Purpose: To develop a fully automated deep learning system, AutoLugano, for end-to-end lymphoma classification by performing lesion segmentation, anatomical localization, and automated Lugano staging from baseline FDG-PET/CT scans. Methods: The AutoLugano system processes baseline FDG-PET/CT scans through three sequential modules:(1) Anatomy-Informed Lesion Segmentation, a 3D nnU-Net model, trained on multi-channel inputs, performs automated lesion detection (2) Atlas-based Anatomical Localization, which leverages the TotalSegmentator toolkit to map segmented lesions to 21 predefined lymph node regions using deterministic anatomical rules; and (3) Automated Lugano Staging, where the spatial distribution of involved regions is translated into Lugano stages and therapeutic groups (Limited vs. Advanced Stage).The system was trained on the public autoPET dataset (n=1,007) and externally validated on an independent cohort of 67 patients. Performance was assessed using accuracy, sensitivity, specificity, F1-scorefor regional involvement detection and staging agreement. Results: On the external validation set, the proposed model demonstrated robust performance, achieving an overall accuracy of 88.31%, sensitivity of 74.47%, Specificity of 94.21% and an F1-score of 80.80% for regional involvement detection,outperforming baseline models. Most notably, for the critical clinical task of therapeutic stratification (Limited vs. Advanced Stage), the system achieved a high accuracy of 85.07%, with a specificity of 90.48% and a sensitivity of 82.61%.Conclusion: AutoLugano represents the first fully automated, end-to-end pipeline that translates a single baseline FDG-PET/CT scan into a complete Lugano stage. This study demonstrates its strong potential to assist in initial staging, treatment stratification, and supporting clinical decision-making.

Skin cancer is a life-threatening disease where early detection significantly improves patient outcomes. Automated diagnosis from dermoscopic images is challenging due to high intra-class variability and subtle inter-class differences. Many deep learning models operate as "black boxes," limiting clinical trust. In this work, we propose a dual-encoder attention-based framework that leverages both segmented lesions and clinical metadata to enhance skin lesion classification in terms of both accuracy and interpretability. A novel Deep-UNet architecture with Dual Attention Gates (DAG) and Atrous Spatial Pyramid Pooling (ASPP) is first employed to segment lesions. The classification stage uses two DenseNet201 encoders-one on the original image and another on the segmented lesion whose features are fused via multi-head cross-attention. This dual-input design guides the model to focus on salient pathological regions. In addition, a transformer-based module incorporates patient metadata (age, sex, lesion site) into the prediction. We evaluate our approach on the HAM10000 dataset and the ISIC 2018 and 2019 challenges. The proposed method achieves state-of-the-art segmentation performance and significantly improves classification accuracy and average AUC compared to baseline models. To validate our model's reliability, we use Gradient-weighted Class Activation Mapping (Grad-CAM) to generate heatmaps. These visualizations confirm that our model's predictions are based on the lesion area, unlike models that rely on spurious background features. These results demonstrate that integrating precise lesion segmentation and clinical data with attention-based fusion leads to a more accurate and interpretable skin cancer classification model.

Segmentation models are important tools for the detection and analysis of lesions in brain MRI. Depending on the type of brain pathology that is imaged, MRI scanners can acquire multiple, different image modalities (contrasts). Most segmentation models for multimodal brain MRI are restricted to fixed modalities and cannot effectively process new ones at inference. Some models generalize to unseen modalities but may lose discriminative modality-specific information. This work aims to develop a model that can perform inference on data that contain image modalities unseen during training, previously seen modalities, and heterogeneous combinations of both, thus allowing a user to utilize any available imaging modalities. We demonstrate this is possible with a simple, thus practical alteration to the U-net architecture, by integrating a modality-agnostic input channel or pathway, alongside modality-specific input channels. To train this modality-agnostic component, we develop an image augmentation scheme that synthesizes artificial MRI modalities. Augmentations differentially alter the appearance of pathological and healthy brain tissue to create artificial contrasts between them while maintaining realistic anatomical integrity. We evaluate the method using 8 MRI databases that include 5 types of pathologies (stroke, tumours, traumatic brain injury, multiple sclerosis and white matter hyperintensities) and 8 modalities (T1, T1+contrast, T2, PD, SWI, DWI, ADC and FLAIR). The results demonstrate that the approach preserves the ability to effectively process MRI modalities encountered during training, while being able to process new, unseen modalities to improve its segmentation. Project code: https://github.com/Anthony-P-Addison/AGN-MOD-SEG

