arXiv subjects

Mohammad Yaqub

Publications and source records attributed to Mohammad Yaqub.

At least 37 records · Page 2Linked to original sources

arXiv2026

MMRINet: Efficient Mamba-Based Segmentation with Dual-Path Refinement for Low-Resource MRI Analysis

Automated brain tumor segmentation in multi-parametric MRI remains a critical yet underserved challenge in resource-constrained clinical settings, where deep 3D networks requiring high-end GPUs are not viable. This is particularly acute across sub-Saharan Africa (SSA), where low-field scanners, heterogeneous patient demographics, and severe data scarcity compound the difficulty of applying standard deep learning pipelines. We present MMRINet, a lightweight segmentation architecture purpose-built for these constraints. At its core, MMRINet replaces quadratic-complexity self-attention with linear-complexity Mamba state-space models, enabling efficient long-range volumetric context modeling without the computational overhead of Transformer-based approaches. We combine two lightweight refinement components:Dual-Path Feature Refinement (DPFR), which extracts complementary detail and contextual representations to improve feature diversity under limited data, and Progressive Feature Aggregation (PFA), which hierarchically fuses multi-scale decoder outputs for sharper segmentation boundaries. Evaluated on the BraTS-Lighthouse SSA 2025 challenge dataset, comprising 3D MRI scans from Nigerian clinical sites, MMRINet achieves an average Dice score of 0.752 and an average HD95 of 12.23 mm with only ~2.5M parameters, outperforming all evaluated baselines, including UNETR, Swin-UNETR, SegMamba, and SegResNet3D. These results indicate that strong validation-set segmentation performance can be achieved with substantially reduced computation, offering a practical step toward AI-assisted neuro-oncology in low-resource clinical environments. Our GitHub repository can be accessed here: BioMedIA-MBZUAI/MMRINet.

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arXiv2026

CardioBench: Do Echocardiography Foundation Models Generalize Beyond the Lab?

Foundation models are reshaping medical imaging, yet their application in echocardiography remains limited, hindered by a heavy reliance on private datasets that prevent reproducible comparison. Echocardiography poses unique challenges, including noisy acquisitions, high frame redundancy, and limited diverse public datasets. To address this, we introduce CardioBench, a comprehensive benchmark for echocardiography foundation models. Specifically, CardioBench unifies eight publicly available datasets into a standardized suite spanning four regression and five classification tasks, covering functional, structural, diagnostic, and view recognition endpoints. Leveraging this framework, we evaluate several leading foundation models, including cardiac-specific, biomedical, and general-purpose encoders, under consistent zero-shot, probing, and alignment protocols. Our analysis reveals that while general-purpose encoders transfer well and often close the gap with probing, they struggle significantly with fine-grained distinctions like view classification and subtle pathology recognition. Results indicate that models capturing temporal cardiac dynamics perform best on functional tasks, while retrieval-based approaches generalize more consistently across datasets. By releasing preprocessing, splits, and public evaluation pipelines, CardioBench establishes a reproducible reference point to guide the architectural design of future echocardiography and possibly other medical imaging foundation models.

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arXiv2026

Intuitive Surgical SurgToolLoc and SurgVU Challenges Results: 2022-2025

Robotic assisted (RA) surgery promises to transform surgical intervention. Intuitive Surgical is committed to fostering these changes and the machine learning models and algorithms that will enable them. With these goals in mind we have invited the surgical data science community to participate in a yearly competition hosted through the Medical Imaging Computing and Computer Assisted Interventions (MICCAI) conference. With varying changes from year to year, we have challenged the community to solve difficult machine learning problems in the context of advanced RA applications. Here we document the results of these challenges, focusing on surgical tool localization (SurgToolLoc) and surgical visual understanding (SurgVU). The publicly released dataset that accompanies these challenges is detailed in a separate paper arXiv:2501.09209 [1].

