MG-3D: Multi-Grained Knowledge-Enhanced 3D Medical Vision-Language Pre-training

3D medical image analysis is pivotal in numerous clinical applications. However, the scarcity of labeled data and limited generalization capabilities hinder the advancement of AI-empowered models. Radiology reports are easily accessible and can serve as weakly-supervised signals. However, large-scale vision-language pre-training (VLP) remains underexplored in 3D medical image analysis. Specifically, the insufficient investigation into multi-grained radiology semantics and their correlations across patients leads to underutilization of large-scale volume-report data. Considering intra-patient cross-modal semantic consistency and inter-patient semantic correlations, we propose a multi-task VLP method, MG-3D, pre-trained on large-scale data (47.1K), addressing the challenges by the following two aspects: 1) Establishing the correspondence between volume semantics and multi-grained medical knowledge of each patient with cross-modal global alignment and complementary modality-guided local reconstruction, ensuring intra-patient features of different modalities cohesively represent the same semantic content; 2) Correlating inter-patient visual semantics based on fine-grained report correlations across patients, and keeping sensitivity to global individual differences via contrastive learning, enhancing the discriminative feature representation. Furthermore, we delve into the scaling law to explore potential performance improvements. Comprehensive evaluations across nine uni- and cross-modal clinical tasks are carried out to assess model efficacy. Extensive experiments on both internal and external datasets demonstrate the superior transferability, scalability, and generalization of MG-3D, showcasing its potential in advancing feature representation for 3D medical image analysis. Code will be available: https://github.com/Xuefeng-Ni/MG-3D.

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.

See it, Think it, Sorted: Large Multimodal Models are Few-shot Time Series Anomaly Analyzers

Time series anomaly detection (TSAD) is becoming increasingly vital due to the rapid growth of time series data across various sectors. Anomalies in web service data, for example, can signal critical incidents such as system failures or server malfunctions, necessitating timely detection and response. However, most existing TSAD methodologies rely heavily on manual feature engineering or require extensive labeled training data, while also offering limited interpretability. To address these challenges, we introduce a pioneering framework called the Time Series Anomaly Multimodal Analyzer (TAMA), which leverages the power of Large Multimodal Models (LMMs) to enhance both the detection and interpretation of anomalies in time series data. By converting time series into visual formats that LMMs can efficiently process, TAMA leverages few-shot in-context learning capabilities to reduce dependence on extensive labeled datasets. Our methodology is validated through rigorous experimentation on multiple real-world datasets, where TAMA consistently outperforms state-of-the-art methods in TSAD tasks. Additionally, TAMA provides rich, natural language-based semantic analysis, offering deeper insights into the nature of detected anomalies. Furthermore, we contribute one of the first open-source datasets that includes anomaly detection labels, anomaly type labels, and contextual description, facilitating broader exploration and advancement within this critical field. Ultimately, TAMA not only excels in anomaly detection but also provides a comprehensive approach for understanding the underlying causes of anomalies, pushing TSAD forward through innovative methodologies and insights.

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.

Unleashing the Denoising Capability of Diffusion Prior for Solving Inverse Problems

The recent emergence of diffusion models has significantly advanced the precision of learnable priors, presenting innovative avenues for addressing inverse problems. Since inverse problems inherently entail maximum a posteriori estimation, previous works have endeavored to integrate diffusion priors into the optimization frameworks. However, prevailing optimization-based inverse algorithms primarily exploit the prior information within the diffusion models while neglecting their denoising capability. To bridge this gap, this work leverages the diffusion process to reframe noisy inverse problems as a two-variable constrained optimization task by introducing an auxiliary optimization variable. By employing gradient truncation, the projection gradient descent method is efficiently utilized to solve the corresponding optimization problem. The proposed algorithm, termed ProjDiff, effectively harnesses the prior information and the denoising capability of a pre-trained diffusion model within the optimization framework. Extensive experiments on the image restoration tasks and source separation and partial generation tasks demonstrate that ProjDiff exhibits superior performance across various linear and nonlinear inverse problems, highlighting its potential for practical applications. Code is available at https://github.com/weigerzan/ProjDiff/.

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.

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.

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.

RMNet: Equivalently Removing Residual Connection from Networks

Although residual connection enables training very deep neural networks, it is not friendly for online inference due to its multi-branch topology. This encourages many researchers to work on designing DNNs without residual connections at inference. For example, RepVGG re-parameterizes multi-branch topology to a VGG-like (single-branch) model when deploying, showing great performance when the network is relatively shallow. However, RepVGG can not transform ResNet to VGG equivalently because re-parameterizing methods can only be applied to linear blocks and the non-linear layers (ReLU) have to be put outside of the residual connection which results in limited representation ability, especially for deeper networks. In this paper, we aim to remedy this problem and propose to remove the residual connection in a vanilla ResNet equivalently by a reserving and merging (RM) operation on ResBlock. Specifically, the RM operation allows input feature maps to pass through the block while reserving their information and merges all the information at the end of each block, which can remove residual connections without changing the original output. As a plug-in method, RM Operation basically has three advantages: 1) its implementation makes it naturally friendly for high ratio network pruning. 2) it helps break the depth limitation of RepVGG. 3) it leads to better accuracy-speed trade-off network (RMNet) compared to ResNet and RepVGG. We believe the ideology of RM Operation can inspire many insights on model design for the community in the future. Code is available at: https://github.com/fxmeng/RMNet.