 37.508 on the BraTS Pediatric dataset. Our GitHub repository can be accessed here: Project Repository : https://github.com/python-arch/BioMbz-Optimizing-Brain-Tumor-Segmentation-with-MedNeXt-BraTS-2024-SSA-and-Pediatrics

eess.IV↗

arXiv2024

MINDSETS: Multi-omics Integration with Neuroimaging for Dementia Subtyping and Effective Temporal Study

In the complex realm of cognitive disorders, Alzheimer's disease (AD) and vascular dementia (VaD) are the two most prevalent dementia types, presenting entangled symptoms yet requiring distinct treatment approaches. The crux of effective treatment in slowing neurodegeneration lies in early, accurate diagnosis, as this significantly assists doctors in determining the appropriate course of action. However, current diagnostic practices often delay VaD diagnosis, impeding timely intervention and adversely affecting patient prognosis. This paper presents an innovative multi-omics approach to accurately differentiate AD from VaD, achieving a diagnostic accuracy of 89.25%. The proposed method segments the longitudinal MRI scans and extracts advanced radiomics features. Subsequently, it synergistically integrates the radiomics features with an ensemble of clinical, cognitive, and genetic data to provide state-of-the-art diagnostic accuracy, setting a new benchmark in classification accuracy on a large public dataset. The paper's primary contribution is proposing a comprehensive methodology utilizing multi-omics data to provide a nuanced understanding of dementia subtypes. Additionally, the paper introduces an interpretable model to enhance clinical decision-making coupled with a novel model architecture for evaluating treatment efficacy. These advancements lay the groundwork for future work not only aimed at improving differential diagnosis but also mitigating and preventing the progression of dementia.

eess.IV↗

arXiv2024

ConDiSR: Contrastive Disentanglement and Style Regularization for Single Domain Generalization

Medical data often exhibits distribution shifts, which cause test-time performance degradation for deep learning models trained using standard supervised learning pipelines. This challenge is addressed in the field of Domain Generalization (DG) with the sub-field of Single Domain Generalization (SDG) being specifically interesting due to the privacy- or logistics-related issues often associated with medical data. Existing disentanglement-based SDG methods heavily rely on structural information embedded in segmentation masks, however classification labels do not provide such dense information. This work introduces a novel SDG method aimed at medical image classification that leverages channel-wise contrastive disentanglement. It is further enhanced with reconstruction-based style regularization to ensure extraction of distinct style and structure feature representations. We evaluate our method on the complex task of multicenter histopathology image classification, comparing it against state-of-the-art (SOTA) SDG baselines. Results demonstrate that our method surpasses the SOTA by a margin of 1% in average accuracy while also showing more stable performance. This study highlights the importance and challenges of exploring SDG frameworks in the context of the classification task. The code is publicly available at https://github.com/BioMedIA-MBZUAI/ConDiSR

cs.CV↗

arXiv2024

XReal: Realistic Anatomy and Pathology-Aware X-ray Generation via Controllable Diffusion Model

Large-scale generative models have demonstrated impressive capabilities in producing visually compelling images, with increasing applications in medical imaging. However, they continue to grapple with hallucination challenges and the generation of anatomically inaccurate outputs. These limitations are mainly due to the reliance on textual inputs and lack of spatial control over the generated images, hindering the potential usefulness of such models in real-life settings. In this work, we present XReal, a novel controllable diffusion model for generating realistic chest X-ray images through precise anatomy and pathology location control. Our lightweight method comprises an Anatomy Controller and a Pathology Controller to introduce spatial control over anatomy and pathology in a pre-trained Text-to-Image Diffusion Model, respectively, without fine-tuning the model. XReal outperforms state-of-the-art X-ray diffusion models in quantitative metrics and radiologists' ratings, showing significant gains in anatomy and pathology realism. Our model holds promise for advancing generative models in medical imaging, offering greater precision and adaptability while inviting further exploration in this evolving field. The code and pre-trained model weights are publicly available at https://github.com/BioMedIA-MBZUAI/XReal.

