Eduardo Reis

Louis Blankemeier, Arjun Desai, Juan Manuel Zambrano Chaves et al.

Computed tomography (CT) is routinely used in clinical practice to evaluate a wide variety of medical conditions. While CT scans provide diagnoses, they also offer the ability to extract quantitative body composition metrics to analyze tissue volume and quality. Extracting quantitative body composition measures manually from CT scans is a cumbersome and time-consuming task. Proprietary software has been developed recently to automate this process, but the closed-source nature impedes widespread use. There is a growing need for fully automated body composition software that is more accessible and easier to use, especially for clinicians and researchers who are not experts in medical image processing. To this end, we have built Comp2Comp, an open-source Python package for rapid and automated body composition analysis of CT scans. This package offers models, post-processing heuristics, body composition metrics, automated batching, and polychromatic visualizations. Comp2Comp currently computes body composition measures for bone, skeletal muscle, visceral adipose tissue, and subcutaneous adipose tissue on CT scans of the abdomen. We have created two pipelines for this purpose. The first pipeline computes vertebral measures, as well as muscle and adipose tissue measures, at the T12 - L5 vertebral levels from abdominal CT scans. The second pipeline computes muscle and adipose tissue measures on user-specified 2D axial slices. In this guide, we discuss the architecture of the Comp2Comp pipelines, provide usage instructions, and report internal and external validation results to measure the quality of segmentations and body composition measures. Comp2Comp can be found at https://github.com/StanfordMIMI/Comp2Comp.

Edward H. Lee, Brendan Kelly, Emre Altinmakas et al.

While it is well known that population differences from genetics, sex, race, and environmental factors contribute to disease, AI studies in medicine have largely focused on locoregional patient cohorts with less diverse data sources. Such limitation stems from barriers to large-scale data share and ethical concerns over data privacy. Federated learning (FL) is one potential pathway for AI development that enables learning across hospitals without data share. In this study, we show the results of various FL strategies on one of the largest and most diverse COVID-19 chest CT datasets: 21 participating hospitals across five continents that comprise >10,000 patients with >1 million images. We also propose an FL strategy that leverages synthetically generated data to overcome class and size imbalances. We also describe the sources of data heterogeneity in the context of FL, and show how even among the correctly labeled populations, disparities can arise due to these biases.

Benjamin Hilprecht, Christian Hammacher, Eduardo Reis et al.

In this paper, we present our vision of differentiable ML pipelines called DiffML to automate the construction of ML pipelines in an end-to-end fashion. The idea is that DiffML allows to jointly train not just the ML model itself but also the entire pipeline including data preprocessing steps, e.g., data cleaning, feature selection, etc. Our core idea is to formulate all pipeline steps in a differentiable way such that the entire pipeline can be trained using backpropagation. However, this is a non-trivial problem and opens up many new research questions. To show the feasibility of this direction, we demonstrate initial ideas and a general principle of how typical preprocessing steps such as data cleaning, feature selection and dataset selection can be formulated as differentiable programs and jointly learned with the ML model. Moreover, we discuss a research roadmap and core challenges that have to be systematically tackled to enable fully differentiable ML pipelines.

Adrit Rao, Malte Jensen, Andrea T. Fisher et al.

Artificial intelligence allows automatic extraction of imaging biomarkers from already-acquired radiologic images. This paradigm of opportunistic imaging adds value to medical imaging without additional imaging costs or patient radiation exposure. However, many open-source image analysis solutions lack rigorous validation while commercial solutions lack transparency, leading to unexpected failures when deployed. Here, we report development and validation for two of the first fully open-sourced, FDA-510(k)-cleared deep learning pipelines to mitigate both challenges: Abdominal Aortic Quantification (AAQ) and Bone Mineral Density (BMD) estimation are both offered within the Comp2Comp package for opportunistic analysis of computed tomography scans. AAQ segments the abdominal aorta to assess aneurysm size; BMD segments vertebral bodies to estimate trabecular bone density and osteoporosis risk. AAQ-derived maximal aortic diameters were compared against radiologist ground-truth measurements on 258 patient scans enriched for abdominal aortic aneurysms from four external institutions. BMD binary classifications (low vs. normal bone density) were compared against concurrent DXA scan ground truths obtained on 371 patient scans from four external institutions. AAQ had an overall mean absolute error of 1.57 mm (95% CI 1.38-1.80 mm). BMD had a sensitivity of 81.0% (95% CI 74.0-86.8%) and specificity of 78.4% (95% CI 72.3-83.7%). Comp2Comp AAQ and BMD demonstrated sufficient accuracy for clinical use. Open-sourcing these algorithms improves transparency of typically opaque FDA clearance processes, allows hospitals to test the algorithms before cumbersome clinical pilots, and provides researchers with best-in-class methods.

Samuel Schmidgall, Rojin Ziaei, Carl Harris et al.

