arXiv subjects

Mohammad Yaqub

Publications and source records attributed to Mohammad Yaqub.

At least 55 records · Page 3Linked to original sources

arXiv2025

Decoupling Clinical and Class-Agnostic Features for Reliable Few-Shot Adaptation under Shift

Medical vision-language models (VLMs) offer promise for clinical decision support, yet their reliability under distribution shifts remains a major concern for safe deployment. These models often learn task-agnostic correlations due to variability in imaging protocols and free-text reports, limiting their generalizability and increasing the risk of failure in real-world settings. We propose DRiFt, a structured feature decoupling framework that explicitly separates clinically relevant signals from task-agnostic noise using parameter-efficient tuning (LoRA) and learnable prompt tokens. To enhance cross-modal alignment and reduce uncertainty, we curate high-quality, clinically grounded image-text pairs by generating captions for a diverse medical dataset. Our approach improves in-distribution performance by +11.4% Top-1 accuracy and +3.3% Macro-F1 over prior prompt-based methods, while maintaining strong robustness across unseen datasets. Ablation studies reveal that disentangling task-relevant features and careful alignment significantly enhance model generalization and reduce unpredictable behavior under domain shift. These insights contribute toward building safer, more trustworthy VLMs for clinical use. The code is available at https://github.com/rumaima/DRiFt.

cs.CV↗

arXiv2025

Predicting Brain Tumor Response to Therapy using a Hybrid Deep Learning and Radiomics Approach

Accurate evaluation of the response of glioblastoma to therapy is crucial for clinical decision-making and patient management. The Response Assessment in Neuro-Oncology (RANO) criteria provide a standardized framework to assess patients' clinical response, but their application can be complex and subject to observer variability. This paper presents an automated method for classifying the intervention response from longitudinal MRI scans, developed to predict tumor response during therapy as part of the BraTS 2025 challenge. We propose a novel hybrid framework that combines deep learning derived feature extraction and an extensive set of radiomics and clinically chosen features. Our approach utilizes a fine-tuned ResNet-18 model to extract features from 2D regions of interest across four MRI modalities. These deep features are then fused with a rich set of more than 4800 radiomic and clinically driven features, including 3D radiomics of tumor growth and shrinkage masks, volumetric changes relative to the nadir, and tumor centroid shift. Using the fused feature set, a CatBoost classifier achieves a mean ROC AUC of 0.81 and a Macro F1 score of 0.50 in the 4-class response prediction task (Complete Response, Partial Response, Stable Disease, Progressive Disease). Our results highlight that synergizing learned image representations with domain-targeted radiomic features provides a robust and effective solution for automated treatment response assessment in neuro-oncology.

cs.CV↗

arXiv2025

TPA: Temporal Prompt Alignment for Fetal Congenital Heart Defect Classification

Congenital heart defect (CHD) detection in ultrasound videos is hindered by image noise and probe positioning variability. While automated methods can reduce operator dependence, current machine learning approaches often neglect temporal information, limit themselves to binary classification, and do not account for prediction calibration. We propose Temporal Prompt Alignment (TPA), a method leveraging foundation image-text model and prompt-aware contrastive learning to classify fetal CHD on cardiac ultrasound videos. TPA extracts features from each frame of video subclips using an image encoder, aggregates them with a trainable temporal extractor to capture heart motion, and aligns the video representation with class-specific text prompts via a margin-hinge contrastive loss. To enhance calibration for clinical reliability, we introduce a Conditional Variational Autoencoder Style Modulation (CVAESM) module, which learns a latent style vector to modulate embeddings and quantifies classification uncertainty. Evaluated on a private dataset for CHD detection and on a large public dataset, EchoNet-Dynamic, for systolic dysfunction, TPA achieves state-of-the-art macro F1 scores of 85.40% for CHD diagnosis, while also reducing expected calibration error by 5.38% and adaptive ECE by 6.8%. On EchoNet-Dynamic's three-class task, it boosts macro F1 by 4.73% (from 53.89% to 58.62%). Temporal Prompt Alignment (TPA) is a framework for fetal congenital heart defect (CHD) classification in ultrasound videos that integrates temporal modeling, prompt-aware contrastive learning, and uncertainty quantification.

