arXiv:2406.06512v2 Announce Type: replace-cross Abstract: 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.

arXiv:2510.14581v3 Announce Type: replace-cross Abstract: Obtaining high-quality labels for large datasets is expensive, requiring massive annotations from human experts. While AI models offer a cost-effective alternative by predicting labels, their label quality is compromised by the unavoidable labeling errors. Existing methods mitigate this issue through selective labeling, where AI labels a subset and human labels the remainder. However, these methods lack theoretical guarantees on the quality of AI-assigned labels, often resulting in unacceptably high labeling error within the AI-labeled subset. To address this, we introduce \textbf{Conformal Labeling}, a novel method to identify instances where AI predictions can be provably trusted. This is achieved by controlling the false discovery rate (FDR), the proportion of incorrect labels within the selected subset. In particular, we construct a conformal $p$-value for each test instance by comparing AI models' predicted confidence to those of calibration instances mislabeled by AI models. Then, we select test instances whose $p$-values are below a data-dependent threshold, certifying AI models' predictions as trustworthy. We provide theoretical guarantees that Conformal Labeling controls the FDR below the nominal level, ensuring that a predefined fraction of AI-assigned labels is correct on average. Extensive experiments demonstrate that our method achieves tight FDR control with high power across various tasks, including image and text labeling, and LLM QA.