eess.IV↗

arXiv2024

Continual Learning in Medical Imaging: A Survey and Practical Analysis

Deep Learning has shown great success in reshaping medical imaging, yet it faces numerous challenges hindering widespread application. Issues like catastrophic forgetting and distribution shifts in the continuously evolving data stream increase the gap between research and applications. Continual Learning offers promise in addressing these hurdles by enabling the sequential acquisition of new knowledge without forgetting previous learnings in neural networks. In this survey, we comprehensively review the recent literature on continual learning in the medical domain, highlight recent trends, and point out the practical issues. Specifically, we survey the continual learning studies on classification, segmentation, detection, and other tasks in the medical domain. Furthermore, we develop a taxonomy for the reviewed studies, identify the challenges, and provide insights to overcome them. We also critically discuss the current state of continual learning in medical imaging, including identifying open problems and outlining promising future directions. We hope this survey will provide researchers with a useful overview of the developments in the field and will further increase interest in the community. To keep up with the fast-paced advancements in this field, we plan to routinely update the repository with the latest relevant papers at https://github.com/BioMedIA-MBZUAI/awesome-cl-in-medical .

cs.CV↗

arXiv2024

TransResNet: Integrating the Strengths of ViTs and CNNs for High Resolution Medical Image Segmentation via Feature Grafting

High-resolution images are preferable in medical imaging domain as they significantly improve the diagnostic capability of the underlying method. In particular, high resolution helps substantially in improving automatic image segmentation. However, most of the existing deep learning-based techniques for medical image segmentation are optimized for input images having small spatial dimensions and perform poorly on high-resolution images. To address this shortcoming, we propose a parallel-in-branch architecture called TransResNet, which incorporates Transformer and CNN in a parallel manner to extract features from multi-resolution images independently. In TransResNet, we introduce Cross Grafting Module (CGM), which generates the grafted features, enriched in both global semantic and low-level spatial details, by combining the feature maps from Transformer and CNN branches through fusion and self-attention mechanism. Moreover, we use these grafted features in the decoding process, increasing the information flow for better prediction of the segmentation mask. Extensive experiments on ten datasets demonstrate that TransResNet achieves either state-of-the-art or competitive results on several segmentation tasks, including skin lesion, retinal vessel, and polyp segmentation. The source code and pre-trained models are available at https://github.com/Sharifmhamza/TransResNet.

eess.IV↗

arXiv2024

Y-CA-Net: A Convolutional Attention Based Network for Volumetric Medical Image Segmentation

Recent attention-based volumetric segmentation (VS) methods have achieved remarkable performance in the medical domain which focuses on modeling long-range dependencies. However, for voxel-wise prediction tasks, discriminative local features are key components for the performance of the VS models which is missing in attention-based VS methods. Aiming at resolving this issue, we deliberately incorporate the convolutional encoder branch with transformer backbone to extract local and global features in a parallel manner and aggregate them in Cross Feature Mixer Module (CFMM) for better prediction of segmentation mask. Consequently, we observe that the derived model, Y-CT-Net, achieves competitive performance on multiple medical segmentation tasks. For example, on multi-organ segmentation, Y-CT-Net achieves an 82.4% dice score, surpassing well-tuned VS Transformer/CNN-like baselines UNETR/ResNet-3D by 2.9%/1.4%. With the success of Y-CT-Net, we extend this concept with hybrid attention models, that derived Y-CH-Net model, which brings a 3% improvement in terms of HD95 score for same segmentation task. The effectiveness of both models Y-CT-Net and Y-CH-Net verifies our hypothesis and motivates us to initiate the concept of Y-CA-Net, a versatile generic architecture based upon any two encoders and a decoder backbones, to fully exploit the complementary strengths of both convolution and attention mechanisms. Based on experimental results, we argue Y-CA-Net is a key player in achieving superior results for volumetric segmentation.

cs.CV↗

arXiv2024

SurvCORN: Survival Analysis with Conditional Ordinal Ranking Neural Network

Survival analysis plays a crucial role in estimating the likelihood of future events for patients by modeling time-to-event data, particularly in healthcare settings where predictions about outcomes such as death and disease recurrence are essential. However, this analysis poses challenges due to the presence of censored data, where time-to-event information is missing for certain data points. Yet, censored data can offer valuable insights, provided we appropriately incorporate the censoring time during modeling. In this paper, we propose SurvCORN, a novel method utilizing conditional ordinal ranking networks to predict survival curves directly. Additionally, we introduce SurvMAE, a metric designed to evaluate the accuracy of model predictions in estimating time-to-event outcomes. Through empirical evaluation on two real-world cancer datasets, we demonstrate SurvCORN's ability to maintain accurate ordering between patient outcomes while improving individual time-to-event predictions. Our contributions extend recent advancements in ordinal regression to survival analysis, offering valuable insights into accurate prognosis in healthcare settings.

cs.LG↗