Taha Koleilat

Taha Koleilat, Hojat Asgariandehkordi, Hassan Rivaz et al.

Segmentation of anatomical structures and pathological regions in medical images is essential for modern clinical diagnosis, disease research, and treatment planning. While significant advancements have been made in deep learning-based segmentation techniques, many of these methods still suffer from limitations in data efficiency, generalizability, and interactivity. As a result, developing precise segmentation methods that require fewer labeled datasets remains a critical challenge in medical image analysis. Recently, the introduction of foundation models like CLIP and Segment-Anything-Model (SAM), with robust cross-domain representations, has paved the way for interactive and universal image segmentation. However, further exploration of these models for data-efficient segmentation in medical imaging is still needed and highly relevant. In this paper, we introduce MedCLIP-SAMv2, a novel framework that integrates the CLIP and SAM models to perform segmentation on clinical scans using text prompts, in both zero-shot and weakly supervised settings. Our approach includes fine-tuning the BiomedCLIP model with a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss, and leveraging the Multi-modal Information Bottleneck (M2IB) to create visual prompts for generating segmentation masks from SAM in the zero-shot setting. We also investigate using zero-shot segmentation labels within a weakly supervised paradigm to enhance segmentation quality further. Extensive testing across four diverse segmentation tasks and medical imaging modalities (breast tumor ultrasound, brain tumor MRI, lung X-ray, and lung CT) demonstrates the high accuracy of our proposed framework. Our code is available at https://github.com/HealthX-Lab/MedCLIP-SAMv2.

Taha Koleilat, Hassan Rivaz, Yiming Xiao

Parameter-efficient adaptation of vision-language foundation models is crucial for precise multimodal understanding of biomedical images, yet existing methods remain deterministic and often struggle under domain shift or ambiguous image-text alignment. This limitation is particularly critical in the clinic, where models should remain robust in low-data regimes and domain shifts. We present Evi-Steer, an evidential cross-modal low-dimensional steering framework for BiomedCLIP that enables uncertainty-aware parameter-efficient fine-tuning while updating only 0.11% of total model parameters. Our approach performs lightweight low-dimensional token updates in both vision and text encoders while simultaneously estimating epistemic uncertainty. These uncertainty estimates update gate residuals, allowing the model to adapt conservatively when evidence is weak. Furthermore, we introduce cross-modal confidence fusion based on Dempster-Shafer theory, enabling visual adaptation to be conditioned on textual confidence and suppressing conflicting or uncertain cross-modal updates. We conduct a comprehensive evaluation on 15 biomedical imaging datasets spanning 8 organs and 8 imaging modalities under few-shot learning and domain generalization settings. Evi-Steer consistently outperforms state-of-the-art methods under few-shot learning and domain shift settings, demonstrating a practical and robust pathway for deploying vision-language models in real-world clinical settings. Code is available at https://github.com/HealthX-Lab/Evi-Steer.

Taha Koleilat, Hojat Asgariandehkordi, Hassan Rivaz et al.

Medical image segmentation of anatomical structures and pathology is crucial in modern clinical diagnosis, disease study, and treatment planning. To date, great progress has been made in deep learning-based segmentation techniques, but most methods still lack data efficiency, generalizability, and interactability. Consequently, the development of new, precise segmentation methods that demand fewer labeled datasets is of utmost importance in medical image analysis. Recently, the emergence of foundation models, such as CLIP and Segment-Anything-Model (SAM), with comprehensive cross-domain representation opened the door for interactive and universal image segmentation. However, exploration of these models for data-efficient medical image segmentation is still limited, but is highly necessary. In this paper, we propose a novel framework, called MedCLIP-SAM that combines CLIP and SAM models to generate segmentation of clinical scans using text prompts in both zero-shot and weakly supervised settings. To achieve this, we employed a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss to fine-tune the BiomedCLIP model and the recent gScoreCAM to generate prompts to obtain segmentation masks from SAM in a zero-shot setting. Additionally, we explored the use of zero-shot segmentation labels in a weakly supervised paradigm to improve the segmentation quality further. By extensively testing three diverse segmentation tasks and medical image modalities (breast tumor ultrasound, brain tumor MRI, and lung X-ray), our proposed framework has demonstrated excellent accuracy. Code is available at https://github.com/HealthX-Lab/MedCLIP-SAM.

Taha Koleilat, Hojat Asgariandehkordi, Hassan Rivaz et al.