Breast ultrasound imaging is a valuable tool for early breast cancer detection, but automated tumor segmentation is challenging due to inherent noise, variations in scale of lesions, and fuzzy boundaries. To address these challenges, we propose a novel hybrid attention-based network for lesion segmentation. Our proposed architecture integrates a pre-trained DenseNet121 in the encoder part for robust feature extraction with a multi-branch attention-enhanced decoder tailored for breast ultrasound images. The bottleneck incorporates Global Spatial Attention (GSA), Position Encoding (PE), and Scaled Dot-Product Attention (SDPA) to learn global context, spatial relationships, and relative positional features. The Spatial Feature Enhancement Block (SFEB) is embedded at skip connections to refine and enhance spatial features, enabling the network to focus more effectively on tumor regions. A hybrid loss function combining Binary Cross-Entropy (BCE) and Jaccard Index loss optimizes both pixel-level accuracy and region-level overlap metrics, enhancing robustness to class imbalance and irregular tumor shapes. Experiments on public datasets demonstrate that our method outperforms existing approaches, highlighting its potential to assist radiologists in early and accurate breast cancer diagnosis.

--While modern segmentation models often prioritize performance over practicality, we advocate a design philosophy prioritizing simplicity and efficiency, and attempted high-performance segmentation model design. This paper presents SimpleUNet, a scalable ultra-lightweight medical image segmentation model with three key innovations: (1) A partial feature selection mechanism in skip connections for redundancy reduction while enhancing segmentation performance; (2) A fixed-width architecture that prevents exponential parameter growth across network stages; (3) An adaptive feature fusion module achieving enhanced representation with minimal computational overhead. With a record-breaking 16 KB parameter configuration, Simple-UNet outperforms LBUNet and other lightweight benchmarks across multiple public datasets. The 0.67 MB variant achieves superior efficiency (8.60 GFLOPs) and accuracy, attaining a mean DSC/IoU of 85.76 %/75.60% on multi-center breast lesion datasets, surpassing both U-Net and TransUNet. Evaluations on skin lesion datasets (ISIC 2017/2018: mDice 84.86 %/88.77%) and endoscopic polyp segmentation (KV ASIR-SEG: 86.46 % /76.48% mDice/mIoU) confirm consistent dominance over state-of-the-art models. This work demonstrates that extreme model compression need not compromise performance, providing new insights for efficient and accurate medical image segmentation. Codes can be found at https://github.com/Frankyu5666666/SimpleUNet. N medical image segmentation, U-Net has been acknowledged as a successful and robust framework distinguished by its unique U-shaped architecture comprising an encoder-decoder pathway [1]-[4]. Generally, the skip connections between the encoder and the decoder are considered to concatenate the lower-level features from the decoder to the high-level features from the encoder for hierarchical feature fusion, mitigating issues like gradient vanishing or explosion, and thus leading to higher performance. The modular design has made U-Net a popular choice for semantic segmentation, especially in medical image segmentation scenarios where available datasets are limited. However, the model's progressively increasing width and the feature concatenation mechanism inherently introduce more parameters in the decoder path for information fusion, potentially resulting in information redundancy and reduced efficiency. Recent advances have sought to enhance segmentation performance by introducing novel computing operations and attention modules [5]-[8]. Although these innovations have improved accuracy, they often come at an expensive cost regarding parameter and computational complexity that challenges practical deployment in resource-constrained environments. In light of these limitations, researchers in the area endeavored to develop lightweight yet high-performance models for medical image segmentation, such as those utilizing depthwise convolution and state-space-based models [9]-[11].

In the U.S., lung cancer is the second major cause of death. Early detection of suspicious lung nodules is crucial for patient treatment planning, management, and improving outcomes. Many approaches for lung nodule segmentation and volumetric analysis have been proposed, but few have looked at longitudinal changes in total lung tumor burden. In this work, we trained two 3D models (nnUNet) with and without anatomical priors to automatically segment lung lesions and quantified total lesion burden for each patient. The 3D model without priors significantly outperformed ($p < .001$) the model trained with anatomy priors. For detecting clinically significant lesions $>$ 1cm, a precision of 71.3\%, sensitivity of 68.4\%, and F1-score of 69.8\% was achieved. For segmentation, a Dice score of 77.1 $\pm$ 20.3 and Hausdorff distance error of 11.7 $\pm$ 24.1 mm was obtained. The median lesion burden was 6.4 cc (IQR: 2.1, 18.1) and the median volume difference between manual and automated measurements was 0.02 cc (IQR: -2.8, 1.2). Agreements were also evaluated with linear regression and Bland-Altman plots. The proposed approach can produce a personalized evaluation of the total tumor burden for a patient and facilitate interval change tracking over time.

