RadGPT: Constructing 3D Image-Text Tumor Datasets

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

ScaleMAI: Accelerating the Development of Trusted Datasets and AI Models

Building trusted datasets is critical for transparent and responsible Medical AI (MAI) research, but creating even small, high-quality datasets can take years of effort from multidisciplinary teams. This process often delays AI benefits, as human-centric data creation and AI-centric model development are treated as separate, sequential steps. To overcome this, we propose ScaleMAI, an agent of AI-integrated data curation and annotation, allowing data quality and AI performance to improve in a self-reinforcing cycle and reducing development time from years to months. We adopt pancreatic tumor detection as an example. First, ScaleMAI progressively creates a dataset of 25,362 CT scans, including per-voxel annotations for benign/malignant tumors and 24 anatomical structures. Second, through progressive human-in-the-loop iterations, ScaleMAI provides Flagship AI Model that can approach the proficiency of expert annotators (30-year experience) in detecting pancreatic tumors. Flagship Model significantly outperforms models developed from smaller, fixed-quality datasets, with substantial gains in tumor detection (+14%), segmentation (+5%), and classification (72%) on three prestigious benchmarks. In summary, ScaleMAI transforms the speed, scale, and reliability of medical dataset creation, paving the way for a variety of impactful, data-driven applications.

Text-Driven Tumor Synthesis

Tumor synthesis can generate examples that AI often misses or over-detects, improving AI performance by training on these challenging cases. However, existing synthesis methods, which are typically unconditional -- generating images from random variables -- or conditioned only by tumor shapes, lack controllability over specific tumor characteristics such as texture, heterogeneity, boundaries, and pathology type. As a result, the generated tumors may be overly similar or duplicates of existing training data, failing to effectively address AI's weaknesses. We propose a new text-driven tumor synthesis approach, termed TextoMorph, that provides textual control over tumor characteristics. This is particularly beneficial for examples that confuse the AI the most, such as early tumor detection (increasing Sensitivity by +8.5%), tumor segmentation for precise radiotherapy (increasing DSC by +6.3%), and classification between benign and malignant tumors (improving Sensitivity by +8.2%). By incorporating text mined from radiology reports into the synthesis process, we increase the variability and controllability of the synthetic tumors to target AI's failure cases more precisely. Moreover, TextoMorph uses contrastive learning across different texts and CT scans, significantly reducing dependence on scarce image-report pairs (only 141 pairs used in this study) by leveraging a large corpus of 34,035 radiology reports. Finally, we have developed rigorous tests to evaluate synthetic tumors, including Text-Driven Visual Turing Test and Radiomics Pattern Analysis, showing that our synthetic tumors is realistic and diverse in texture, heterogeneity, boundaries, and pathology.

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).

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

Explanation is All You Need in Distillation: Mitigating Bias and Shortcut Learning

Bias and spurious correlations in data can cause shortcut learning, undermining out-of-distribution (OOD) generalization in deep neural networks. Most methods require unbiased data during training (and/or hyper-parameter tuning) to counteract shortcut learning. Here, we propose the use of explanation distillation to hinder shortcut learning. The technique does not assume any access to unbiased data, and it allows an arbitrarily sized student network to learn the reasons behind the decisions of an unbiased teacher, such as a vision-language model or a network processing debiased images. We found that it is possible to train a neural network with explanation (e.g by Layer Relevance Propagation, LRP) distillation only, and that the technique leads to high resistance to shortcut learning, surpassing group-invariant learning, explanation background minimization, and alternative distillation techniques. In the COLOURED MNIST dataset, LRP distillation achieved 98.2% OOD accuracy, while deep feature distillation and IRM achieved 92.1% and 60.2%, respectively. In COCO-on-Places, the undesirable generalization gap between in-distribution and OOD accuracy is only of 4.4% for LRP distillation, while the other two techniques present gaps of 15.1% and 52.1%, respectively.