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arXiv2026

DARK: Diagonal-Anchored Repulsive Knowledge Distillation for Vision-Language Models under Extreme Compression

Compressing vision-language models for on-device deployment is increasingly important in clinical settings, but knowledge distillation (KD) degrades sharply when the teacher-student capacity gap spans an order of magnitude or more. We argue that, under such gaps, strict imitation of the teacher is a poor objective: much of the teacher's pairwise similarity structure reflects its own architectural biases rather than information a compact student can efficiently represent. We propose \textbf{Diagonal-Anchored Repulsive Knowledge Distillation (DARK)}, a contrastive KD framework that decomposes the distillation loss into a diagonal term (matched image-text pairs) and an off-diagonal term (non-target similarities). The diagonal term anchors matched-pair alignment throughout training; the off-diagonal term is annealed from positive to negative weighting, transitioning the student from imitating to \emph{repelling} the teacher's non-target similarity structure. We instantiate DARK by distilling FetalCLIP, a 427M-parameter fetal ultrasound vision-language model, into \textbf{MobileFetalCLIP}, a 75M-parameter student model with a $26\times$ smaller visual encoder, running in 1.6\,ms on an iPhone~16~Pro. The student matches or exceeds its teacher on three zero-shot benchmarks, including HC18 biometry validity (88.6\% vs.\ 83.5\%) and brain sub-plane F1 (0.784 vs.\ 0.702). Embedding-geometry and logit analyses show that DARK induces \emph{structured decorrelation}: the student preserves teacher-aligned per-image confidence while diverging from inherited inter-class confusion, suggesting that controlled repulsion can be more efficient than imitation under extreme compression.

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arXiv2026

Kalman Filter Enhanced GRPO for Reinforcement Learning-Based Language Model Reasoning

The advantage function is a central concept in RL that helps reduce variance in policy gradient estimates. For language modeling, Group Relative Policy Optimization (GRPO) was proposed to use the within-group sample mean as a baseline for advantage normalization. This estimator can be sensitive to small group size and rollout-level stochasticity, which may lead to suboptimal advantage estimates in some settings. In this paper, we propose Kalman Filter Enhanced Group Relative Policy Optimization (KRPO), a lightweight variant that treats per-group rewards as noisy observations of a latent prompt-level reward baseline and uses a 1D Kalman filter to estimate both the baseline and its uncertainty. KRPO introduces no additional learned parameters and can be integrated into GRPO with minimal computational overhead. On mathematical reasoning benchmarks, KRPO consistently improves training reward curves and final accuracy over GRPO. These results suggest that adaptive advantage estimation is a promising direction for critic-free reinforcement learning in language model reasoning. The code is available at https://github.com/billhhh/KRPO_LLMs_RL.

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arXiv2026

FETAL-GAUGE: A Benchmark for Assessing Vision-Language Models in Fetal Ultrasound

The growing demand for prenatal ultrasound imaging has intensified a global shortage of trained sonographers, creating barriers to essential fetal health monitoring. Deep learning has the potential to enhance sonographers' efficiency and support the training of new practitioners. Vision-Language Models (VLMs) are particularly promising for ultrasound interpretation, as they can jointly process images and text to perform multiple clinical tasks within a single framework. However, despite the expansion of VLMs, no standardized benchmark exists to evaluate their performance in fetal ultrasound imaging. This gap is primarily due to the modality's challenging nature, operator dependency, and the limited public availability of datasets. To address this gap, we present Fetal-Gauge, the first and largest visual question answering benchmark specifically designed to evaluate VLMs across various fetal ultrasound tasks. Our benchmark comprises over 42,000 images and 93,000 question-answer pairs, spanning anatomical plane identification, visual grounding of anatomical structures, fetal orientation assessment, clinical view conformity, and clinical diagnosis. We systematically evaluate several state-of-the-art VLMs, including general-purpose and medical-specific models, and reveal a substantial performance gap: the best-performing model achieves only 55\% accuracy, far below clinical requirements. Our analysis identifies critical limitations of current VLMs in fetal ultrasound interpretation, highlighting the urgent need for domain-adapted architectures and specialized training approaches. Fetal-Gauge establishes a rigorous foundation for advancing multimodal deep learning in prenatal care and provides a pathway toward addressing global healthcare accessibility challenges. Our benchmark will be publicly available once the paper gets accepted.