cs.CV↗

arXiv2025

SALT: Parameter-Efficient Fine-Tuning via Singular Value Adaptation with Low-Rank Transformation

The complex nature of medical image segmentation calls for models that are specifically designed to capture detailed, domain-specific features. Large foundation models offer considerable flexibility, yet the cost of fine-tuning these models remains a significant barrier. Parameter-Efficient Fine-Tuning (PEFT) methods, such as Low-Rank Adaptation (LoRA), efficiently update model weights with low-rank matrices but may suffer from underfitting when the chosen rank is insufficient to capture domain-specific nuances. Conversely, full-rank Singular Value Decomposition (SVD) based methods provide comprehensive updates by modifying all singular values, yet they often lack flexibility and exhibit variable performance across datasets. We propose SALT (Singular Value Adaptation with Low-Rank Transformation), a method that selectively adapts the most influential singular values using trainable scale and shift parameters while complementing this with a low-rank update for the remaining subspace. This hybrid approach harnesses the advantages of both LoRA and SVD, enabling effective adaptation without relying on increasing model size or depth. Evaluated on 5 challenging medical datasets, ranging from as few as 20 samples to 1000, SALT outperforms state-of-the-art PEFT (LoRA and SVD) by 2% to 5% in Dice with only 3.9% trainable parameters, demonstrating robust adaptation even in low-resource settings. The code for SALT is available at: https://github.com/BioMedIA-MBZUAI/SALT

eess.IV↗

arXiv2025

Meta-Learned Modality-Weighted Knowledge Distillation for Robust Multi-Modal Learning with Missing Data

In multi-modal learning, some modalities are more influential than others, and their absence can have a significant impact on classification/segmentation accuracy. Addressing this challenge, we propose a novel approach called Meta-learned Modality-weighted Knowledge Distillation (MetaKD), which enables multi-modal models to maintain high accuracy even when key modalities are missing. MetaKD adaptively estimates the importance weight of each modality through a meta-learning process. These learned importance weights guide a pairwise modality-weighted knowledge distillation process, allowing high-importance modalities to transfer knowledge to lower-importance ones, resulting in robust performance despite missing inputs. Unlike previous methods in the field, which are often task-specific and require significant modifications, our approach is designed to work in multiple tasks (e.g., segmentation and classification) with minimal adaptation. Experimental results on five prevalent datasets, including three Brain Tumor Segmentation datasets (BraTS2018, BraTS2019 and BraTS2020), the Alzheimer's Disease Neuroimaging Initiative (ADNI) classification dataset and the Audiovision-MNIST classification dataset, demonstrate the proposed model is able to outperform the compared models by a large margin. The code is available at https://github.com/billhhh/MetaKD.

cs.CV↗

arXiv2025

UNICON: UNIfied CONtinual Learning for Medical Foundational Models

Foundational models are trained on extensive datasets to capture the general trends of a domain. However, in medical imaging, the scarcity of data makes pre-training for every domain, modality, or task challenging. Continual learning offers a solution by fine-tuning a model sequentially on different domains or tasks, enabling it to integrate new knowledge without requiring large datasets for each training phase. In this paper, we propose UNIfied CONtinual Learning for Medical Foundational Models (UNICON), a framework that enables the seamless adaptation of foundation models to diverse domains, tasks, and modalities. Unlike conventional adaptation methods that treat these changes in isolation, UNICON provides a unified, perpetually expandable framework. Through careful integration, we show that foundation models can dynamically expand across imaging modalities, anatomical regions, and clinical objectives without catastrophic forgetting or task interference. Empirically, we validate our approach by adapting a chest CT foundation model initially trained for classification to a prognosis and segmentation task. Our results show improved performance across both additional tasks. Furthermore, we continually incorporated PET scans and achieved a 5\% improvement in Dice score compared to respective baselines. These findings establish that foundation models are not inherently constrained to their initial training scope but can evolve, paving the way toward generalist AI models for medical imaging.

