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Researcher profile

Mohammad Yaqub

Mohammad Yaqub contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer Visioneess.IVMachine LearningArtificial IntelligenceQuantitative Methods

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Published work

14 published item(s)

preprint2026arXiv

Lost in Volume: The CT-SpatialVQA Benchmark for Evaluating Semantic-Spatial Understanding of 3D Medical Vision-Language Models

Recent advances in 3D medical vision-language models have enabled joint reasoning over volumetric images and text, showing strong performance in medical visual question-answering (VQA) and report generation. Despite this progress, it remains unclear whether these models learn spatially grounded anatomy from 3D volumes or rely primarily on learned priors and language correlations. This uncertainty stems from the lack of systematic evaluation of semantic-spatial reasoning in volumetric medical VLMs for clinically reliable decision support. To address this gap, we introduce CT-SpatialVQA, a benchmark designed to evaluate semantic-spatial reasoning in 3D CT data. The benchmark comprises 9077 clinically grounded question-answer (QA) pairs derived directly from 1601 radiology reports and CT volumes, which are validated via a robust LLM-assisted pipeline with a 95% human consensus agreement rate. Our dataset requires explicit anatomical localization, laterality awareness, structural comparison, and 3D inter-structure relational reasoning. We also introduce a standardized evaluation protocol and benchmark eight 3D medical VLMs, finding severe degradation on semantic-spatial reasoning tasks, averaging 34% accuracy and often below random, highlighting the need for deeper integration of volumetric evidence for trustworthy clinical use.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

An Ensemble Approach for Patient Prognosis of Head and Neck Tumor Using Multimodal Data

Accurate prognosis of a tumor can help doctors provide a proper course of treatment and, therefore, save the lives of many. Traditional machine learning algorithms have been eminently useful in crafting prognostic models in the last few decades. Recently, deep learning algorithms have shown significant improvement when developing diagnosis and prognosis solutions to different healthcare problems. However, most of these solutions rely solely on either imaging or clinical data. Utilizing patient tabular data such as demographics and patient medical history alongside imaging data in a multimodal approach to solve a prognosis task has started to gain more interest recently and has the potential to create more accurate solutions. The main issue when using clinical and imaging data to train a deep learning model is to decide on how to combine the information from these sources. We propose a multimodal network that ensembles deep multi-task logistic regression (MTLR), Cox proportional hazard (CoxPH) and CNN models to predict prognostic outcomes for patients with head and neck tumors using patients' clinical and imaging (CT and PET) data. Features from CT and PET scans are fused and then combined with patients' electronic health records for the prediction. The proposed model is trained and tested on 224 and 101 patient records respectively. Experimental results show that our proposed ensemble solution achieves a C-index of 0.72 on The HECKTOR test set that saved us the first place in prognosis task of the HECKTOR challenge. The full implementation based on PyTorch is available on \url{https://github.com/numanai/BioMedIA-Hecktor2021}.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Automatic Segmentation of Head and Neck Tumor: How Powerful Transformers Are?

Cancer is one of the leading causes of death worldwide, and head and neck (H&N) cancer is amongst the most prevalent types. Positron emission tomography and computed tomography are used to detect, segment and quantify the tumor region. Clinically, tumor segmentation is extensively time-consuming and prone to error. Machine learning, and deep learning in particular, can assist to automate this process, yielding results as accurate as the results of a clinician. In this paper, we investigate a vision transformer-based method to automatically delineate H&N tumor, and compare its results to leading convolutional neural network (CNN)-based models. We use multi-modal data from CT and PET scans to perform the segmentation task. We show that a solution with a transformer-based model has the potential to achieve comparable results to CNN-based ones. With cross validation, the model achieves a mean dice similarity coefficient (DSC) of 0.736, mean precision of 0.766 and mean recall of 0.766. This is only 0.021 less than the 2020 competition winning model (cross validated in-house) in terms of the DSC score. On the testing set, the model performs similarly, with DSC of 0.736, precision of 0.773, and recall of 0.760, which is only 0.023 lower in DSC than the 2020 competition winning model. This work shows that cancer segmentation via transformer-based models is a promising research area to further explore.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Color Space-based HoVer-Net for Nuclei Instance Segmentation and Classification