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arXiv2026

MedObvious: Exposing the Medical Moravec's Paradox in VLMs via Clinical Triage

Vision Language Models (VLMs) are increasingly used for tasks like medical report generation and visual question answering. However, fluent diagnostic text does not guarantee safe visual understanding. In clinical practice, interpretation begins with pre-diagnostic sanity checks: verifying that the input is valid to read (correct modality and anatomy, plausible viewpoint and orientation, and no obvious integrity violations). Existing benchmarks largely assume this step is solved, and therefore miss a critical failure mode: a model can produce plausible narratives even when the input is inconsistent or invalid. We introduce MedObvious, a 1,880-task benchmark that isolates input validation as a set-level consistency capability over small multi-panel image sets: the model must identify whether any panel violates expected coherence. MedObvious spans five progressive tiers, from basic orientation/modality mismatches to clinically motivated anatomy/viewpoint verification and triage-style cues, and includes five evaluation formats to test robustness across interfaces. Evaluating 17 different VLMs, we find that sanity checking remains unreliable: several models hallucinate anomalies on normal (negative-control) inputs, performance degrades when scaling to larger image sets, and measured accuracy varies substantially between multiple-choice and open-ended settings. These results show that pre-diagnostic verification remains unsolved for medical VLMs and should be treated as a distinct, safety-critical capability before deployment.

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arXiv2026

Beyond Benchmarks of IUGC: Rethinking Requirements of Deep Learning Methods for Intrapartum Ultrasound Biometry from Fetal Ultrasound Videos

A substantial proportion (45\%) of maternal deaths, neonatal deaths, and stillbirths occur during the intrapartum phase, with a particularly high burden in low- and middle-income countries. Intrapartum biometry plays a critical role in monitoring labor progression; however, the routine use of ultrasound in resource-limited settings is hindered by a shortage of trained sonographers. To address this challenge, the Intrapartum Ultrasound Grand Challenge (IUGC), co-hosted with MICCAI 2024, was launched. The IUGC introduces a clinically oriented multi-task automatic measurement framework that integrates standard plane classification, fetal head-pubic symphysis segmentation, and biometry, enabling algorithms to exploit complementary task information for more accurate estimation. Furthermore, the challenge releases the largest multi-center intrapartum ultrasound video dataset to date, comprising 774 videos (68,106 frames) collected from three hospitals, providing a robust foundation for model training and evaluation. In this study, we present a comprehensive overview of the challenge design, review the submissions from eight participating teams, and analyze their methods from five perspectives: preprocessing, data augmentation, learning strategy, model architecture, and post-processing. In addition, we perform a systematic analysis of the benchmark results to identify key bottlenecks, explore potential solutions, and highlight open challenges for future research. Although encouraging performance has been achieved, our findings indicate that the field remains at an early stage, and further in-depth investigation is required before large-scale clinical deployment. All benchmark solutions and the complete dataset have been publicly released to facilitate reproducible research and promote continued advances in automatic intrapartum ultrasound biometry.

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arXiv2026

FUGC: Benchmarking Semi-Supervised Learning Methods for Cervical Segmentation

Accurate segmentation of cervical structures in transvaginal ultrasound (TVS) is critical for assessing the risk of spontaneous preterm birth (PTB), yet the scarcity of labeled data limits the performance of supervised learning approaches. This paper introduces the Fetal Ultrasound Grand Challenge (FUGC), the first benchmark for semi-supervised learning in cervical segmentation, hosted at ISBI 2025. FUGC provides a dataset of 890 TVS images, including 500 training images, 90 validation images, and 300 test images. Methods were evaluated using the Dice Similarity Coefficient (DSC), Hausdorff Distance (HD), and runtime (RT), with a weighted combination of 0.4/0.4/0.2. The challenge attracted 10 teams with 82 participants submitting innovative solutions. The best-performing methods for each individual metric achieved 90.26\% mDSC, 38.88 mHD, and 32.85 ms RT, respectively. FUGC establishes a standardized benchmark for cervical segmentation, demonstrates the efficacy of semi-supervised methods with limited labeled data, and provides a foundation for AI-assisted clinical PTB risk assessment.

