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.

Label Critic: Design Data Before Models

As medical datasets rapidly expand, creating detailed annotations of different body structures becomes increasingly expensive and time-consuming. We consider that requesting radiologists to create detailed annotations is unnecessarily burdensome and that pre-existing AI models can largely automate this process. Following the spirit don't use a sledgehammer on a nut, we find that, rather than creating annotations from scratch, radiologists only have to review and edit errors if the Best-AI Labels have mistakes. To obtain the Best-AI Labels among multiple AI Labels, we developed an automatic tool, called Label Critic, that can assess label quality through tireless pairwise comparisons. Extensive experiments demonstrate that, when incorporated with our developed Image-Prompt pairs, pre-existing Large Vision-Language Models (LVLM), trained on natural images and texts, achieve 96.5% accuracy when choosing the best label in a pair-wise comparison, without extra fine-tuning. By transforming the manual annotation task (30-60 min/scan) into an automatic comparison task (15 sec/scan), we effectively reduce the manual efforts required from radiologists by an order of magnitude. When the Best-AI Labels are sufficiently accurate (81% depending on body structures), they will be directly adopted as the gold-standard annotations for the dataset, with lower-quality AI Labels automatically discarded. Label Critic can also check the label quality of a single AI Label with 71.8% accuracy when no alternatives are available for comparison, prompting radiologists to review and edit if the estimated quality is low (19% depending on body structures).

Analyzing Tumors by Synthesis

Computer-aided tumor detection has shown great potential in enhancing the interpretation of over 80 million CT scans performed annually in the United States. However, challenges arise due to the rarity of CT scans with tumors, especially early-stage tumors. Developing AI with real tumor data faces issues of scarcity, annotation difficulty, and low prevalence. Tumor synthesis addresses these challenges by generating numerous tumor examples in medical images, aiding AI training for tumor detection and segmentation. Successful synthesis requires realistic and generalizable synthetic tumors across various organs. This chapter reviews AI development on real and synthetic data and summarizes two key trends in synthetic data for cancer imaging research: modeling-based and learning-based approaches. Modeling-based methods, like Pixel2Cancer, simulate tumor development over time using generic rules, while learning-based methods, like DiffTumor, learn from a few annotated examples in one organ to generate synthetic tumors in others. Reader studies with expert radiologists show that synthetic tumors can be convincingly realistic. We also present case studies in the liver, pancreas, and kidneys reveal that AI trained on synthetic tumors can achieve performance comparable to, or better than, AI only trained on real data. Tumor synthesis holds significant promise for expanding datasets, enhancing AI reliability, improving tumor detection performance, and preserving patient privacy.

AbdomenAtlas: A Large-Scale, Detailed-Annotated, & Multi-Center Dataset for Efficient Transfer Learning and Open Algorithmic Benchmarking

We introduce the largest abdominal CT dataset (termed AbdomenAtlas) of 20,460 three-dimensional CT volumes sourced from 112 hospitals across diverse populations, geographies, and facilities. AbdomenAtlas provides 673K high-quality masks of anatomical structures in the abdominal region annotated by a team of 10 radiologists with the help of AI algorithms. We start by having expert radiologists manually annotate 22 anatomical structures in 5,246 CT volumes. Following this, a semi-automatic annotation procedure is performed for the remaining CT volumes, where radiologists revise the annotations predicted by AI, and in turn, AI improves its predictions by learning from revised annotations. Such a large-scale, detailed-annotated, and multi-center dataset is needed for two reasons. Firstly, AbdomenAtlas provides important resources for AI development at scale, branded as large pre-trained models, which can alleviate the annotation workload of expert radiologists to transfer to broader clinical applications. Secondly, AbdomenAtlas establishes a large-scale benchmark for evaluating AI algorithms -- the more data we use to test the algorithms, the better we can guarantee reliable performance in complex clinical scenarios. An ISBI & MICCAI challenge named BodyMaps: Towards 3D Atlas of Human Body was launched using a subset of our AbdomenAtlas, aiming to stimulate AI innovation and to benchmark segmentation accuracy, inference efficiency, and domain generalizability. We hope our AbdomenAtlas can set the stage for larger-scale clinical trials and offer exceptional opportunities to practitioners in the medical imaging community. Codes, models, and datasets are available at https://www.zongweiz.com/dataset