Recent advancements in vision-language models (VLMs), such as CLIP, have demonstrated substantial success in self-supervised representation learning for vision tasks. However, effectively adapting VLMs to downstream applications remains challenging, as their accuracy often depends on time-intensive and expertise-demanding prompt engineering, while full model fine-tuning is costly. This is particularly true for biomedical images, which, unlike natural images, typically suffer from limited annotated datasets, unintuitive image contrasts, and nuanced visual features. Recent prompt learning techniques, such as Context Optimization (CoOp) intend to tackle these issues, but still fall short in generalizability. Meanwhile, explorations in prompt learning for biomedical image analysis are still highly limited. In this work, we propose BiomedCoOp, a novel prompt learning framework that enables efficient adaptation of BiomedCLIP for accurate and highly generalizable few-shot biomedical image classification. Our approach achieves effective prompt context learning by leveraging semantic consistency with average prompt ensembles from Large Language Models (LLMs) and knowledge distillation with a statistics-based prompt selection strategy. We conducted comprehensive validation of our proposed framework on 11 medical datasets across 9 modalities and 10 organs against existing state-of-the-art methods, demonstrating significant improvements in both accuracy and generalizability. The code is publicly available at https://github.com/HealthX-Lab/BiomedCoOp.

Omid Nejati Manzari, Hojat Asgariandehkordi, Taha Koleilat et al.

Large vision-language models (VLMs) excel on general benchmarks but often lack robustness in medical imaging, where heterogeneous supervision induces cross-dataset interference and sensitivity to data regime (i.e., how the supervisory signals are mixed). In realistic clinical workflows, data and tasks arrive sequentially, so naive continual training further leads to catastrophic forgetting. To address these challenges, we propose MedQwen, a parameter-efficient medical VLM that couples a spectrally routed Mixture-of-Experts (MoE) with a theoretically grounded scaling rule that aligns low-rank updates with a full-rank, fully fine-tuned MoE, without changing the base architecture. Concretely, we initialize each expert from non-overlapping singular value decomposition (SVD) segments of the pretrained weight and introduce a residual compensation and scaling scheme to enable stable expert specialization and consistent routing under distribution shift. Across 23 medical datasets covering visual question answering, report generation, radiology classification, and hallucination mitigation, MedQwen achieves strong, reliable performance: it approaches full fine-tuning on zero-shot classification with 339$\times$ fewer trainable parameters, and reduces sequential forgetting to $\sim$5\% where strong baselines degrade by $>$20-50\%.

Taha Koleilat, Hojat Asgariandehkordi, Omid Nejati Manzari et al.

Medical image segmentation remains challenging due to limited annotations for training, ambiguous anatomical features, and domain shifts. While vision-language models such as CLIP offer strong cross-modal representations, their potential for dense, text-guided medical image segmentation remains underexplored. We present MedCLIPSeg, a novel framework that adapts CLIP for robust, data-efficient, and uncertainty-aware medical image segmentation. Our approach leverages patch-level CLIP embeddings through probabilistic cross-modal attention, enabling bidirectional interaction between image and text tokens and explicit modeling of predictive uncertainty. Together with a soft patch-level contrastive loss that encourages more nuanced semantic learning across diverse textual prompts, MedCLIPSeg effectively improves data efficiency and domain generalizability. Extensive experiments across 16 datasets spanning five imaging modalities and six organs demonstrate that MedCLIPSeg outperforms prior methods in accuracy, efficiency, and robustness, while providing interpretable uncertainty maps that highlight local reliability of segmentation results. This work demonstrates the potential of probabilistic vision-language modeling for text-driven medical image segmentation.

Pascal Spiegler, Taha Koleilat, Arash Harirpoush et al.

Pancreatic cancer carries a poor prognosis and relies on endoscopic ultrasound (EUS) for targeted biopsy and radiotherapy. However, the speckle noise, low contrast, and unintuitive appearance of EUS make segmentation of pancreatic tumors with fully supervised deep learning (DL) models both error-prone and dependent on large, expert-curated annotation datasets. To address these challenges, we present TextSAM-EUS, a novel, lightweight, text-driven adaptation of the Segment Anything Model (SAM) that requires no manual geometric prompts at inference. Our approach leverages text prompt learning (context optimization) through the BiomedCLIP text encoder in conjunction with a LoRA-based adaptation of SAM's architecture to enable automatic pancreatic tumor segmentation in EUS, tuning only 0.86% of the total parameters. On the public Endoscopic Ultrasound Database of the Pancreas, TextSAM-EUS with automatic prompts attains 82.69% Dice and 85.28% normalized surface distance (NSD), and with manual geometric prompts reaches 83.10% Dice and 85.70% NSD, outperforming both existing state-of-the-art (SOTA) supervised DL models and foundation models (e.g., SAM and its variants). As the first attempt to incorporate prompt learning in SAM-based medical image segmentation, TextSAM-EUS offers a practical option for efficient and robust automatic EUS segmentation. Code is available at https://github.com/HealthX-Lab/TextSAM-EUS .