eess.IV↗

arXiv2025

Deep Learning-Based Automated Segmentation of Uterine Myomas

Uterine fibroids (myomas) are the most common benign tumors of the female reproductive system, particularly among women of childbearing age. With a prevalence exceeding 70%, they pose a significant burden on female reproductive health. Clinical symptoms such as abnormal uterine bleeding, infertility, pelvic pain, and pressure-related discomfort play a crucial role in guiding treatment decisions, which are largely influenced by the size, number, and anatomical location of the fibroids. Magnetic Resonance Imaging (MRI) is a non-invasive and highly accurate imaging modality commonly used by clinicians for the diagnosis of uterine fibroids. Segmenting uterine fibroids requires a precise assessment of both the uterus and fibroids on MRI scans, including measurements of volume, shape, and spatial location. However, this process is labor intensive and time consuming and subjected to variability due to intra- and inter-expert differences at both pre- and post-treatment stages. As a result, there is a critical need for an accurate and automated segmentation method for uterine fibroids. In recent years, deep learning algorithms have shown re-markable improvements in medical image segmentation, outperforming traditional methods. These approaches offer the potential for fully automated segmentation. Several studies have explored the use of deep learning models to achieve automated segmentation of uterine fibroids. However, most of the previous work has been conducted using private datasets, which poses challenges for validation and comparison between studies. In this study, we leverage the publicly available Uterine Myoma MRI Dataset (UMD) to establish a baseline for automated segmentation of uterine fibroids, enabling standardized evaluation and facilitating future research in this domain.

eess.IV↗

arXiv2025

Advancing Fetal Ultrasound Image Quality Assessment in Low-Resource Settings

Accurate fetal biometric measurements, such as abdominal circumference, play a vital role in prenatal care. However, obtaining high-quality ultrasound images for these measurements heavily depends on the expertise of sonographers, posing a significant challenge in low-income countries due to the scarcity of trained personnel. To address this issue, we leverage FetalCLIP, a vision-language model pretrained on a curated dataset of over 210,000 fetal ultrasound image-caption pairs, to perform automated fetal ultrasound image quality assessment (IQA) on blind-sweep ultrasound data. We introduce FetalCLIP$_{CLS}$, an IQA model adapted from FetalCLIP using Low-Rank Adaptation (LoRA), and evaluate it on the ACOUSLIC-AI dataset against six CNN and Transformer baselines. FetalCLIP$_{CLS}$ achieves the highest F1 score of 0.757. Moreover, we show that an adapted segmentation model, when repurposed for classification, further improves performance, achieving an F1 score of 0.771. Our work demonstrates how parameter-efficient fine-tuning of fetal ultrasound foundation models can enable task-specific adaptations, advancing prenatal care in resource-limited settings. The experimental code is available at: https://github.com/donglihe-hub/FetalCLIP-IQA.

cs.CV↗

arXiv2025

Not Only Grey Matter: OmniBrain for Robust Multimodal Classification of Alzheimer's Disease

Alzheimer's disease affects over 55 million people worldwide and is projected to more than double by 2050, necessitating rapid, accurate, and scalable diagnostics. However, existing approaches are limited because they cannot achieve clinically acceptable accuracy, generalization across datasets, robustness to missing modalities, and explainability all at the same time. This inability to satisfy all these requirements simultaneously undermines their reliability in clinical settings. We propose OmniBrain, a multimodal framework that integrates brain MRI, radiomics, gene expression, and clinical data using a unified model with cross-attention and modality dropout. OmniBrain achieves $92.2 \pm 2.4\%$accuracy on the ANMerge dataset and generalizes to the MRI-only ADNI dataset with $70.4 \pm 2.7\%$ accuracy, outperforming unimodal and prior multimodal approaches. Explainability analyses highlight neuropathologically relevant brain regions and genes, enhancing clinical trust. OmniBrain offers a robust, interpretable, and practical solution for real-world Alzheimer's diagnosis.

