Benchmarks for out-of-distribution (OOD) generalization frequently show a strong positive correlation between in-distribution (ID) and OOD accuracy across models, termed "accuracy-on-the-line." This pattern is often taken to imply that spurious correlations - correlations that improve ID but reduce OOD performance - are rare in practice. We find that this positive correlation is often an artifact of aggregating heterogeneous OOD examples. Using a simple gradient-based method, OODSelect, we identify semantically coherent OOD subsets where accuracy on the line does not hold. Across widely used distribution shift benchmarks, the OODSelect uncovers subsets, sometimes over half of the standard OOD set, where higher ID accuracy predicts lower OOD accuracy. Our findings indicate that aggregate metrics can obscure important failure modes of OOD robustness. We release code and the identified subsets to facilitate further research.

Medical object detection suffers when a single detector is trained on mixed medical modalities (e.g., CXR, CT, MRI) due to heterogeneous statistics and disjoint representation spaces. To address this challenge, we turn to representation alignment, an approach that has proven effective for bringing features from different sources into a shared space. Specifically, we target the representations of DETR-style object queries and propose a simple, detector-agnostic framework to align them with modality context. First, we define modality tokens: compact, text-derived embeddings encoding imaging modality that are lightweight and require no extra annotations. We integrate the modality tokens into the detection process via Multimodality Context Attention (MoCA), mixing object-query representations via self-attention to propagate modality context within the query set. This preserves DETR-style architectures and adds negligible latency while injecting modality cues into object queries. We further introduce QueryREPA, a short pretraining stage that aligns query representations to their modality tokens using a task-specific contrastive objective with modality-balanced batches. Together, MoCA and QueryREPA produce modality-aware, class-faithful queries that transfer effectively to downstream training. Across diverse modalities trained altogether, the proposed approach consistently improves AP with minimal overhead and no architectural modifications, offering a practical path toward robust multimodality medical object detection. Project page: https://araseo.github.io/alignyourquery/.

Chest radiographs (CXRs) are among the most common tests in medicine. Automated image interpretation may reduce radiologists\' workload and expand access to diagnostic expertise. Deep learning multi-task and foundation models have shown strong performance for CXR interpretation but are vulnerable to shortcut learning, where models rely on spurious and off-target correlations rather than clinically relevant features to make decisions. We introduce RoentMod, a counterfactual image editing framework that generates anatomically realistic CXRs with user-specified, synthetic pathology while preserving unrelated anatomical features of the original scan. RoentMod combines an open-source medical image generator (RoentGen) with an image-to-image modification model without requiring retraining. In reader studies with board-certified radiologists and radiology residents, RoentMod-produced images appeared realistic in 93\% of cases, correctly incorporated the specified finding in 89-99\% of cases, and preserved native anatomy comparable to real follow-up CXRs. Using RoentMod, we demonstrate that state-of-the-art multi-task and foundation models frequently exploit off-target pathology as shortcuts, limiting their specificity. Incorporating RoentMod-generated counterfactual images during training mitigated this vulnerability, improving model discrimination across multiple pathologies by 3-19\% AUC in internal validation and by 1-11\% for 5 out of 6 tested pathologies in external testing. These findings establish RoentMod as a broadly applicable tool for probing and correcting shortcut learning in medical AI. By enabling controlled counterfactual interventions, RoentMod enhances the robustness and interpretability of CXR interpretation models and provides a generalizable strategy for improving foundation models in medical imaging.