Hamza Rasaee, Taha Koleilat, Hassan Rivaz

Accurate and generalizable object segmentation in ultrasound imaging remains a significant challenge due to anatomical variability, diverse imaging protocols, and limited annotated data. In this study, we propose a prompt-driven vision-language model (VLM) that integrates Grounding DINO with SAM2 (Segment Anything Model2) to enable object segmentation across multiple ultrasound organs. A total of 18 public ultrasound datasets, encompassing the breast, thyroid, liver, prostate, kidney, and paraspinal muscle, were utilized. These datasets were divided into 15 for fine-tuning and validation of Grounding DINO using Low Rank Adaptation (LoRA) to the ultrasound domain, and 3 were held out entirely for testing to evaluate performance in unseen distributions. Comprehensive experiments demonstrate that our approach outperforms state-of-the-art segmentation methods, including UniverSeg, MedSAM, MedCLIP-SAM, BiomedParse, and SAMUS on most seen datasets while maintaining strong performance on unseen datasets without additional fine-tuning. These results underscore the promise of VLMs in scalable and robust ultrasound image analysis, reducing dependence on large, organ-specific annotated datasets. We will publish our code on code.sonography.ai after acceptance.

Taha Koleilat, Hassan Rivaz, Yiming Xiao

Vision-language models (VLMs) like CLIP have shown impressive zero-shot and few-shot learning capabilities across diverse applications. However, adapting these models to new fine-grained domains remains difficult due to reliance on prompt engineering and the high cost of full model fine-tuning. Existing adaptation approaches rely on augmented components, such as prompt tokens and adapter modules, which could limit adaptation quality, destabilize the model, and compromise the rich knowledge learned during pretraining. In this work, we present CLIP-SVD, a novel multi-modal and parameter-efficient adaptation technique that leverages Singular Value Decomposition (SVD) to modify the internal parameter space of CLIP without injecting additional modules. Specifically, we fine-tune only the singular values of the CLIP parameter matrices to rescale the basis vectors for domain adaptation while retaining the pretrained model. This design enables enhanced adaptation performance using only 0.04% of the model's total parameters and better preservation of its generalization ability. CLIP-SVD achieves state-of-the-art classification results on 11 natural and 10 biomedical datasets, outperforming previous methods in both accuracy and generalization under few-shot settings. Additionally, we leverage a natural language-based approach to analyze the effectiveness and dynamics of the CLIP adaptation to allow interpretability of CLIP-SVD. The code is publicly available at https://github.com/HealthX-Lab/CLIP-SVD.

Omid Nejati Manzari, Hojat Asgariandehkordi, Taha Koleilat et al.

Convolutional networks, transformers, hybrid models, and Mamba-based architectures have demonstrated strong performance across various medical image classification tasks. However, these methods were primarily designed to classify clean images using labeled data. In contrast, real-world clinical data often involve image corruptions that are unique to multi-center studies and stem from variations in imaging equipment across manufacturers. In this paper, we introduce the Medical Vision Transformer (MedViTV2), a novel architecture incorporating Kolmogorov-Arnold Network (KAN) layers into the transformer architecture for the first time, aiming for generalized medical image classification. We have developed an efficient KAN block to reduce computational load while enhancing the accuracy of the original MedViT. Additionally, to counteract the fragility of our MedViT when scaled up, we propose an enhanced Dilated Neighborhood Attention (DiNA), an adaptation of the efficient fused dot-product attention kernel capable of capturing global context and expanding receptive fields to scale the model effectively and addressing feature collapse issues. Moreover, a hierarchical hybrid strategy is introduced to stack our Local Feature Perception and Global Feature Perception blocks in an efficient manner, which balances local and global feature perceptions to boost performance. Extensive experiments on 17 medical image classification datasets and 12 corrupted medical image datasets demonstrate that MedViTV2 achieved state-of-the-art results in 27 out of 29 experiments with reduced computational complexity. MedViTV2 is 44\% more computationally efficient than the previous version and significantly enhances accuracy, achieving improvements of 4.6\% on MedMNIST, 5.8\% on NonMNIST, and 13.4\% on the MedMNIST-C benchmark.