cs.CV↗

arXiv2025

Forget-MI: Machine Unlearning for Forgetting Multimodal Information in Healthcare Settings

Privacy preservation in AI is crucial, especially in healthcare, where models rely on sensitive patient data. In the emerging field of machine unlearning, existing methodologies struggle to remove patient data from trained multimodal architectures, which are widely used in healthcare. We propose Forget-MI, a novel machine unlearning method for multimodal medical data, by establishing loss functions and perturbation techniques. Our approach unlearns unimodal and joint representations of the data requested to be forgotten while preserving knowledge from the remaining data and maintaining comparable performance to the original model. We evaluate our results using performance on the forget dataset, performance on the test dataset, and Membership Inference Attack (MIA), which measures the attacker's ability to distinguish the forget dataset from the training dataset. Our model outperforms the existing approaches that aim to reduce MIA and the performance on the forget dataset while keeping an equivalent performance on the test set. Specifically, our approach reduces MIA by 0.202 and decreases AUC and F1 scores on the forget set by 0.221 and 0.305, respectively. Additionally, our performance on the test set matches that of the retrained model, while allowing forgetting. Code is available at https://github.com/BioMedIA-MBZUAI/Forget-MI.git

cs.LG↗

arXiv2025

MOTOR: Multimodal Optimal Transport via Grounded Retrieval in Medical Visual Question Answering

Medical visual question answering (MedVQA) plays a vital role in clinical decision-making by providing contextually rich answers to image-based queries. Although vision-language models (VLMs) are widely used for this task, they often generate factually incorrect answers. Retrieval-augmented generation addresses this challenge by providing information from external sources, but risks retrieving irrelevant context, which can degrade the reasoning capabilities of VLMs. Re-ranking retrievals, as introduced in existing approaches, enhances retrieval relevance by focusing on query-text alignment. However, these approaches neglect the visual or multimodal context, which is particularly crucial for medical diagnosis. We propose MOTOR, a novel multimodal retrieval and re-ranking approach that leverages grounded captions and optimal transport. It captures the underlying relationships between the query and the retrieved context based on textual and visual information. Consequently, our approach identifies more clinically relevant contexts to augment the VLM input. Empirical analysis and human expert evaluation demonstrate that MOTOR achieves higher accuracy on MedVQA datasets, outperforming state-of-the-art methods by an average of 6.45%. Code is available at https://github.com/BioMedIA-MBZUAI/MOTOR.

cs.CV↗

arXiv2025

DiMPLe -- Disentangled Multi-Modal Prompt Learning: Enhancing Out-Of-Distribution Alignment with Invariant and Spurious Feature Separation

We introduce DiMPLe (Disentangled Multi-Modal Prompt Learning), a novel approach to disentangle invariant and spurious features across vision and language modalities in multi-modal learning. Spurious correlations in visual data often hinder out-of-distribution (OOD) performance. Unlike prior methods focusing solely on image features, DiMPLe disentangles features within and across modalities while maintaining consistent alignment, enabling better generalization to novel classes and robustness to distribution shifts. Our method combines three key objectives: (1) mutual information minimization between invariant and spurious features, (2) spurious feature regularization, and (3) contrastive learning on invariant features. Extensive experiments demonstrate DiMPLe demonstrates superior performance compared to CoOp-OOD, when averaged across 11 diverse datasets, and achieves absolute gains of 15.27 in base class accuracy and 44.31 in novel class accuracy.

