Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Large-Scale 3D Medical Image Pre-training with Geometric Context Priors

The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.

FreeTumor: Advance Tumor Segmentation via Large-Scale Tumor Synthesis

AI-driven tumor analysis has garnered increasing attention in healthcare. However, its progress is significantly hindered by the lack of annotated tumor cases, which requires radiologists to invest a lot of effort in collecting and annotation. In this paper, we introduce a highly practical solution for robust tumor synthesis and segmentation, termed FreeTumor, which refers to annotation-free synthetic tumors and our desire to free patients that suffering from tumors. Instead of pursuing sophisticated technical synthesis modules, we aim to design a simple yet effective tumor synthesis paradigm to unleash the power of large-scale data. Specifically, FreeTumor advances existing methods mainly from three aspects: (1) Existing methods only leverage small-scale labeled data for synthesis training, which limits their ability to generalize well on unseen data from different sources. To this end, we introduce the adversarial training strategy to leverage large-scale and diversified unlabeled data in synthesis training, significantly improving tumor synthesis. (2) Existing methods largely ignored the negative impact of low-quality synthetic tumors in segmentation training. Thus, we employ an adversarial-based discriminator to automatically filter out the low-quality synthetic tumors, which effectively alleviates their negative impact. (3) Existing methods only used hundreds of cases in tumor segmentation. In FreeTumor, we investigate the data scaling law in tumor segmentation by scaling up the dataset to 11k cases. Extensive experiments demonstrate the superiority of FreeTumor, e.g., on three tumor segmentation benchmarks, average $+8.9\%$ DSC over the baseline that only using real tumors and $+6.6\%$ DSC over the state-of-the-art tumor synthesis method. Code will be available.

MiM: Mask in Mask Self-Supervised Pre-Training for 3D Medical Image Analysis

The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Mask AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various medical vision tasks. However, due to large spatial sizes with much higher dimensions of 3D medical images, the lack of hierarchical design for MAE may hinder the performance of downstream tasks. In this paper, we propose a novel \textit{Mask in Mask (MiM)} pre-training framework for 3D medical images, which aims to advance MAE by learning discriminative representation from hierarchical visual tokens across varying scales. We introduce multiple levels of granularity for masked inputs from the volume, which are then reconstructed simultaneously ranging at both fine and coarse levels. Additionally, a cross-level alignment mechanism is applied to adjacent level volumes to enforce anatomical similarity hierarchically. Furthermore, we adopt a hybrid backbone to enhance the hierarchical representation learning efficiently during the pre-training. MiM was pre-trained on a large scale of available 3D volumetric images, \textit{i.e.,} Computed Tomography (CT) images containing various body parts. Extensive experiments on thirteen public datasets demonstrate the superiority of MiM over other SSL methods in organ/lesion/tumor segmentation and disease classification. We further scale up the MiM to large pre-training datasets with more than 10k volumes, showing that large-scale pre-training can further enhance the performance of downstream tasks. The improvement also concluded that the research community should pay more attention to the scale of the pre-training dataset towards the healthcare foundation model for 3D medical images.

Modeling the Label Distributions for Weakly-Supervised Semantic Segmentation

Weakly-Supervised Semantic Segmentation (WSSS) aims to train segmentation models by weak labels, which is receiving significant attention due to its low annotation cost. Existing approaches focus on generating pseudo labels for supervision while largely ignoring to leverage the inherent semantic correlation among different pseudo labels. We observe that pseudo-labeled pixels that are close to each other in the feature space are more likely to share the same class, and those closer to the distribution centers tend to have higher confidence. Motivated by this, we propose to model the underlying label distributions and employ cross-label constraints to generate more accurate pseudo labels. In this paper, we develop a unified WSSS framework named Adaptive Gaussian Mixtures Model, which leverages a GMM to model the label distributions. Specifically, we calculate the feature distribution centers of pseudo-labeled pixels and build the GMM by measuring the distance between the centers and each pseudo-labeled pixel. Then, we introduce an Online Expectation-Maximization (OEM) algorithm and a novel maximization loss to optimize the GMM adaptively, aiming to learn more discriminative decision boundaries between different class-wise Gaussian mixtures. Based on the label distributions, we leverage the GMM to generate high-quality pseudo labels for more reliable supervision. Our framework is capable of solving different forms of weak labels: image-level labels, points, scribbles, blocks, and bounding-boxes. Extensive experiments on PASCAL, COCO, Cityscapes, and ADE20K datasets demonstrate that our framework can effectively provide more reliable supervision and outperform the state-of-the-art methods under all settings. Code will be available at https://github.com/Luffy03/AGMM-SASS.

