Enhancing Brain MRI Anomaly Detection and Reasoning with ROI Rethink and Synthetic Data

Vision-language models (VLMs) read an image and produce text in a single forward pass, whereas radiologists typically inspect an image several times and consult the literature before writing a report. We introduce GAZE (Grounded Agentic Zero-shot Evaluation), a framework that lets a medical VLM work in this iterative way by calling viewer-level tools (zoom, windowing, contrast, edge detection) and two retrieval tools backed by the U.S. National Library of Medicine (PubMed for medical literature, Open-i for radiological images), with structured outputs validated against a schema and full tool-call traces recorded for auditability. On NOVA, a benchmark of 906 brain MRI cases covering 281 rare neurological conditions, GAZE reaches 58.2 mean average precision (mAP) at intersection-over-union (IoU) 0.3 for lesion localisation and 34.9% Top-1 diagnostic accuracy under a joint protocol that scores captioning, diagnosis, and localisation from the image alone, without task-specific fine-tuning. Before any tool is used, structured prompting and schema-validated outputs already improve over the published Gemini 2.0 Flash baseline (20.2 to 29.4 mAP@0.3), so framework design is itself an experimental variable. Tool use helps rare pathologies disproportionately: the fraction of cases with IoU > 0.3 rises from 17% to 58% for diagnoses with three or fewer examples versus 25% to 68% for common conditions ($\geq$10 cases), with gains tracking engagement (Gemini 3 Flash: Cohen's d = 0.79, 11.8 tool calls per case; Gemini 2.0 Flash: tools used in 8.2% of cases, no significant benefit). Retrieval ablations additionally reveal a model-dependent trade-off in which gains in diagnosis can coincide with losses in localisation, reinforcing the case for joint evaluation of diagnosis, localisation, and captioning in medical VLMs.

Spatial reasoning and visual grounding are core capabilities for vision-language models (VLMs), yet most medical VLMs produce predictions without transparent reasoning or spatial evidence. Existing benchmarks also evaluate VLMs on isolated 2D images, overlooking the volumetric nature of clinical imaging, where findings can span multiple frames or appear on only a few slices. We introduce Spatially Grounded MRI Visual Question Answering (SGMRI-VQA), a 41,307-pair benchmark for multi-frame, spatially grounded reasoning on volumetric MRI. Built from expert radiologist annotations in the fastMRI+ dataset across brain and knee studies, each QA pair includes a clinician-aligned chain-of-thought trace with frame-indexed bounding box coordinates. Tasks are organized hierarchically across detection, localization, counting/classification, and captioning, requiring models to jointly reason about what is present, where it is, and across which frames it extends. We benchmark 10 VLMs and show that supervised fine-tuning of Qwen3-VL-8B with bounding box supervision consistently improves grounding performance over strong zero-shot baselines, indicating that targeted spatial supervision is an effective path toward grounded clinical reasoning.

Vision-language models (VLMs), including medical specialists, are increasingly proposed for medical imaging, yet their stated confidence is rarely evaluated separately from correctness. We use brain MRI as a controlled, high-stakes testbed for a broader failure mode in frontier multimodal systems: models can appear competent while lacking reliable self-knowledge. We present an automatically graded behavioral audit and pilot study of six instruction-tuned VLMs (five general-purpose and one medical specialist) on 4,102 images (4,032 axial/coronal/sagittal MRI slices from 250 subjects plus 70 non-brain/noise controls), with labels derived from public metadata and released expert segmentation masks rather than new human annotation. Across models, answer coverage is near-complete, but verbalized-confidence calibration is poor: ECE ranges from 0.27 to 0.40, mean confidence on incorrect answers ranges from 0.82 to 0.97, and 33-46% of answered items are high-confidence errors. The most accurate model is also the most confident on its errors, while a base/specialist family contrast suggests that medical adaptation improves tumor-presence detection without improving confidence reliability. Open-ended diagnostics further show that hallucination and abstention vary separately from multiple-choice accuracy. These findings argue that medical-image VLM evaluation should report verbalized-confidence reliability, confident error, hallucination, and abstention alongside accuracy.