cs.CV↗

arXiv2025

Structurally Different Neural Network Blocks for the Segmentation of Atrial and Aortic Perivascular Adipose Tissue in Multi-centre CT Angiography Scans

Since the emergence of convolutional neural networks (CNNs) and, later, vision transformers (ViTs), deep learning architectures have predominantly relied on identical block types with varying hyperparameters. We propose a novel block alternation strategy to leverage the complementary strengths of different architectural designs, assembling structurally distinct components similar to Lego blocks. We introduce LegoNet, a deep learning framework that alternates CNN-based and SwinViT-based blocks to enhance feature learning for medical image segmentation. We investigate three variations of LegoNet and apply this concept to a previously unexplored clinical problem: the segmentation of the internal mammary artery (IMA), aorta, and perivascular adipose tissue (PVAT) from computed tomography angiography (CTA) scans. These PVAT regions have been shown to possess prognostic value in assessing cardiovascular risk and primary clinical outcomes. We evaluate LegoNet on large datasets, achieving superior performance to other leading architectures. Furthermore, we assess the model's generalizability on external testing cohorts, where an expert clinician corrects the model's segmentations, achieving DSC > 0.90 across various external, international, and public cohorts. To further validate the model's clinical reliability, we perform intra- and inter-observer variability analysis, demonstrating strong agreement with human annotations. The proposed methodology has significant implications for diagnostic cardiovascular management and early prognosis, offering a robust, automated solution for vascular and perivascular segmentation and risk assessment in clinical practice, paving the way for personalised medicine.

eess.IV↗

arXiv2025

On the Robustness of Medical Vision-Language Models: Are they Truly Generalizable?

Medical Vision-Language Models (MVLMs) have achieved par excellence generalization in medical image analysis, yet their performance under noisy, corrupted conditions remains largely untested. Clinical imaging is inherently susceptible to acquisition artifacts and noise; however, existing evaluations predominantly assess generally clean datasets, overlooking robustness -- i.e., the model's ability to perform under real-world distortions. To address this gap, we first introduce MediMeta-C, a corruption benchmark that systematically applies several perturbations across multiple medical imaging datasets. Combined with MedMNIST-C, this establishes a comprehensive robustness evaluation framework for MVLMs. We further propose RobustMedCLIP, a visual encoder adaptation of a pretrained MVLM that incorporates few-shot tuning to enhance resilience against corruptions. Through extensive experiments, we benchmark 5 major MVLMs across 5 medical imaging modalities, revealing that existing models exhibit severe degradation under corruption and struggle with domain-modality tradeoffs. Our findings highlight the necessity of diverse training and robust adaptation strategies, demonstrating that efficient low-rank adaptation when paired with few-shot tuning, improves robustness while preserving generalization across modalities.

cs.CV↗

arXiv2025

In-Model Merging for Enhancing the Robustness of Medical Imaging Classification Models

Model merging is an effective strategy to merge multiple models for enhancing model performances, and more efficient than ensemble learning as it will not introduce extra computation into inference. However, limited research explores if the merging process can occur within one model and enhance the model's robustness, which is particularly critical in the medical image domain. In the paper, we are the first to propose in-model merging (InMerge), a novel approach that enhances the model's robustness by selectively merging similar convolutional kernels in the deep layers of a single convolutional neural network (CNN) during the training process for classification. We also analytically reveal important characteristics that affect how in-model merging should be performed, serving as an insightful reference for the community. We demonstrate the feasibility and effectiveness of this technique for different CNN architectures on 4 prevalent datasets. The proposed InMerge-trained model surpasses the typically-trained model by a substantial margin. The code will be made public.