Evaluating large language models (LLM) in clinical scenarios is crucial to assessing their potential clinical utility. Existing benchmarks rely heavily on static question-answering, which does not accurately depict the complex, sequential nature of clinical decision-making. Here, we introduce AgentClinic, a multimodal agent benchmark for evaluating LLMs in simulated clinical environments that include patient interactions, multimodal data collection under incomplete information, and the usage of various tools, resulting in an in-depth evaluation across nine medical specialties and seven languages. We find that solving MedQA problems in the sequential decision-making format of AgentClinic is considerably more challenging, resulting in diagnostic accuracies that can drop to below a tenth of the original accuracy. Overall, we observe that agents sourced from Claude-3.5 outperform other LLM backbones in most settings. Nevertheless, we see stark differences in the LLMs' ability to make use of tools, such as experiential learning, adaptive retrieval, and reflection cycles. Strikingly, Llama-3 shows up to 92% relative improvements with the notebook tool that allows for writing and editing notes that persist across cases. To further scrutinize our clinical simulations, we leverage real-world electronic health records, perform a clinical reader study, perturb agents with biases, and explore novel patient-centric metrics that this interactive environment firstly enables.

Louis Blankemeier, Ashwin Kumar, Joseph Paul Cohen et al.

The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.

Jean-Benoit Delbrouck, Justin Xu, Johannes Moll et al. · oxford, stanford

Automated radiology report generation from chest X-ray (CXR) images has the potential to improve clinical efficiency and reduce radiologists' workload. However, most datasets, including the publicly available MIMIC-CXR and CheXpert Plus, consist entirely of free-form reports, which are inherently variable and unstructured. This variability poses challenges for both generation and evaluation: existing models struggle to produce consistent, clinically meaningful reports, and standard evaluation metrics fail to capture the nuances of radiological interpretation. To address this, we introduce Structured Radiology Report Generation (SRRG), a new task that reformulates free-text radiology reports into a standardized format, ensuring clarity, consistency, and structured clinical reporting. We create a novel dataset by restructuring reports using large language models (LLMs) following strict structured reporting desiderata. Additionally, we introduce SRR-BERT, a fine-grained disease classification model trained on 55 labels, enabling more precise and clinically informed evaluation of structured reports. To assess report quality, we propose F1-SRR-BERT, a metric that leverages SRR-BERT's hierarchical disease taxonomy to bridge the gap between free-text variability and structured clinical reporting. We validate our dataset through a reader study conducted by five board-certified radiologists and extensive benchmarking experiments.

Rohan Sanda, Asad Aali, Andrew Johnston et al.

Magnetic resonance imaging (MRI) requires long acquisition times, raising costs, reducing accessibility, and making scans more susceptible to motion artifacts. Diffusion probabilistic models that learn data-driven priors can potentially assist in reducing acquisition time. However, they typically require large training datasets that can be prohibitively expensive to collect. Patch-based diffusion models have shown promise in learning effective data-driven priors over small real-valued datasets, but have not yet demonstrated clinical value in MRI. We extend the Patch-based Diffusion Inverse Solver (PaDIS) to complex-valued, multi-coil MRI reconstruction, and compare it against a state-of-the-art whole-image diffusion baseline (FastMRI-EDM) for 7x undersampled MRI reconstruction on the FastMRI brain dataset. We show that PaDIS-MRI models trained on small datasets of as few as 25 k-space images outperform FastMRI-EDM on image quality metrics (PSNR, SSIM, NRMSE), pixel-level uncertainty, cross-contrast generalization, and robustness to severe k-space undersampling. In a blinded study with three radiologists, PaDIS-MRI reconstructions were chosen as diagnostically superior in 91.7% of cases, compared to baselines (i) FastMRI-EDM and (ii) classical convex reconstruction with wavelet sparsity. These findings highlight the potential of patch-based diffusion priors for high-fidelity MRI reconstruction in data-scarce clinical settings where diagnostic confidence matters.

Eduardo Reis, Thangarajah Akilan, Mohammed Khalid

Recent research in deep learning (DL) has investigated the use of the Fast Fourier Transform (FFT) to accelerate the computations involved in Convolutional Neural Networks (CNNs) by replacing spatial convolution with element-wise multiplications on the spectral domain. These approaches mainly rely on the FFT to reduce the number of operations, which can be further decreased by adopting the Real-Valued FFT. In this paper, we propose using the phasor form, a polar representation of complex numbers, as a more efficient alternative to the traditional approach. The experimental results, evaluated on the CIFAR-10, demonstrate that our method achieves superior speed improvements of up to a factor of 1.376 (average of 1.316) during training and up to 1.390 (average of 1.321) during inference when compared to the traditional rectangular form employed in modern CNN architectures. Similarly, when evaluated on the CIFAR-100, our method achieves superior speed improvements of up to a factor of 1.375 (average of 1.299) during training and up to 1.387 (average of 1.300) during inference. Most importantly, given the modular aspect of our approach, the proposed method can be applied to any existing convolution-based DL model without design changes.