Embracing Massive Medical Data

As massive medical data become available with an increasing number of scans, expanding classes, and varying sources, prevalent training paradigms -- where AI is trained with multiple passes over fixed, finite datasets -- face significant challenges. First, training AI all at once on such massive data is impractical as new scans/sources/classes continuously arrive. Second, training AI continuously on new scans/sources/classes can lead to catastrophic forgetting, where AI forgets old data as it learns new data, and vice versa. To address these two challenges, we propose an online learning method that enables training AI from massive medical data. Instead of repeatedly training AI on randomly selected data samples, our method identifies the most significant samples for the current AI model based on their data uniqueness and prediction uncertainty, then trains the AI on these selective data samples. Compared with prevalent training paradigms, our method not only improves data efficiency by enabling training on continual data streams, but also mitigates catastrophic forgetting by selectively training AI on significant data samples that might otherwise be forgotten, outperforming by 15% in Dice score for multi-organ and tumor segmentation. The code is available at https://github.com/MrGiovanni/OnlineLearning

Quality Sentinel: Estimating Label Quality and Errors in Medical Segmentation Datasets

An increasing number of public datasets have shown a transformative impact on automated medical segmentation. However, these datasets are often with varying label quality, ranging from manual expert annotations to AI-generated pseudo-annotations. There is no systematic, reliable, and automatic quality control (QC). To fill in this bridge, we introduce a regression model, Quality Sentinel, to estimate label quality compared with manual annotations in medical segmentation datasets. This regression model was trained on over 4 million image-label pairs created by us. Each pair presents a varying but quantified label quality based on manual annotations, which enable us to predict the label quality of any image-label pairs in the inference. Our Quality Sentinel can predict the label quality of 142 body structures. The predicted label quality quantified by Dice Similarity Coefficient (DSC) shares a strong correlation with ground truth quality, with a positive correlation coefficient (r=0.902). Quality Sentinel has found multiple impactful use cases. (I) We evaluated label quality in publicly available datasets, where quality highly varies across different datasets. Our analysis also uncovers that male and younger subjects exhibit significantly higher quality. (II) We identified and corrected poorly annotated labels, achieving 1/3 reduction in annotation costs with optimal budgeting on TotalSegmentator. (III) We enhanced AI training efficiency and performance by focusing on high-quality pseudo labels, resulting in a 33%--88% performance boost over entropy-based methods, with a cost of 31% time and 4.5% memory. The data and model are released.

Universal and Extensible Language-Vision Models for Organ Segmentation and Tumor Detection from Abdominal Computed Tomography

The advancement of artificial intelligence (AI) for organ segmentation and tumor detection is propelled by the growing availability of computed tomography (CT) datasets with detailed, per-voxel annotations. However, these AI models often struggle with flexibility for partially annotated datasets and extensibility for new classes due to limitations in the one-hot encoding, architectural design, and learning scheme. To overcome these limitations, we propose a universal, extensible framework enabling a single model, termed Universal Model, to deal with multiple public datasets and adapt to new classes (e.g., organs/tumors). Firstly, we introduce a novel language-driven parameter generator that leverages language embeddings from large language models, enriching semantic encoding compared with one-hot encoding. Secondly, the conventional output layers are replaced with lightweight, class-specific heads, allowing Universal Model to simultaneously segment 25 organs and six types of tumors and ease the addition of new classes. We train our Universal Model on 3,410 CT volumes assembled from 14 publicly available datasets and then test it on 6,173 CT volumes from four external datasets. Universal Model achieves first place on six CT tasks in the Medical Segmentation Decathlon (MSD) public leaderboard and leading performance on the Beyond The Cranial Vault (BTCV) dataset. In summary, Universal Model exhibits remarkable computational efficiency (6x faster than other dataset-specific models), demonstrates strong generalization across different hospitals, transfers well to numerous downstream tasks, and more importantly, facilitates the extensibility to new classes while alleviating the catastrophic forgetting of previously learned classes. Codes, models, and datasets are available at https://github.com/ljwztc/CLIP-Driven-Universal-Model