Nuclei segmentation and classification is the first and most crucial step that is utilized for many different microscopy medical analysis applications. However, it suffers from many issues such as the segmentation of small objects, imbalance, and fine-grained differences between types of nuclei. In this paper, multiple different contributions were done tackling these problems present. Firstly, the recently released "ConvNeXt" was used as the encoder for HoVer-Net model since it leverages the key components of transformers that make them perform well. Secondly, to enhance the visual differences between nuclei, a multi-channel color space-based approach is used to aid the model in extracting distinguishing features. Thirdly, Unified Focal loss (UFL) was used to tackle the background-foreground imbalance. Finally, Sharpness-Aware Minimization (SAM) was used to ensure generalizability of the model. Overall, we were able to outperform the current state-of-the-art (SOTA), HoVer-Net, on the preliminary test set of the CoNiC Challenge 2022 by 12.489% mPQ+.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Contrastive Pretraining for Echocardiography Segmentation with Limited Data

Contrastive learning has proven useful in many applications where access to labelled data is limited. The lack of annotated data is particularly problematic in medical image segmentation as it is difficult to have clinical experts manually annotate large volumes of data such as cardiac structures in ultrasound images of the heart. In this paper, We propose a self supervised contrastive learning method to segment the left ventricle from echocardiography when limited annotated images exist. Furthermore, we study the effect of contrastive pretraining on two well-known segmentation networks, UNet and DeepLabV3. Our results show that contrastive pretraining helps improve the performance on left ventricle segmentation, particularly when annotated data is scarce. We show how to achieve comparable results to state-of-the-art fully supervised algorithms when we train our models in a self-supervised fashion followed by fine-tuning on just 5\% of the data. We show that our solution outperforms what is currently published on a large public dataset (EchoNet-Dynamic) achieving a Dice score of 0.9252. We also compare the performance of our solution on another smaller dataset (CAMUS) to demonstrate the generalizability of our proposed solution. The code is available at (https://github.com/BioMedIA-MBZUAI/contrastive-echo).

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deep Learning-based Quality Assessment of Clinical Protocol Adherence in Fetal Ultrasound Dating Scans

To assess fetal health during pregnancy, doctors use the gestational age (GA) calculation based on the Crown Rump Length (CRL) measurement in order to check for fetal size and growth trajectory. However, GA estimation based on CRL, requires proper positioning of calipers on the fetal crown and rump view, which is not always an easy plane to find, especially for an inexperienced sonographer. Finding a slightly oblique view from the true CRL view could lead to a different CRL value and therefore incorrect estimation of GA. This study presents an AI-based method for a quality assessment of the CRL view by verifying 7 clinical scoring criteria that are used to verify the correctness of the acquired plane. We show how our proposed solution achieves high accuracy on the majority of the scoring criteria when compared to an expert. We also show that if such scoring system is used, it helps identify poorly acquired images accurately and hence may help sonographers acquire better images which could potentially lead to a better assessment of conditions such as Intrauterine Growth Restriction (IUGR).

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

EchoCoTr: Estimation of the Left Ventricular Ejection Fraction from Spatiotemporal Echocardiography

Learning spatiotemporal features is an important task for efficient video understanding especially in medical images such as echocardiograms. Convolutional neural networks (CNNs) and more recent vision transformers (ViTs) are the most commonly used methods with limitations per each. CNNs are good at capturing local context but fail to learn global information across video frames. On the other hand, vision transformers can incorporate global details and long sequences but are computationally expensive and typically require more data to train. In this paper, we propose a method that addresses the limitations we typically face when training on medical video data such as echocardiographic scans. The algorithm we propose (EchoCoTr) utilizes the strength of vision transformers and CNNs to tackle the problem of estimating the left ventricular ejection fraction (LVEF) on ultrasound videos. We demonstrate how the proposed method outperforms state-of-the-art work to-date on the EchoNet-Dynamic dataset with MAE of 3.95 and $R^2$ of 0.82. These results show noticeable improvement compared to all published research. In addition, we show extensive ablations and comparisons with several algorithms, including ViT and BERT. The code is available at https://github.com/BioMedIA-MBZUAI/EchoCoTr.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