cs.CV↗

arXiv2025

MedNNS: Supernet-based Medical Task-Adaptive Neural Network Search

Deep learning (DL) has achieved remarkable progress in the field of medical imaging. However, adapting DL models to medical tasks remains a significant challenge, primarily due to two key factors: (1) architecture selection, as different tasks necessitate specialized model designs, and (2) weight initialization, which directly impacts the convergence speed and final performance of the models. Although transfer learning from ImageNet is a widely adopted strategy, its effectiveness is constrained by the substantial differences between natural and medical images. To address these challenges, we introduce Medical Neural Network Search (MedNNS), the first Neural Network Search framework for medical imaging applications. MedNNS jointly optimizes architecture selection and weight initialization by constructing a meta-space that encodes datasets and models based on how well they perform together. We build this space using a Supernetwork-based approach, expanding the model zoo size by 51x times over previous state-of-the-art (SOTA) methods. Moreover, we introduce rank loss and Fréchet Inception Distance (FID) loss into the construction of the space to capture inter-model and inter-dataset relationships, thereby achieving more accurate alignment in the meta-space. Experimental results across multiple datasets demonstrate that MedNNS significantly outperforms both ImageNet pre-trained DL models and SOTA Neural Architecture Search (NAS) methods, achieving an average accuracy improvement of 1.7% across datasets while converging substantially faster. The code and the processed meta-space is available at https://github.com/BioMedIA-MBZUAI/MedNNS.

cs.CV↗

arXiv2025

Efficient Parameter Adaptation for Multi-Modal Medical Image Segmentation and Prognosis

Cancer detection and prognosis relies heavily on medical imaging, particularly CT and PET scans. Deep Neural Networks (DNNs) have shown promise in tumor segmentation by fusing information from these modalities. However, a critical bottleneck exists: the dependency on CT-PET data concurrently for training and inference, posing a challenge due to the limited availability of PET scans. Hence, there is a clear need for a flexible and efficient framework that can be trained with the widely available CT scans and can be still adapted for PET scans when they become available. In this work, we propose a parameter-efficient multi-modal adaptation (PEMMA) framework for lightweight upgrading of a transformer-based segmentation model trained only on CT scans such that it can be efficiently adapted for use with PET scans when they become available. This framework is further extended to perform prognosis task maintaining the same efficient cross-modal fine-tuning approach. The proposed approach is tested with two well-known segementation backbones, namely UNETR and Swin UNETR. Our approach offers two main advantages. Firstly, we leverage the inherent modularity of the transformer architecture and perform low-rank adaptation (LoRA) as well as decomposed low-rank adaptation (DoRA) of the attention weights to achieve parameter-efficient adaptation. Secondly, by minimizing cross-modal entanglement, PEMMA allows updates using only one modality without causing catastrophic forgetting in the other. Our method achieves comparable performance to early fusion, but with only 8% of the trainable parameters, and demonstrates a significant +28% Dice score improvement on PET scans when trained with a single modality. Furthermore, in prognosis, our method improves the concordance index by +10% when adapting a CT-pretrained model to include PET scans, and by +23% when adapting for both PET and EHR data.

cs.CV↗

arXiv2025

MedMerge: Merging Models for Effective Transfer Learning to Medical Imaging Tasks

Transfer learning has become a powerful tool to initialize deep learning models to achieve faster convergence and higher performance. This is especially useful in the medical imaging analysis domain, where data scarcity limits possible performance gains for deep learning models. Some advancements have been made in boosting the transfer learning performance gain by merging models starting from the same initialization. However, in the medical imaging analysis domain, there is an opportunity to merge models starting from different initializations, thus combining the features learned from different tasks. In this work, we propose MedMerge, a method whereby the weights of different models can be merged, and their features can be effectively utilized to boost performance on a new task. With MedMerge, we learn kernel-level weights that can later be used to merge the models into a single model, even when starting from different initializations. Testing on various medical imaging analysis tasks, we show that our merged model can achieve significant performance gains, with up to 7% improvement on the F1 score. The code implementation of this work is available at github.com/BioMedIA-MBZUAI/MedMerge.

cs.CV↗