Amirreza Fateh

Amirhossein Movahedisefat, Amirreza Fateh, Mohammad Reza Mohammadi

Semantic segmentation in medical imaging is a critical yet challenging task due to data scarcity and high variability across modalities. While foundation models like the Segment Anything Model (SAM) show promise, they often struggle with medical images without specific adaptation. Moreover, point prompts, despite being the most natural form of user interaction, provide insufficient spatial context for reliable segmentation, particularly when target structures are irregular or poorly contrasted. In this paper, we propose an enhanced segmentation framework that integrates a lightweight Box Predictor module into the MedSAM architecture. The Box Predictor estimates an approximate bounding box from a single user click using localized image embedding features, providing spatial guidance that reduces the ambiguity of point prompts, while introducing only 1.6M additional parameters and negligible inference overhead. We introduce a two-stage training pipeline where the Box Predictor is trained independently before being integrated into MedSAM. To validate the generalization capability of our method, we conduct extensive evaluations on four diverse datasets (FLARE22, BRISC, BUSI, LungSegDB) spanning distinct imaging modalities, including CT, MRI, and Ultrasound. Our method improves segmentation accuracy and robustness across varied anatomical structures and imaging domains, achieving Dice scores of 0.89 (BUSI), 0.93 (FLARE22), 0.88 (BRISC), and 0.98 (LungSegDB). Code is available at https://github.com/Amirhosseinmovahedi/MedSAM-BoxPredictor

Amirreza Fateh, Mohammad Reza Mohammadi, Mohammad Reza Jahed Motlagh

Few-shot Semantic Segmentation addresses the challenge of segmenting objects in query images with only a handful of annotated examples. However, many previous state-of-the-art methods either have to discard intricate local semantic features or suffer from high computational complexity. To address these challenges, we propose a new Few-shot Semantic Segmentation framework based on the Transformer architecture. Our approach introduces the spatial transformer decoder and the contextual mask generation module to improve the relational understanding between support and query images. Moreover, we introduce a multi scale decoder to refine the segmentation mask by incorporating features from different resolutions in a hierarchical manner. Additionally, our approach integrates global features from intermediate encoder stages to improve contextual understanding, while maintaining a lightweight structure to reduce complexity. This balance between performance and efficiency enables our method to achieve competitive results on benchmark datasets such as PASCAL-5^i and COCO-20^i in both 1-shot and 5-shot settings. Notably, our model with only 1.5 million parameters demonstrates competitive performance while overcoming limitations of existing methodologies. https://github.com/amirrezafateh/MSDNet

Fatemeh Askari, Amirreza Fateh, Mohammad Reza Mohammadi

In the context of few-shot classification, the goal is to train a classifier using a limited number of samples while maintaining satisfactory performance. However, traditional metric-based methods exhibit certain limitations in achieving this objective. These methods typically rely on a single distance value between the query feature and support feature, thereby overlooking the contribution of shallow features. To overcome this challenge, we propose a novel approach in this paper. Our approach involves utilizing a multi-output embedding network that maps samples into distinct feature spaces. The proposed method extracts feature vectors at different stages, enabling the model to capture both global and abstract features. By utilizing these diverse feature spaces, our model enhances its performance. Moreover, employing a self-attention mechanism improves the refinement of features at each stage, leading to even more robust representations and improved overall performance. Furthermore, assigning learnable weights to each stage significantly improved performance and results. We conducted comprehensive evaluations on the MiniImageNet and FC100 datasets, specifically in the 5-way 1-shot and 5-way 5-shot scenarios. Additionally, we performed cross-domain tasks across eight benchmark datasets, achieving high accuracy in the testing domains. These evaluations demonstrate the efficacy of our proposed method in comparison to state-of-the-art approaches. https://github.com/FatemehAskari/MSENet

Alireza Saber, Amirreza Fateh, Pouria Parhami et al.