GARDNet: Robust Multi-View Network for Glaucoma Classification in Color Fundus Images

Glaucoma is one of the most severe eye diseases, characterized by rapid progression and leading to irreversible blindness. It is often the case that diagnostics is carried out when one's sight has already significantly degraded due to the lack of noticeable symptoms at early stage of the disease. Regular glaucoma screenings of the population shall improve early-stage detection, however the desirable frequency of etymological checkups is often not feasible due to the excessive load imposed by manual diagnostics on limited number of specialists. Considering the basic methodology to detect glaucoma is to analyze fundus images for the optic-disc-to-optic-cup ratio, Machine Learning algorithms can offer sophisticated methods for image processing and classification. In our work, we propose an advanced image pre-processing technique combined with a multi-view network of deep classification models to categorize glaucoma. Our Glaucoma Automated Retinal Detection Network (GARDNet) has been successfully tested on Rotterdam EyePACS AIROGS dataset with an AUC of 0.92, and then additionally fine-tuned and tested on RIM-ONE DL dataset with an AUC of 0.9308 outperforming the state-of-the-art of 0.9272. Our code is available on https://github.com/ahmed1996said/gardnet

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Hyperparameter Optimization for COVID-19 Chest X-Ray Classification

Despite the introduction of vaccines, Coronavirus disease (COVID-19) remains a worldwide dilemma, continuously developing new variants such as Delta and the recent Omicron. The current standard for testing is through polymerase chain reaction (PCR). However, PCRs can be expensive, slow, and/or inaccessible to many people. X-rays on the other hand have been readily used since the early 20th century and are relatively cheaper, quicker to obtain, and typically covered by health insurance. With a careful selection of model, hyperparameters, and augmentations, we show that it is possible to develop models with 83% accuracy in binary classification and 64% in multi-class for detecting COVID-19 infections from chest x-rays.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Is it Possible to Predict MGMT Promoter Methylation from Brain Tumor MRI Scans using Deep Learning Models?

Glioblastoma is a common brain malignancy that tends to occur in older adults and is almost always lethal. The effectiveness of chemotherapy, being the standard treatment for most cancer types, can be improved if a particular genetic sequence in the tumor known as MGMT promoter is methylated. However, to identify the state of the MGMT promoter, the conventional approach is to perform a biopsy for genetic analysis, which is time and effort consuming. A couple of recent publications proposed a connection between the MGMT promoter state and the MRI scans of the tumor and hence suggested the use of deep learning models for this purpose. Therefore, in this work, we use one of the most extensive datasets, BraTS 2021, to study the potency of employing deep learning solutions, including 2D and 3D CNN models and vision transformers. After conducting a thorough analysis of the models' performance, we concluded that there seems to be no connection between the MRI scans and the state of the MGMT promoter.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Self-Ensembling Vision Transformer (SEViT) for Robust Medical Image Classification

