Andrea Cavalli

Wenxuan Li, Pedro R. A. S. Bassi, Lizhou Wu et al.

Pancreatic ductal adenocarcinoma (PDAC), one of the deadliest solid malignancies, is often detected at a late and inoperable stage. Retrospective reviews of prediagnostic CT scans, when conducted by expert radiologists aware that the patient later developed PDAC, frequently reveal lesions that were previously overlooked. To help detecting these lesions earlier, we developed an automated system named ePAI (early Pancreatic cancer detection with Artificial Intelligence). It was trained on data from 1,598 patients from a single medical center. In the internal test involving 1,009 patients, ePAI achieved an area under the receiver operating characteristic curve (AUC) of 0.939-0.999, a sensitivity of 95.3%, and a specificity of 98.7% for detecting small PDAC less than 2 cm in diameter, precisely localizing PDAC as small as 2 mm. In an external test involving 7,158 patients across 6 centers, ePAI achieved an AUC of 0.918-0.945, a sensitivity of 91.5%, and a specificity of 88.0%, precisely localizing PDAC as small as 5 mm. Importantly, ePAI detected PDACs on prediagnostic CT scans obtained 3 to 36 months before clinical diagnosis that had originally been overlooked by radiologists. It successfully detected and localized PDACs in 75 of 159 patients, with a median lead time of 347 days before clinical diagnosis. Our multi-reader study showed that ePAI significantly outperformed 30 board-certified radiologists by 50.3% (P < 0.05) in sensitivity while maintaining a comparable specificity of 95.4% in detecting PDACs early and prediagnostic. These findings suggest its potential of ePAI as an assistive tool to improve early detection of pancreatic cancer.

Pedro R. A. S. Bassi, Haydr A. H. Ali, Andrea Cavalli et al.

Application of Artificial Intelligence (AI) in critical domains, like the medical one, is often hampered by shortcut learning, which hinders AI generalization to diverse hospitals and patients. Shortcut learning can be caused, for example, by background biases -- features in image backgrounds that are spuriously correlated to classification labels (e.g., words in X-rays). To mitigate the influence of image background and foreground bias on AI, we introduce a new training paradigm, dubbed Training with Explanations Alone (TEA). TEA trains a classifier (TEA student) only by making its explanation heatmaps match target heatmaps from a larger teacher model. By learning from its explanation heatmaps, the TEA student pays attention to the same image features as the teacher. For example, a teacher uses a large segmenter to remove image backgrounds before classification, thus ignoring background bias. By learning from the teacher's explanation heatmaps, the TEA student learns to also ignore backgrounds -- but it does not need a segmenter. With different teachers, the TEA student can also resist bias in the image foreground. Surprisingly, by training with heatmaps alone the student output naturally matches the teacher output -- with no loss function applied to the student output. We compared the TEA student against 14 state-of-the-art methods in 5 datasets with strong background or foreground bias, including Waterbirds and an X-Ray dataset for COVID-19 and pneumonia classification. The TEA student had better resistance to bias, strongly surpassing state-of-the-art methods, and generalizing better to hospitals not seen in training.

Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.

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.

Pedro R. A. S. Bassi, Mehmet Can Yavuz, Kang Wang et al.

Cancers identified in CT scans are usually accompanied by detailed radiology reports, but publicly available CT datasets often lack these essential reports. This absence limits their usefulness for developing accurate report generation AI. To address this gap, we present AbdomenAtlas 3.0, the first public, high-quality abdominal CT dataset with detailed, expert-reviewed radiology reports. All reports are paired with per-voxel masks and they describe liver, kidney and pancreatic tumors. AbdomenAtlas 3.0 has 9,262 triplets of CT, mask and report--3,955 with tumors. These CT scans come from 17 public datasets. Besides creating the reports for these datasets, we expanded their number of tumor masks by 4.2x, identifying 3,011 new tumor cases. Notably, the reports in AbdomenAtlas 3.0 are more standardized, and generated faster than traditional human-made reports. They provide details like tumor size, location, attenuation and surgical resectability. These reports were created by 12 board-certified radiologists using our proposed RadGPT, a novel framework that converted radiologist-revised tumor segmentation masks into structured and narrative reports. Besides being a dataset creation tool, RadGPT can also become a fully-automatic, segmentation-assisted report generation method. We benchmarked this method and 5 state-of-the-art report generation vision-language models. Our results show that segmentation strongly improves tumor detection in AI-made reports.

Pedro R. A. S. Bassi, Qilong Wu, Wenxuan Li et al.

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).

Pedro R. A. S. Bassi, Sergio Decherchi, Andrea Cavalli

Bias or spurious correlations in image backgrounds can impact neural networks, causing shortcut learning (Clever Hans Effect) and hampering generalization to real-world data. ISNet, a recently introduced architecture, proposed the optimization of Layer-Wise Relevance Propagation (LRP, an explanation technique) heatmaps, to mitigate the influence of backgrounds on deep classifiers. However, ISNet's training time scales linearly with the number of classes in an application. Here, we propose reformulated architectures whose training time becomes independent from this number. Additionally, we introduce a concise and model-agnostic LRP implementation. We challenge the proposed architectures using synthetic background bias, and COVID-19 detection in chest X-rays, an application that commonly presents background bias. The networks hindered background attention and shortcut learning, surpassing multiple state-of-the-art models on out-of-distribution test datasets. Representing a potentially massive training speed improvement over ISNet, the proposed architectures introduce LRP optimization into a gamut of applications that the original model cannot feasibly handle.

Pedro R. A. S. Bassi, Sergio S. J. Dertkigil, Andrea Cavalli

Features in images' backgrounds can spuriously correlate with the images' classes, representing background bias. They can influence the classifier's decisions, causing shortcut learning (Clever Hans effect). The phenomenon generates deep neural networks (DNNs) that perform well on standard evaluation datasets but generalize poorly to real-world data. Layer-wise Relevance Propagation (LRP) explains DNNs' decisions. Here, we show that the optimization of LRP heatmaps can minimize the background bias influence on deep classifiers, hindering shortcut learning. By not increasing run-time computational cost, the approach is light and fast. Furthermore, it applies to virtually any classification architecture. After injecting synthetic bias in images' backgrounds, we compared our approach (dubbed ISNet) to eight state-of-the-art DNNs, quantitatively demonstrating its superior robustness to background bias. Mixed datasets are common for COVID-19 and tuberculosis classification with chest X-rays, fostering background bias. By focusing on the lungs, the ISNet reduced shortcut learning. Thus, its generalization performance on external (out-of-distribution) test databases significantly surpassed all implemented benchmark models.