Achieving robust performance and fairness across diverse patient populations remains a challenge in developing clinically deployable deep learning models for diagnostic imaging. Synthetic data generation has emerged as a promising strategy to address limitations in dataset scale and diversity. We introduce RoentGen-v2, a text-to-image diffusion model for chest radiographs that enables fine-grained control over both radiographic findings and patient demographic attributes, including sex, age, and race/ethnicity. RoentGen-v2 is the first model to generate clinically plausible images with demographic conditioning, facilitating the creation of a large, demographically balanced synthetic dataset comprising over 565,000 images. We use this large synthetic dataset to evaluate optimal training pipelines for downstream disease classification models. In contrast to prior work that combines real and synthetic data naively, we propose an improved training strategy that leverages synthetic data for supervised pretraining, followed by fine-tuning on real data. Through extensive evaluation on over 137,000 chest radiographs from five institutions, we demonstrate that synthetic pretraining consistently improves model performance, generalization to out-of-distribution settings, and fairness across demographic subgroups. Across datasets, synthetic pretraining led to a 6.5% accuracy increase in the performance of downstream classification models, compared to a modest 2.7% increase when naively combining real and synthetic data. We observe this performance improvement simultaneously with the reduction of the underdiagnosis fairness gap by 19.3%. These results highlight the potential of synthetic imaging to advance equitable and generalizable medical deep learning under real-world data constraints. We open source our code, trained models, and synthetic dataset at https://github.com/StanfordMIMI/RoentGen-v2 .

In intensive care units (ICUs), patients with complex clinical conditions require vigilant monitoring and prompt interventions. Chest X-rays (CXRs) are a vital diagnostic tool, providing insights into clinical trajectories, but their irregular acquisition limits their utility. Existing tools for CXR interpretation are constrained by cross-sectional analysis, failing to capture temporal dynamics. To address this, we introduce CXR-TFT, a novel multi-modal framework that integrates temporally sparse CXR imaging and radiology reports with high-frequency clinical data, such as vital signs, laboratory values, and respiratory flow sheets, to predict the trajectory of CXR findings in critically ill patients. CXR-TFT leverages latent embeddings from a vision encoder that are temporally aligned with hourly clinical data through interpolation. A transformer model is then trained to predict CXR embeddings at each hour, conditioned on previous embeddings and clinical measurements. In a retrospective study of 20,000 ICU patients, CXR-TFT demonstrated high accuracy in forecasting abnormal CXR findings up to 12 hours before they became radiographically evident. This predictive capability in clinical data holds significant potential for enhancing the management of time-sensitive conditions like acute respiratory distress syndrome, where early intervention is crucial and diagnoses are often delayed. By providing distinctive temporal resolution in prognostic CXR analysis, CXR-TFT offers actionable 'whole patient' insights that can directly improve clinical outcomes.

Accurate and interpretable multi-disease diagnosis remains a critical challenge in medical research, particularly when leveraging heterogeneous multimodal medical data. Current approaches often rely on single-modal data, limiting their ability to comprehensively understand complex diseases. To address this, we propose MedTVT-R1, a novel Multimodal Large Language Model (MLLM) framework designed to integrate clinical multimodal data for reasoning and diagnosing multiple diseases. We construct MedTVT-QA, a curated instruction dataset that provides question-answer pairs for physiological-level interpretations and disease-level diagnoses with a Chain of Evidence approach. MedTVT-R1 incorporates a modality perception layer to capture inter-modal dependencies and adaptively weight modality contributions. Additionally, we employ Group Relative Policy Optimization (GRPO)-based Reinforcement Fine-Tuning with a Jaccard Reward function to enhance diagnostic reasoning. Experimental results demonstrate MedTVT-R1's superiority in multimodal feature utilization and multi-disease diagnosis, offering significant potential for clinical applications such as diagnostic report generation and comorbidity reasoning. The dataset and code are available at https://github.com/keke-nice/MedTVT-R1.

Modern diagnostic workflows are increasingly multimodal, integrating diverse data sources such as medical images, structured records, and physiological time series. Among these, electrocardiograms (ECGs) and chest X-rays (CXRs) are two of the most widely used modalities for cardiac assessment. While CXRs provide rich diagnostic information, ECGs are more accessible and can support scalable early warning systems. In this work, we propose CroMoTEX, a novel contrastive learning-based framework that leverages chest X-rays during training to learn clinically informative ECG representations for multiple cardiac-related pathologies: cardiomegaly, pleural effusion, and edema. Our method aligns ECG and CXR representations using a novel supervised cross-modal contrastive objective with adaptive hard negative weighting, enabling robust and task-relevant feature learning. At test time, CroMoTEX relies solely on ECG input, allowing scalable deployment in real-world settings where CXRs may be unavailable. Evaluated on the large-scale MIMIC-IV-ECG and MIMIC-CXR datasets, CroMoTEX outperforms baselines across all three pathologies, achieving up to 78.31 AUROC on edema. Our code is available at github.com/vineetpmoorty/cromotex.