In the setting of clinical imaging, differences in between vendors, hospitals and sequences can yield highly inhomogeneous imaging data. In MRI in particular, voxel dimension, slice spacing and acquisition plane can vary substantially. For clinical applications, therefore, algorithms must be trained to handle data with various voxel resolutions. The usual strategy to deal with heterogeneity of resolution is harmonization: resampling imaging data to a common (usually isovoxel) resolution. This can lead to loss of fidelity arising from interpolation artifacts out-of-plane and downsampling in-plane. We present in this paper a network architecture designed to be able to learn directly from spatially heterogeneous data, without resampling: a segmentation network based on the e3nn framework that leverages a spherical harmonic, rather than voxel-grid, parameterization of convolutional kernels, with a fixed physical radius. Networks based on these kernels can be resampled to their input voxel dimensions. We trained and tested our network on a publicly available dataset assembled from three centres, and on an in-house dataset of Multiple Sclerosis cases with a high degree of spatial inhomogeneity. We compared our approach to a standard U-Net with two strategies for handling inhomogeneous data: training directly on the data without resampling, and resampling to a common resolution of 1mm isovoxels. We show that our network is able to learn from various combinations of voxel sizes and outperforms classical U-Nets on 2D testing cases and most 3D testing cases. This shows an ability to generalize well when tested on image resolutions not seen during training. Our code can be found at: http://github.com/SCAN-NRAD/e3nn\_U-Net.

In oncology, Positron Emission Tomography-Computed Tomography (PET/CT) is widely used in cancer diagnosis, staging, and treatment monitoring, as it combines anatomical details from CT with functional metabolic activity and molecular marker expression information from PET. However, existing artificial intelligence-driven PET/CT analyses rely predominantly on task-specific models trained from scratch or on limited datasets, limiting their generalizability and robustness. To address this, we propose a foundation model approach specifically designed for multimodal PET/CT imaging. We introduce the Cross-Fraternal Twin Masked Autoencoder (FratMAE), a novel framework that effectively integrates whole-body anatomical and functional or molecular information. FratMAE employs separate Vision Transformer (ViT) encoders for PET and CT scans, along with cross-attention decoders that enable synergistic interactions between modalities during masked autoencoder training. Additionally, it incorporates textual metadata to enhance PET representation learning.

In this work, we present LesionLocator, a framework for zero-shot longitudinal lesion tracking and segmentation in 3D medical imaging, establishing the first end-to-end model capable of 4D tracking with dense spatial prompts. Our model leverages an extensive dataset of 23,262 annotated medical scans, as well as synthesized longitudinal data across diverse lesion types. The diversity and scale of our dataset significantly enhances model generalizability to real-world medical imaging challenges and addresses key limitations in longitudinal data availability. LesionLocator outperforms all existing promptable models in lesion segmentation by nearly 10 dice points, reaching human-level performance, and achieves state-of-the-art results in lesion tracking, with superior lesion retrieval and segmentation accuracy. LesionLocator not only sets a new benchmark in universal promptable lesion segmentation and automated longitudinal lesion tracking but also provides the first open-access solution of its kind, releasing our synthetic 4D dataset and model to the community, empowering future advancements in medical imaging. Code is available at: www.github.com/MIC-DKFZ/LesionLocator

Magnetic resonance imaging (MRI) is a potent diagnostic tool for detecting pathological tissues in various diseases. Different MRI sequences have different contrast mechanisms and sensitivities for different types of lesions, which pose challenges to accurate and consistent lesion segmentation. In clinical practice, radiologists commonly use the sub-sequence feature, i.e. the difference between post contrast-enhanced T1-weighted (post) and pre-contrast-enhanced (pre) sequences, to locate lesions. Inspired by this, we propose a residual fusion method to learn subsequence representation for MRI lesion segmentation. Specifically, we iteratively and adaptively fuse features from pre- and post-contrast sequences at multiple resolutions, using dynamic weights to achieve optimal fusion and address diverse lesion enhancement patterns. Our method achieves state-of-the-art performances on BraTS2023 dataset for brain tumor segmentation and our in-house breast MRI dataset for breast lesion segmentation. Our method is clinically inspired and has the potential to facilitate lesion segmentation in various applications.