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arXiv2025

Beyond Generative AI: World Models for Clinical Prediction, Counterfactuals, and Planning

Healthcare requires AI that is predictive, reliable, and data-efficient. However, recent generative models lack physical foundation and temporal reasoning required for clinical decision support. As scaling language models show diminishing returns for grounded clinical reasoning, world models are gaining traction because they learn multimodal, temporally coherent, and action-conditioned representations that reflect the physical and causal structure of care. This paper reviews World Models for healthcare systems that learn predictive dynamics to enable multistep rollouts, counterfactual evaluation and planning. We survey recent work across three domains: (i) medical imaging and diagnostics (e.g., longitudinal tumor simulation, projection-transition modeling, and Joint Embedding Predictive Architecture i.e., JEPA-style predictive representation learning), (ii) disease progression modeling from electronic health records (generative event forecasting at scale), and (iii) robotic surgery and surgical planning (action-conditioned guidance and control). We also introduce a capability rubric: L1 temporal prediction, L2 action-conditioned prediction, L3 counterfactual rollouts for decision support, and L4 planning/control. Most reviewed systems achieve L1--L2, with fewer instances of L3 and rare L4. We identify cross-cutting gaps that limit clinical reliability; under-specified action spaces and safety constraints, weak interventional validation, incomplete multimodal state construction, and limited trajectory-level uncertainty calibration. This review outlines a research agenda for clinically robust prediction-first world models that integrate generative backbones (transformers, diffusion, VAE) with causal/mechanical foundation for safe decision support in healthcare.

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arXiv2025

TransPrune: Token Transition Pruning for Efficient Large Vision-Language Model

Large Vision-Language Models (LVLMs) have advanced multimodal learning but face high computational costs due to the large number of visual tokens, motivating token pruning to improve inference efficiency. The key challenge lies in identifying which tokens are truly important. Most existing approaches rely on attention-based criteria to estimate token importance. However, they inherently suffer from certain limitations, such as positional bias. In this work, we explore a new perspective on token importance based on token transitions in LVLMs. We observe that the transition of token representations provides a meaningful signal of semantic information. Based on this insight, we propose TransPrune, a training-free and efficient token pruning method. Specifically, TransPrune progressively prunes tokens by assessing their importance through a combination of Token Transition Variation (TTV)-which measures changes in both the magnitude and direction of token representations-and Instruction-Guided Attention (IGA), which measures how strongly the instruction attends to image tokens via attention. Extensive experiments demonstrate that TransPrune achieves comparable multimodal performance to original LVLMs, such as LLaVA-v1.5 and LLaVA-Next, across eight benchmarks, while reducing inference TFLOPs by more than half. Moreover, TTV alone can serve as an effective criterion without relying on attention, achieving performance comparable to attention-based methods. The code will be made publicly available upon acceptance of the paper at https://github.com/liaolea/TransPrune.

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arXiv2025

MAFM^3: Modular Adaptation of Foundation Models for Multi-Modal Medical AI

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. Instead of building separate models, we propose MAFM^3 (Modular Adaptation of Foundation Models for Multi-Modal Medical AI), a framework that enables a single foundation model to expand into diverse domains, tasks, and modalities through lightweight modular components. These components serve as specialized skill sets that allow the system to flexibly activate the appropriate capability at the inference time, depending on the input type or clinical objective. Unlike conventional adaptation methods that treat each new task or modality in isolation, MAFM^3 provides a unified and expandable framework for efficient multitask and multimodality adaptation. Empirically, we validate our approach by adapting a chest CT foundation model initially trained for classification into prognosis and segmentation modules. Our results show improved performance on both tasks. Furthermore, by incorporating PET scans, MAFM^3 achieved an improvement in the Dice score 5% compared to the respective baselines. These findings establish that foundation models, when equipped with modular components, are not inherently constrained to their initial training scope but can evolve into multitask, multimodality systems for medical imaging. The code implementation of this work can be found at https://github.com/Areeb2735/CTscan_prognosis_VLM