Exploiting Structural Consistency of Chest Anatomy for Unsupervised Anomaly Detection in Radiography Images

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. Exploiting this structured information could potentially ease the detection of anomalies from radiography images. To this end, we propose a Simple Space-Aware Memory Matrix for In-painting and Detecting anomalies from radiography images (abbreviated as SimSID). We formulate anomaly detection as an image reconstruction task, consisting of a space-aware memory matrix and an in-painting block in the feature space. During the training, SimSID can taxonomize the ingrained anatomical structures into recurrent visual patterns, and in the inference, it can identify anomalies (unseen/modified visual patterns) from the test image. Our SimSID surpasses the state of the arts in unsupervised anomaly detection by +8.0%, +5.0%, and +9.9% AUC scores on ZhangLab, COVIDx, and CheXpert benchmark datasets, respectively. Code: https://github.com/MrGiovanni/SimSID

From Pixel to Cancer: Cellular Automata in Computed Tomography

AI for cancer detection encounters the bottleneck of data scarcity, annotation difficulty, and low prevalence of early tumors. Tumor synthesis seeks to create artificial tumors in medical images, which can greatly diversify the data and annotations for AI training. However, current tumor synthesis approaches are not applicable across different organs due to their need for specific expertise and design. This paper establishes a set of generic rules to simulate tumor development. Each cell (pixel) is initially assigned a state between zero and ten to represent the tumor population, and a tumor can be developed based on three rules to describe the process of growth, invasion, and death. We apply these three generic rules to simulate tumor development--from pixel to cancer--using cellular automata. We then integrate the tumor state into the original computed tomography (CT) images to generate synthetic tumors across different organs. This tumor synthesis approach allows for sampling tumors at multiple stages and analyzing tumor-organ interaction. Clinically, a reader study involving three expert radiologists reveals that the synthetic tumors and their developing trajectories are convincingly realistic. Technically, we generate tumors at varied stages in 9,262 raw, unlabeled CT images sourced from 68 hospitals worldwide. The performance in segmenting tumors in the liver, pancreas, and kidneys exceeds prevailing literature benchmarks, underlining the immense potential of tumor synthesis, especially for earlier cancer detection. The code and models are available at https://github.com/MrGiovanni/Pixel2Cancer

Radiative Gaussian Splatting for Efficient X-ray Novel View Synthesis

X-ray is widely applied for transmission imaging due to its stronger penetration than natural light. When rendering novel view X-ray projections, existing methods mainly based on NeRF suffer from long training time and slow inference speed. In this paper, we propose a 3D Gaussian splatting-based framework, namely X-Gaussian, for X-ray novel view synthesis. Firstly, we redesign a radiative Gaussian point cloud model inspired by the isotropic nature of X-ray imaging. Our model excludes the influence of view direction when learning to predict the radiation intensity of 3D points. Based on this model, we develop a Differentiable Radiative Rasterization (DRR) with CUDA implementation. Secondly, we customize an Angle-pose Cuboid Uniform Initialization (ACUI) strategy that directly uses the parameters of the X-ray scanner to compute the camera information and then uniformly samples point positions within a cuboid enclosing the scanned object. Experiments show that our X-Gaussian outperforms state-of-the-art methods by 6.5 dB while enjoying less than 15% training time and over 73x inference speed. The application on sparse-view CT reconstruction also reveals the practical values of our method. Code and models will be publicly available at https://github.com/caiyuanhao1998/X-Gaussian . A video demo of the training process visualization is at https://www.youtube.com/watch?v=gDVf_Ngeghg .