We present a novel approach to Chest X-ray (CXR) Visual Question Answering (VQA), addressing both single-image image-difference questions. Single-image questions focus on abnormalities within a specific CXR ("What abnormalities are seen in image X?"), while image-difference questions compare two longitudinal CXRs acquired at different time points ("What are the differences between image X and Y?"). We further explore how the integration of radiology reports can enhance the performance of VQA models. While previous approaches have demonstrated the utility of radiology reports during the pre-training phase, we extend this idea by showing that the reports can also be leveraged as additional input to improve the VQA model's predicted answers. First, we propose a unified method that handles both types of questions and auto-regressively generates the answers. For single-image questions, the model is provided with a single CXR. For image-difference questions, the model is provided with two CXRs from the same patient, captured at different time points, enabling the model to detect and describe temporal changes. Taking inspiration from 'Chain-of-Thought reasoning', we demonstrate that performance on the CXR VQA task can be improved by grounding the answer generator module with a radiology report predicted for the same CXR. In our approach, the VQA model is divided into two steps: i) Report Generation (RG) and ii) Answer Generation (AG). Our results demonstrate that incorporating predicted radiology reports as evidence to the AG model enhances performance on both single-image and image-difference questions, achieving state-of-the-art results on the Medical-Diff-VQA dataset.

Computed tomography (CT) is a key imaging modality for diagnosis, yet its clinical utility is marred by high radiation exposure and long turnaround times, restricting its use for larger-scale screening. Although chest radiography (CXR) is more accessible and safer, existing CXR foundation models focus primarily on detecting diseases that are readily visible on the CXR. Recently, works have explored training disease classification models on simulated CXRs, but they remain limited to recognizing a single disease type from CT. CT foundation models have also emerged with significantly improved detection of pathologies in CT. However, the generalized application of CT-derived labels on CXR has remained illusive. In this study, we propose X2CT-CLIP, a tri-modal knowledge transfer learning framework that bridges the modality gap between CT and CXR while reducing the computational burden of model training. Our approach is the first work to enable multi-abnormality classification in CT, using CXR, by transferring knowledge from 3D CT volumes and associated radiology reports to a CXR encoder via a carefully designed tri-modal alignment mechanism in latent space. Extensive evaluations on three multi-label CT datasets demonstrate that our method outperforms state-of-the-art baselines in cross-modal retrieval, few-shot adaptation, and external validation. These results highlight the potential of CXR, enriched with knowledge derived from CT, as a viable efficient alternative for disease detection in resource-limited settings.

Anatomical abnormality detection and report generation of chest X-ray (CXR) are two essential tasks in clinical practice. The former aims at localizing and characterizing cardiopulmonary radiological findings in CXRs, while the latter summarizes the findings in a detailed report for further diagnosis and treatment. Existing methods often focused on either task separately, ignoring their correlation. This work proposes a co-evolutionary abnormality detection and report generation (CoE-DG) framework. The framework utilizes both fully labeled (with bounding box annotations and clinical reports) and weakly labeled (with reports only) data to achieve mutual promotion between the abnormality detection and report generation tasks. Specifically, we introduce a bi-directional information interaction strategy with generator-guided information propagation (GIP) and detector-guided information propagation (DIP). For semi-supervised abnormality detection, GIP takes the informative feature extracted by the generator as an auxiliary input to the detector and uses the generator's prediction to refine the detector's pseudo labels. We further propose an intra-image-modal self-adaptive non-maximum suppression module (SA-NMS). This module dynamically rectifies pseudo detection labels generated by the teacher detection model with high-confidence predictions by the student.Inversely, for report generation, DIP takes the abnormalities' categories and locations predicted by the detector as input and guidance for the generator to improve the generated reports.