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arXiv2025

T3: Test-Time Model Merging in VLMs for Zero-Shot Medical Imaging Analysis

In medical imaging, vision-language models face a critical duality: pretrained networks offer broad robustness but lack subtle, modality-specific characteristics, while fine-tuned expert models achieve high in-distribution accuracy yet falter under modality shift. Existing model-merging techniques, designed for natural-image benchmarks, are simple and efficient but fail to deliver consistent gains across diverse medical modalities; their static interpolation limits reliability in varied clinical tasks. To address this, we introduce Test-Time Task adaptive merging (T^3), a backpropagation-free framework that computes per-sample interpolation coefficients via the Jensen-Shannon divergence between the two models' output distributions. T^3 dynamically preserves local precision when models agree and defers to generalist robustness under drift. To overcome the inference costs of sample-wise merging, we further propose a batch-wise extension, T^3_B, that computes a merging coefficient across a batch of samples, dramatically reducing computational bottleneck. Recognizing the lack of a standardized medical-merging benchmark, we present a rigorous cross-evaluation protocol spanning in-domain, base-to-novel, and corruptions across four modalities. Empirically, T^3 sets new state-of-the-art in Top-1 accuracy and error reduction, outperforming strong baselines while maintaining efficiency, paving the way for adaptive MVLM deployment in clinical settings. Our code is available at https://github.com/Razaimam45/TCube.

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arXiv2025

BRIQA: Balanced Reweighting in Image Quality Assessment of Pediatric Brain MRI

Assessing the severity of artifacts in pediatric brain Magnetic Resonance Imaging (MRI) is critical for diagnostic accuracy, especially in low-field systems where the signal-to-noise ratio is reduced. Manual quality assessment is time-consuming and subjective, motivating the need for robust automated solutions. In this work, we propose BRIQA (Balanced Reweighting in Image Quality Assessment), which addresses class imbalance in artifact severity levels. BRIQA uses gradient-based loss reweighting to dynamically adjust per-class contributions and employs a rotating batching scheme to ensure consistent exposure to underrepresented classes. Through experiments, no single architecture performs best across all artifact types, emphasizing the importance of architectural diversity. The rotating batching configuration improves performance across metrics by promoting balanced learning when combined with cross-entropy loss. BRIQA improves average macro F1 score from 0.659 to 0.706, with notable gains in Noise (0.430), Zipper (0.098), Positioning (0.097), Contrast (0.217), Motion (0.022), and Banding (0.012) artifact severity classification. The code is available at https://github.com/BioMedIA-MBZUAI/BRIQA.

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arXiv2025

FetalCLIP: A Visual-Language Foundation Model for Fetal Ultrasound Image Analysis

Foundation models are becoming increasingly effective in the medical domain, offering pre-trained models on large datasets that can be readily adapted for downstream tasks. Despite progress, fetal ultrasound images remain a challenging domain for foundation models due to their inherent complexity, often requiring substantial additional training and facing limitations due to the scarcity of paired multimodal data. To overcome these challenges, here we introduce FetalCLIP, a vision-language foundation model capable of generating universal representation of fetal ultrasound images. FetalCLIP was pre-trained using a multimodal learning approach on a diverse dataset of 210,035 fetal ultrasound images paired with text. This represents the largest paired dataset of its kind used for foundation model development to date. This unique training approach allows FetalCLIP to effectively learn the intricate anatomical features present in fetal ultrasound images, resulting in robust representations that can be used for a variety of downstream applications. In extensive benchmarking across a range of key fetal ultrasound applications, including classification, gestational age estimation, congenital heart defect (CHD) detection, and fetal structure segmentation, FetalCLIP outperformed all baselines while demonstrating remarkable generalizability and strong performance even with limited labeled data. We plan to release the FetalCLIP model publicly for the benefit of the broader scientific community.

