Resolution Meets Reduction: Efficient Visual Context for 3D Radiology Report Generation
Authors: Jonathan Suprijadi, Raphael Stock, Moritz Langenberg, David Zimmerer, Kim-Celine Kahl, Stefan Denner, Yannick Kirchhoff, Karol Gotkowski, +5 more
Organizations: Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
Abstract
Vision-language models offer a promising path toward automating radiology report generation, but applying them to full 3D CT volumes poses substantial computational challenges. Modern foundation vision encoders (VEs) can produce tens of thousands of vision tokens per scan, making the visual sequence passed to the large language model (LLM) a primary computational bottleneck. Vision-to-language projectors can compress this sequence to reduce computation, but may discard clinically relevant detail; conversely, effective compression can accommodate higher-resolution inputs while keeping the downstream token count fixed. How this vision-token budget should be allocated across input field of view, spatial resolution, and vision-to-language projection therefore remains an open design question. We systematically evaluate four heterogeneous VEs (CNN- and ViT-based), five token-reducing projectors at up to 64x compression alongside a non-reducing MLP projector baseline, and five instruction-tuned LLMs (1.7B--4B) on two large-scale CT report datasets (CT-RATE and Merlin). At matched LLM token budgets, anatomy-guided region of interest cropping is the most consistent strategy, improving clinical macro F1 in 19 of 20 settings by +3.7 points on average for the 3D ViT Primus encoder and +1.1 for the slice-based 2D ViT Curia encoder. Increasing input resolution further is strongly projector-dependent: the PerceiverResampler, paired with higher-resolution Curia features, yields the strongest configuration in the resolution study on both datasets. Our best configurations achieve state-of-the-art clinical macro F1 on the test sets, reaching 49.5 on CT-RATE and 49.0 on Merlin. Code and models will be published upon publication.
Vision-language pre-training (VLP) holds great promise for general-purpose medical AI by leveraging radiology reports as rich textual supervision, yet existing methods struggle with 3D CT imaging due to inefficient visual backbones and coarse semantic alignment. To address these issues, we propose a tailored VLP framework featuring three key components: (1) a CNN-ViT hybrid encoder that replaces ViT's patch embedding with a 3D CNN backbone to efficiently capture local anatomical details while preserving global attention and compatibility with pre-trained cross-modal priors; (2) a disease-level contrastive learning mechanism using learnable query tokens to dynamically extract disease-specific semantics from full reports and align them with corresponding visual features, thereby disentangling distinct diseases within the same anatomical region; and (3) a diagnosis-aware prompt strategy that employs real clinical phrases and aggregated disease prototypes to bridge the pre-training-inference gap and enhance zero-shot diagnostic reliability. Our model achieves state-of-the-art performance on CT-RATE (84.4% AUC, +5.1%) and Rad-ChestCT (75.4% AUC, +5.4%), with even larger gains (+9.8% AUC) on a challenging 60-disease benchmark, and demonstrates strong transferability to radiology report generation, underscoring the generality and clinical utility of our approach.
A 3D CT scan entering a vision-language model produces a long sequence of visual tokens, often thousands to tens of thousands per volume, and this sequence must be compressed before a language model can consume it. Token compression is well studied in general vision, but little of it targets 3D CT specifically. A common baseline is grid average, which pools regular grid cells and can blend distinct anatomy, lesion, and air into one token. We present \textbf{ORCA} (ORgan-Centroid Aggregation), a token compressor for 3D CT. It merges adjacent tokens with organ guidance and adds a sinusoidal encoding of each region's centroid to preserve spatial layout. This preserves the anatomical information a downstream model needs. ORCA is training-free and plug-and-play, producing an adjustable token set without any model change or text query. We evaluate it across two datasets (CT-RATE and Merlin) and five encoders. The evaluation spans two task types: attribute prediction over five families (size, density, location, texture, and disease) and text generation (visual question answering and report generation). At matched token budgets, ORCA improves consistently over existing compression methods. It shrinks the visual context 64× and its KV-cache 50×, and is 31× faster to process each volume. Code released at https://github.com/renjie-liang/ORCA-3DCT.
Modern 3D medical vision-language models (VLMs) can generate fluent radiology-style text while exhibit critically low pathology detection and output diversity, collapsing to generic templates that under-report rare yet critical findings. We identify this failure mode as Template Collapse. This failure stems from the unique constraints of 3D medical imaging, e.g., limited data, severe label imbalance, and weak signals from volumetric encoders. Under these constraints, text-generation objectives encourage shortcut learning and fluent but weakly grounded reports. We systematically diagnose the Template Collapse through clinical fidelity, output diversity, normal-template bias, and rare-finding survival. To mitigate it, we propose CLarGen, a decoupled framework that separates what to say (clinical detection) from how to say it (language synthesis). CLarGen uses (i) a Latent Query Transformer for multi-label pathology detection, (ii) pathology-guided retrieval for clinically matched exemplars, and (iii) a medical language model to synthesize the final report from detected findings and retrieved context. Across state-of-the-art 3D CT report generation baselines, CLarGen mitigates Template Collapse and substantially improves clinical accuracy (macro-F1 0.487 vs. 0.189; CRG 0.472 vs. 0.368) while maintaining fluent reporting. Our results suggest that explicit, measurable clinical grounding is essential for template-collapse-resistant 3D CT report generation. Code is available at https://github.com/ai-med/CLarGen.