Vision Transformers (ViT) are competing to replace Convolutional Neural Networks (CNN) for various computer vision tasks in medical imaging such as classification and segmentation. While the vulnerability of CNNs to adversarial attacks is a well-known problem, recent works have shown that ViTs are also susceptible to such attacks and suffer significant performance degradation under attack. The vulnerability of ViTs to carefully engineered adversarial samples raises serious concerns about their safety in clinical settings. In this paper, we propose a novel self-ensembling method to enhance the robustness of ViT in the presence of adversarial attacks. The proposed Self-Ensembling Vision Transformer (SEViT) leverages the fact that feature representations learned by initial blocks of a ViT are relatively unaffected by adversarial perturbations. Learning multiple classifiers based on these intermediate feature representations and combining these predictions with that of the final ViT classifier can provide robustness against adversarial attacks. Measuring the consistency between the various predictions can also help detect adversarial samples. Experiments on two modalities (chest X-ray and fundoscopy) demonstrate the efficacy of SEViT architecture to defend against various adversarial attacks in the gray-box (attacker has full knowledge of the target model, but not the defense mechanism) setting. Code: https://github.com/faresmalik/SEViT

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Self-Supervision and Multi-Task Learning: Challenges in Fine-Grained COVID-19 Multi-Class Classification from Chest X-rays

Quick and accurate diagnosis is of paramount importance to mitigate the effects of COVID-19 infection, particularly for severe cases. Enormous effort has been put towards developing deep learning methods to classify and detect COVID-19 infections from chest radiography images. However, recently some questions have been raised surrounding the clinical viability and effectiveness of such methods. In this work, we investigate the impact of multi-task learning (classification and segmentation) on the ability of CNNs to differentiate between various appearances of COVID-19 infections in the lung. We also employ self-supervised pre-training approaches, namely MoCo and inpainting-CXR, to eliminate the dependence on expensive ground truth annotations for COVID-19 classification. Finally, we conduct a critical evaluation of the models to assess their deploy-readiness and provide insights into the difficulties of fine-grained COVID-19 multi-class classification from chest X-rays.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

SubOmiEmbed: Self-supervised Representation Learning of Multi-omics Data for Cancer Type Classification

For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of omics data show various aspects of samples. Integration and analysis of multi-omics data give us a broad view of tumours, which can improve clinical decision making. Omics data, mainly DNA methylation and gene expression profiles are usually high dimensional data with a lot of molecular features. In recent years, variational autoencoders (VAE) have been extensively used in embedding image and text data into lower dimensional latent spaces. In our project, we extend the idea of using a VAE model for low dimensional latent space extraction with the self-supervised learning technique of feature subsetting. With VAEs, the key idea is to make the model learn meaningful representations from different types of omics data, which could then be used for downstream tasks such as cancer type classification. The main goals are to overcome the curse of dimensionality and integrate methylation and expression data to combine information about different aspects of same tissue samples, and hopefully extract biologically relevant features. Our extension involves training encoder and decoder to reconstruct the data from just a subset of it. By doing this, we force the model to encode most important information in the latent representation. We also added an identity to the subsets so that the model knows which subset is being fed into it during training and testing. We experimented with our approach and found that SubOmiEmbed produces comparable results to the baseline OmiEmbed with a much smaller network and by using just a subset of the data. This work can be improved to integrate mutation-based genomic data as well.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

TMSS: An End-to-End Transformer-based Multimodal Network for Segmentation and Survival Prediction

When oncologists estimate cancer patient survival, they rely on multimodal data. Even though some multimodal deep learning methods have been proposed in the literature, the majority rely on having two or more independent networks that share knowledge at a later stage in the overall model. On the other hand, oncologists do not do this in their analysis but rather fuse the information in their brain from multiple sources such as medical images and patient history. This work proposes a deep learning method that mimics oncologists' analytical behavior when quantifying cancer and estimating patient survival. We propose TMSS, an end-to-end Transformer based Multimodal network for Segmentation and Survival prediction that leverages the superiority of transformers that lies in their abilities to handle different modalities. The model was trained and validated for segmentation and prognosis tasks on the training dataset from the HEad & NeCK TumOR segmentation and the outcome prediction in PET/CT images challenge (HECKTOR). We show that the proposed prognostic model significantly outperforms state-of-the-art methods with a concordance index of 0.763+/-0.14 while achieving a comparable dice score of 0.772+/-0.030 to a standalone segmentation model. The code is publicly available.

0 citations0 reviewsNo code linkedOpen access