Pneumonia, a prevalent respiratory infection, remains a leading cause of morbidity and mortality worldwide, particularly among vulnerable populations. Chest X-rays serve as a primary tool for pneumonia detection; however, variations in imaging conditions and subtle visual indicators complicate consistent interpretation. Automated tools can enhance traditional methods by improving diagnostic reliability and supporting clinical decision-making. In this study, we propose a novel multi-scale transformer approach for pneumonia detection that integrates lung segmentation and classification into a unified framework. Our method introduces a lightweight transformer-enhanced TransUNet for precise lung segmentation, achieving a Dice score of 95.68% on the "Chest X-ray Masks and Labels" dataset with fewer parameters than traditional transformers. For classification, we employ pre-trained ResNet models (ResNet-50 and ResNet-101) to extract multi-scale feature maps, which are then processed through a modified transformer module to enhance pneumonia detection. This integration of multi-scale feature extraction and lightweight transformer modules ensures robust performance, making our method suitable for resource-constrained clinical environments. Our approach achieves 93.75% accuracy on the "Kermany" dataset and 96.04% accuracy on the "Cohen" dataset, outperforming existing methods while maintaining computational efficiency. This work demonstrates the potential of multi-scale transformer architectures to improve pneumonia diagnosis, offering a scalable and accurate solution to global healthcare challenges. https://github.com/amirrezafateh/Multi-Scale-Transformer-Pneumonia

Sadjad Rezvani, Mansoor Fateh, Yeganeh Jalali et al.

Early detection of lung cancer is crucial as it increases the chances of successful treatment. Automatic lung image segmentation assists doctors in identifying diseases such as lung cancer, COVID-19, and respiratory disorders. However, lung segmentation is challenging due to overlapping features like vascular and bronchial structures, along with pixel-level fusion of brightness, color, and texture. New lung segmentation methods face difficulties in identifying long-range relationships between image components, reliance on convolution operations that may not capture all critical features, and the complex structures of the lungs. Furthermore, semantic gaps between feature maps can hinder the integration of relevant information, reducing model accuracy. Skip connections can also limit the decoder's access to complete information, resulting in partial information loss during encoding. To overcome these challenges, we propose a hybrid approach using the FusionLungNet network, which has a multi-level structure with key components, including the ResNet-50 encoder, Channel-wise Aggregation Attention (CAA) module, Multi-scale Feature Fusion (MFF) block, self refinement (SR) module, and multiple decoders. The refinement sub-network uses convolutional neural networks for image post-processing to improve quality. Our method employs a combination of loss functions, including SSIM, IOU, and focal loss, to optimize image reconstruction quality. We created and publicly released a new dataset for lung segmentation called LungSegDB, including 1800 CT images from the LIDC-IDRI dataset (dataset version 1) and 700 images from the Chest CT Cancer Images from Kaggle dataset (dataset version 2). Our method achieved an IOU score of 98.04, outperforming existing methods and demonstrating significant improvements in segmentation accuracy. https://github.com/sadjadrz/FusionLungNet

Amirreza Fateh, Yasin Rezvani, Sara Moayedi et al.

Accurate segmentation and classification of brain tumors from Magnetic Resonance Imaging (MRI) remain key challenges in medical image analysis, primarily due to the lack of high-quality, balanced, and diverse datasets with expert annotations. In this work, we address this gap by introducing BRISC, a dataset designed for brain tumor segmentation and classification tasks, featuring high-resolution segmentation masks. The dataset comprises 6,000 contrast-enhanced T1-weighted MRI scans, which were collated from multiple public datasets that lacked segmentation labels. Our primary contribution is the subsequent expert annotation of these images, performed by certified radiologists and physicians. It includes three major tumor types, namely glioma, meningioma, and pituitary, as well as non-tumorous cases. Each sample includes high-resolution labels and is categorized across axial, sagittal, and coronal imaging planes to facilitate robust model development and cross-view generalization. To demonstrate the utility of the dataset, we provide benchmark results for both tasks using standard deep learning models. The BRISC dataset is made publicly available. datasetlink: Kaggle (https://www.kaggle.com/datasets/briscdataset/brisc2025/), Figshare (https://doi.org/10.6084/m9.figshare.30533120), Zenodo (https://doi.org/10.5281/zenodo.17524350)