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arXiv2025

EMedNeXt: An Enhanced Brain Tumor Segmentation Framework for Sub-Saharan Africa using MedNeXt V2 with Deep Supervision

Brain cancer affects millions worldwide, and in nearly every clinical setting, doctors rely on magnetic resonance imaging (MRI) to diagnose and monitor gliomas. However, the current standard for tumor quantification through manual segmentation of multi-parametric MRI is time-consuming, requires expert radiologists, and is often infeasible in under-resourced healthcare systems. This problem is especially pronounced in low-income regions, where MRI scanners are of lower quality and radiology expertise is scarce, leading to incorrect segmentation and quantification. In addition, the number of acquired MRI scans in Africa is typically small. To address these challenges, the BraTS-Lighthouse 2025 Challenge focuses on robust tumor segmentation in sub-Saharan Africa (SSA), where resource constraints and image quality degradation introduce significant shifts. In this study, we present EMedNeXt -- an enhanced brain tumor segmentation framework based on MedNeXt V2 with deep supervision and optimized post-processing pipelines tailored for SSA. EMedNeXt introduces three key contributions: a larger region of interest, an improved nnU-Net v2-based architectural skeleton, and a robust model ensembling system. Evaluated on the hidden validation set, our solution achieved an average LesionWise DSC of 0.897 with an average LesionWise NSD of 0.541 and 0.84 at a tolerance of 0.5 mm and 1.0 mm, respectively.

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arXiv2025

DuPLUS: Dual-Prompt Vision-Language Framework for Universal Medical Image Segmentation and Prognosis

Deep learning for medical imaging is hampered by task-specific models that lack generalizability and prognostic capabilities, while existing 'universal' approaches suffer from simplistic conditioning and poor medical semantic understanding. To address these limitations, we introduce DuPLUS, a deep learning framework for efficient multi-modal medical image analysis. DuPLUS introduces a novel vision-language framework that leverages hierarchical semantic prompts for fine-grained control over the analysis task, a capability absent in prior universal models. To enable extensibility to other medical tasks, it includes a hierarchical, text-controlled architecture driven by a unique dual-prompt mechanism. For segmentation, DuPLUS is able to generalize across three imaging modalities, ten different anatomically various medical datasets, encompassing more than 30 organs and tumor types. It outperforms the state-of-the-art task specific and universal models on 8 out of 10 datasets. We demonstrate extensibility of its text-controlled architecture by seamless integration of electronic health record (EHR) data for prognosis prediction, and on a head and neck cancer dataset, DuPLUS achieved a Concordance Index (CI) of 0.69. Parameter-efficient fine-tuning enables rapid adaptation to new tasks and modalities from varying centers, establishing DuPLUS as a versatile and clinically relevant solution for medical image analysis. The code for this work is made available at: https://anonymous.4open.science/r/DuPLUS-6C52

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arXiv2025

A Multimodal and Multi-centric Head and Neck Cancer Dataset for Segmentation, Diagnosis and Outcome Prediction

We present a publicly available multimodal dataset for head and neck cancer research, comprising 1123 annotated Positron Emission Tomography/Computed Tomography (PET/CT) studies from patients with histologically confirmed disease, acquired from 10 international medical centers. All studies contain co-registered PET/CT scans with varying acquisition protocols, reflecting real-world clinical diversity from a long-term, multi-institution retrospective collection. Primary gross tumor volumes (GTVp) and involved lymph nodes (GTVn) were manually segmented by experienced radiation oncologists and radiologists following established guidelines. We provide anonymized NifTi files, expert-annotated segmentation masks, comprehensive clinical metadata, and radiotherapy dose distributions for a patient subset. The metadata include TNM staging, HPV status, demographics, long-term follow-up outcomes, survival times, censoring indicators, and treatment information. To demonstrate its utility, we benchmark three key clinical tasks: automated tumor segmentation, recurrence-free survival prediction, and HPV status classification, using state-of-the-art deep learning models like UNet, SegResNet, and multimodal prognostic frameworks.

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