Faster ISNet for Background Bias Mitigation on Deep Neural Networks

Image background features can constitute background bias (spurious correlations) and impact deep classifiers decisions, causing shortcut learning (Clever Hans effect) and reducing the generalization skill on real-world data. The concept of optimizing Layer-wise Relevance Propagation (LRP) heatmaps, to improve classifier behavior, was recently introduced by a neural network architecture named ISNet. It minimizes background relevance in LRP maps, to mitigate the influence of image background features on deep classifiers decisions, hindering shortcut learning and improving generalization. For each training image, the original ISNet produces one heatmap per possible class in the classification task, hence, its training time scales linearly with the number of classes. Here, we introduce reformulated architectures that allow the training time to become independent from this number, rendering the optimization process much faster. We challenged the enhanced models utilizing the MNIST dataset with synthetic background bias, and COVID-19 detection in chest X-rays, an application that is prone to shortcut learning due to background bias. The trained models minimized background attention and hindered shortcut learning, while retaining high accuracy. Considering external (out-of-distribution) test datasets, they consistently proved more accurate than multiple state-of-the-art deep neural network architectures, including a dedicated image semantic segmenter followed by a classifier. The architectures presented here represent a potentially massive improvement in training speed over the original ISNet, thus introducing LRP optimization into a gamut of applications that could not be feasibly handled by the original model.

ISNet: Costless and Implicit Image Segmentation for Deep Classifiers, with Application in COVID-19 Detection

In this work we propose a novel deep neural network (DNN) architecture, ISNet, to solve the task of image segmentation followed by classification, substituting the common pipeline of two networks by a single model. We designed the ISNet for high flexibility and performance: it allows virtually any classification neural network architecture to analyze a common image as if it had been previously segmented. Furthermore, in relation to the original classifier, the ISNet does not cause any increment in computational cost or architectural changes at run-time. To accomplish this, we introduce the concept of optimizing DNNs for relevance segmentation in heatmaps created by Layer-wise Relevance Propagation (LRP), which proves to be equivalent to the classification of previously segmented images. We apply an ISNet based on a DenseNet121 classifier to solve the task of COVID-19 detection in chest X-rays. We compare the model to a U-net (performing lung segmentation) followed by a DenseNet121, and to a standalone DenseNet121. Due to the implicit segmentation, the ISNet precisely ignored the X-ray regions outside of the lungs; it achieved 94.5 +/-4.1% mean accuracy with an external database, showing strong generalization capability and surpassing the other models' performances by 6 to 7.9%. ISNet presents a fast and light methodology to perform classification preceded by segmentation, while also being more accurate than standard pipelines.

FBCNN: A Deep Neural Network Architecture for Portable and Fast Brain-Computer Interfaces

Objective: To propose a novel deep neural network (DNN) architecture -- the filter bank convolutional neural network (FBCNN) -- to improve SSVEP classification in single-channel BCIs with small data lengths. Methods: We propose two models: the FBCNN-2D and the FBCNN-3D. The FBCNN-2D utilizes a filter bank to create sub-band components of the electroencephalography (EEG) signal, which it transforms using the fast Fourier transform (FFT) and analyzes with a 2D CNN. The FBCNN-3D utilizes the same filter bank, but it transforms the sub-band components into spectrograms via short-time Fourier transform (STFT), and analyzes them with a 3D CNN. We made use of transfer learning. To train the FBCNN-3D, we proposed a new technique, called inter-dimensional transfer learning, to transfer knowledge from a 2D DNN to a 3D DNN. Our BCI was conceived so as not to require calibration from the final user: therefore, the test subject data was separated from training and validation. Results: The mean test accuracy was 85.7% for the FBCCA-2D and 85% for the FBCCA-3D. Mean F1-Scores were 0.858 and 0.853. Alternative classification methods, SVM, FBCCA and a CNN, had mean accuracy of 79.2%, 80.1% and 81.4%, respectively. Conclusion: The FBCNNs surpassed traditional SSVEP classification methods in our simulated BCI, by a considerable margin (about 5% higher accuracy). Transfer learning and inter-dimensional transfer learning made training much faster and more predictable. Significance: We proposed a new and flexible type of DNN, which had a better performance than standard methods in SSVEP classification for portable and fast BCIs.