VoCo: A Simple-yet-Effective Volume Contrastive Learning Framework for 3D Medical Image Analysis

Self-Supervised Learning (SSL) has demonstrated promising results in 3D medical image analysis. However, the lack of high-level semantics in pre-training still heavily hinders the performance of downstream tasks. We observe that 3D medical images contain relatively consistent contextual position information, i.e., consistent geometric relations between different organs, which leads to a potential way for us to learn consistent semantic representations in pre-training. In this paper, we propose a simple-yet-effective Volume Contrast (VoCo) framework to leverage the contextual position priors for pre-training. Specifically, we first generate a group of base crops from different regions while enforcing feature discrepancy among them, where we employ them as class assignments of different regions. Then, we randomly crop sub-volumes and predict them belonging to which class (located at which region) by contrasting their similarity to different base crops, which can be seen as predicting contextual positions of different sub-volumes. Through this pretext task, VoCo implicitly encodes the contextual position priors into model representations without the guidance of annotations, enabling us to effectively improve the performance of downstream tasks that require high-level semantics. Extensive experimental results on six downstream tasks demonstrate the superior effectiveness of VoCo. Code will be available at https://github.com/Luffy03/VoCo.

Deep Covariance Alignment for Domain Adaptive Remote Sensing Image Segmentation

Unsupervised domain adaptive (UDA) image segmentation has recently gained increasing attention, aiming to improve the generalization capability for transferring knowledge from the source domain to the target domain. However, in high spatial resolution remote sensing image (RSI), the same category from different domains (\emph{e.g.}, urban and rural) can appear to be totally different with extremely inconsistent distributions, which heavily limits the UDA accuracy. To address this problem, in this paper, we propose a novel Deep Covariance Alignment (DCA) model for UDA RSI segmentation. The DCA can explicitly align category features to learn shared domain-invariant discriminative feature representations, which enhances the ability of model generalization. Specifically, a Category Feature Pooling (CFP) module is first employed to extract category features by combining the coarse outputs and the deep features. Then, we leverage a novel Covariance Regularization (CR) to enforce the intra-category features to be closer and the inter-category features to be further separate. Compared with the existing category alignment methods, our CR aims to regularize the correlation between different dimensions of the features and thus performs more robustly when dealing with the divergent category features of imbalanced and inconsistent distributions. Finally, we propose a stagewise procedure to train the DCA in order to alleviate the error accumulation. Experiments on both Rural-to-Urban and Urban-to-Rural scenarios of the LoveDA dataset demonstrate the superiority of our proposed DCA over other state-of-the-art UDA segmentation methods. Code is available at https://github.com/Luffy03/DCA.

Iterative Semi-Supervised Learning for Abdominal Organs and Tumor Segmentation

Deep-learning (DL) based methods are playing an important role in the task of abdominal organs and tumors segmentation in CT scans. However, the large requirements of annotated datasets heavily limit its development. The FLARE23 challenge provides a large-scale dataset with both partially and fully annotated data, which also focuses on both segmentation accuracy and computational efficiency. In this study, we propose to use the strategy of Semi-Supervised Learning (SSL) and iterative pseudo labeling to address FLARE23. Initially, a deep model (nn-UNet) trained on datasets with complete organ annotations (about 220 scans) generates pseudo labels for the whole dataset. These pseudo labels are then employed to train a more powerful segmentation model. Employing the FLARE23 dataset, our approach achieves an average DSC score of 89.63% for organs and 46.07% for tumors on online validation leaderboard. For organ segmentation, We obtain 0.9007\% DSC and 0.9493\% NSD. For tumor segmentation, we obtain 0.3785% DSC and 0.2842% NSD. Our code is available at https://github.com/USTguy/Flare23.