Virtual Biopsy for Intracranial Tumors Diagnosis on MRI

Brain tumors represent one of the most critical neurological conditions, where early and accurate diagnosis is directly correlated with patient survival rates. Manual interpretation of Magnetic Resonance Imaging (MRI) scans is time-intensive, subject to inter-observer variability, and demands significant specialist expertise. This paper proposes a deep learning framework for automated four-class brain tumor classification distinguishing glioma, meningioma, pituitary tumor, and healthy brain tissue from a dataset of 7,023 MRI scans. The proposed system employs a Vision Transformer (ViT-B/16) pretrained on ImageNet-21k as the backbone, augmented with a clinically motivated preprocessing and training pipeline. Contrast Limited Adaptive Histogram Equalization (CLAHE) is applied to enhance local contrast and accentuate tumor boundaries invisible to standard normalization. A two-stage fine-tuning strategy is adopted: the classification head is warmed up with the backbone frozen, followed by full fine-tuning with discriminative learning rates. MixUp and CutMix augmentation is applied per batch to improve generalization. Exponential Moving Average (EMA) of weights and Test-Time Augmentation (TTA) further stabilize and boost performance. Attention Rollout visualization provides clinically interpretable heatmaps of the brain regions driving each prediction. The proposed model achieves a test accuracy of 99.29%, macro F1-score of 99.25%, and perfect recall on both healthy and meningioma classes, outperforming all CNN-based baselines

We developed BrainVLM to classify all 12 World Health Organization (WHO) 2021 brain tumor types. BrainVLM integrates an uncertainty quantification strategy to indicate prediction reliability and a module for generating radiology reports to elucidate the clinical rationale. BrainVLM was trained on multi-modal data (MRI scans, demographics, and radiology reports) from 40,043 individuals. It was validated on 5,211 patients with pathologically confirmed brain tumors, including 3,877 held-out patients from the primary hospital and 1,334 patients from 11 independent hospitals. We further conducted two proof-of-concept studies to validate its clinical utility in AI-clinician workflows: 1) a blinded multireader study where 12 neuroradiologists across varying experience levels interpreted 248 retrospective cases with or without AI assistance, and 2) a real-world prospective study in which 1,009 patients were independently and blindly assessed by BrainVLM and radiologists before surgery. Additionally, we demonstrated BrainVLM's utility in preoperative molecular subgroup prediction for adult-type diffuse gliomas, using a multi-center cohort of 632 patients. In primary evaluation, BrainVLM achieved an area under the curve (macro-AUC) of 0.85 (95% CI: 0.84-0.86), and an F1 score of 0.82 (95% CI: 0.81-0.83), surpassing neuroradiologists (F1 = 0.80 (95% CI: 0.79-0.81)). In external validation across 11 centers, BrainVLM achieved an AUC = 0.80 (95% CI: 0.79-0.82) and F1 = 0.75 (95% CI: 0.73-0.78), compared with F1 = 0.71 (95% CI: 0.69-0.73) for neuroradiologists. In prospective real-world evaluation, BrainVLM maintained performance comparable to neuroradiologists. The BrainVLM project page is available at https://hku-healthai.github.io/brainvlm_project.github.io/.

Gliomas are aggressive brain tumors that infiltrate surrounding tissue beyond the visible tumor margins observed on Magnetic Resonance Imaging (MRI). Predicting the spatial extent of this infiltration is essential for surgical planning and radiation therapy, yet existing deep learning approaches focus on segmenting the visible tumor rather than estimating infiltration risk in the surrounding tissue. This paper presents InfiltrNet, a novel dual-branch architecture that combines a convolutional neural network (CNN) encoder with a Swin Transformer encoder through cross-attention fusion modules to predict three-zone infiltration risk maps from multimodal MRI. A label generation strategy based on distance transforms is proposed to derive reproducible infiltration risk zones from standard Brain Tumor Segmentation (BraTS) annotations. InfiltrNet is trained with a combined Dice-CrossEntropy and boundary-aware loss augmented by auxiliary supervision heads at intermediate decoder levels. Extensive experiments on BraTS 2020 and BraTS 2025 demonstrate that InfiltrNet outperforms five established baselines. Explainability analysis using GradCAM++ and Occlusion sensitivity confirms that the model attends to clinically relevant peritumoral regions.