CT-based Anatomical Segmentation for Thoracic Surgical Planning: A Benchmark Study for 3D U-shaped Deep Learning Models

Recent rising interests in patient-specific thoracic surgical planning and simulation require efficient and robust creation of digital anatomical models from automatic medical image segmentation algorithms. Deep learning (DL) is now state-of-the-art in various radiological tasks, and U-shaped DL models have particularly excelled in medical image segmentation since the inception of the 2D UNet. To date, many variants of U-shaped models have been proposed by the integration of different attention mechanisms and network configurations. Leveraging the recent development of large multi-label databases, systematic benchmark studies for these models can provide valuable insights for clinical deployment and future model designs, but such studies are still rare. We conduct the first benchmark study for variants of 3D U-shaped models (3DUNet, STUNet, AttentionUNet, SwinUNETR, FocalSegNet, and a novel 3D SwinUnet with four variants) with a focus on CT-based anatomical segmentation for thoracic surgery. Our study systematically examines the impact of different attention mechanisms, number of resolution stages, and network configurations on segmentation accuracy and computational complexity. To allow cross-reference with other recent benchmarking studies, we also included a performance assessment of the BTCV abdominal structural segmentation. With the STUNet ranking at the top, our study demonstrated the value of CNN-based U-shaped models for the investigated tasks and the benefit of residual blocks in network configuration designs to boost segmentation performance.

VesselShot: Few-shot learning for cerebral blood vessel segmentation

Angiography is widely used to detect, diagnose, and treat cerebrovascular diseases. While numerous techniques have been proposed to segment the vascular network from different imaging modalities, deep learning (DL) has emerged as a promising approach. However, existing DL methods often depend on proprietary datasets and extensive manual annotation. Moreover, the availability of pre-trained networks specifically for medical domains and 3D volumes is limited. To overcome these challenges, we propose a few-shot learning approach called VesselShot for cerebrovascular segmentation. VesselShot leverages knowledge from a few annotated support images and mitigates the scarcity of labeled data and the need for extensive annotation in cerebral blood vessel segmentation. We evaluated the performance of VesselShot using the publicly available TubeTK dataset for the segmentation task, achieving a mean Dice coefficient (DC) of 0.62(0.03).

Precision-Weighted Federated Learning

Federated Learning using the Federated Averaging algorithm has shown great advantages for large-scale applications that rely on collaborative learning, especially when the training data is either unbalanced or inaccessible due to privacy constraints. We hypothesize that Federated Averaging underestimates the full extent of heterogeneity of data when the aggregation is performed. We propose Precision-weighted Federated Learning a novel algorithm that takes into account the variance of the stochastic gradients when computing the weighted average of the parameters of models trained in a Federated Learning setting. With Precision-weighted Federated Learning, we provide an alternate averaging scheme that leverages the heterogeneity of the data when it has a large diversity of features in its composition. Our method was evaluated using standard image classification datasets with two different data partitioning strategies (IID/non-IID) to measure the performance and speed of our method in resource-constrained environments, such as mobile and IoT devices. We obtained a good balance between computational efficiency and convergence rates with Precision-weighted Federated Learning. Our performance evaluations show 9% better predictions with MNIST, 18% with Fashion-MNIST, and 5% with CIFAR-10 in the non-IID setting. Further reliability evaluations ratify the stability in our method by reaching a 99% reliability index with IID partitions and 96% with non-IID partitions. In addition, we obtained a 20x speedup on Fashion-MNIST with only 10 clients and up to 37x with 100 clients participating in the aggregation concurrently per communication round. The results indicate that Precision-weighted Federated Learning is an effective and faster alternative approach for aggregating private data, especially in domains where data is highly heterogeneous.