Brain Tumor Classification

Accurate intraoperative assessment of glioma infiltration is essential for maximizing tumor resection while preserving functional brain tissue. Fluorescence lifetime imaging (FLIm) offers real-time, label-free biochemical contrast, but its clinical utility is challenged by biological heterogeneity, class imbalance, and variability in histopathological labeling. We present a data-centric AI (DC-AI) framework that integrates confident learning (CL), class refinement, and targeted label evaluation to develop a robust multi-class FLIm classifier for glioblastoma (GBM) resection margins. FLIm data were collected from 192 tissue margins across 31 newly diagnosed IDH-wildtype GBM patients and initially labeled into seven tumor cellularity classes by an expert neuropathologist. CL was applied to quantify FLIm point-level confidence, identify label inconsistencies, and guide iterative class merging into a three-class scheme ("low", "moderate", "high"). The resulting high-fidelity dataset enabled training a model that achieved 96% accuracy in the three-class task. SHAP analysis revealed class-specific FLIm feature importance, highlighting distinct optical signatures across the infiltration spectrum. Targeted FLIm analysis further identified biological (e.g., gray matter composition) and acquisition-related (e.g., blood contamination) contributors to low-confidence predictions. Blinded re-evaluation of margins flagged by CL demonstrated intra-pathologist variability, underscoring the value of selective relabeling rather than exhaustive review. Together, these findings demonstrate that a DC-AI framework can systematically improve data reliability, enhance model robustness, and refine biological interpretation of FLIm signals, supporting the development of clinically actionable optical tools for real-time glioma margin assessment.

Early detection and classifying brain tumors using Magnetic Resonance Imaging (MRI) images is highly important but difficult to extract in medical images. Convolutional Neural Networks (CNNs) are good at capturing both local texture and spatial information whereas Vision Transformers (ViTs) are good at capturing long-range global dependencies. We propose a new hybrid architecture that combines a SqueezeNet-style CNN branch with a MobileViT-style global transformer branch, through an Adaptive Attention Gate mechanism, in this paper. The gate learns dynamically per-sample, per-feature weights to weight the contribution of each branch, allowing context-sensitive merging of local and global representations. The proposed model has a test accuracy of 97.60, a precision of 97.30, a recall of 97.50, an F1-score of 97.40, and a macro-average area under the curve (AUC) of 0.9946 with a trained and evaluated on the Brain Tumor MRI Dataset (Kaggle). These scores are higher than single CNN and ViT baselines, and current competitive fusion methods, showing that dynamic feature weighting is an effective way to classify medical images.

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

Accurate diagnosis of pediatric brain tumors, starting with histopathology, presents unique challenges for deep learning, including severe data scarcity, class imbalance, and fine-grained morphologic overlap across diagnostically distinct subtypes. While pathology foundation models have advanced patch-level representation learning, their effective adaptation to weakly supervised pediatric brain tumor classification under limited data remains underexplored. In this work, we introduce an expert-guided contrastive fine-tuning framework for pediatric brain tumor diagnosis from whole-slide images (WSI). Our approach integrates contrastive learning into slide-level multiple instance learning (MIL) to explicitly regularize the geometry of slide-level representations during downstream fine-tuning. We propose both a general supervised contrastive setting and an expert-guided variant that incorporates clinically informed hard negatives targeting diagnostically confusable subtypes. Through comprehensive experiments on pediatric brain tumor WSI classification under realistic low-sample and class-imbalanced conditions, we demonstrate that contrastive fine-tuning yields measurable improvements in fine-grained diagnostic distinctions. Our experimental analyses reveal complementary strengths across different contrastive strategies, with expert-guided hard negatives promoting more compact intra-class representations and improved inter-class separation. This work highlights the importance of explicitly shaping slide-level representations for robust fine-grained classification in data-scarce pediatric pathology settings.

The scarcity of labeled clinical data in oncology makes Few-Shot Learning (FSL) a critical framework for Computer Aided Diagnostics, but we observed that standard Prototypical Networks often struggle with the "prototype instability" caused by morphological noise and high intra-class variance in brain tumor scans. Our work attempts to minimize this by integrating a non-linear Logistic Chaos Module into a fine-tuned ResNet-18 backbone creating the Chaos-Enhanced ProtoNet(CE-ProtoNet). Using the deterministic ergodicity of the logistic chaos map we inject controlled perturbations into support features during episodic training-essentially for "stress testing" the embedding space. This process makes the model to converge on noise-invariant representations without increasing computational overhead. Testing this on a 4-way 5-shot brain tumor classification task, we found that a 15% chaotic injection level worked efficiently to stabilize high-dimensional clusters and reduce class dispersion. Our method achieved a peak test accuracy of 84.52%, outperforming standard ProtoNet. Our results suggest the idea of using chaotic perturbation as an efficient, low-overhead regularization tool, for the data-scarce regimes.

Medical imaging techniques, especially Magnetic Resonance Imaging (MRI), are accepted as the gold standard in the diagnosis and treatment planning of neurological diseases. However, the manual analysis of MRI images is a time-consuming process for radiologists and is prone to human error due to fatigue. In this study, two different Deep Learning approaches were developed and analyzed comparatively for the automatic detection and classification of brain tumors (Glioma, Meningioma, Pituitary, and No Tumor). In the first approach, a custom Convolutional Neural Network (CNN) architecture named "OkanNet", which has a low computational cost and fast training time, was designed from scratch. In the second approach, the Transfer Learning method was applied using the 50-layer ResNet-50 [1] architecture, pre-trained on the ImageNet dataset. In experiments conducted on an extended dataset compiled by Masoud Nickparvar containing a total of $7,023$ MRI images, the Transfer Learning-based ResNet-50 model exhibited superior classification performance, achieving $96.49\%$ Accuracy and $0.963$ Precision. In contrast, the custom OkanNet architecture reached an accuracy rate of $88.10\%$; however, it proved to be a strong alternative for mobile and embedded systems with limited computational power by yielding results approximately $3.2$ times faster ($311$ seconds) than ResNet-50 in terms of training time. This study demonstrates the trade-off between model depth and computational efficiency in medical image analysis through experimental data.

The accurate classification of brain tumors from MRI scans is essential for effective diagnosis and treatment planning. This paper presents a weighted ensemble learning approach that combines deep learning and traditional machine learning models to improve classification performance. The proposed system integrates multiple classifiers, including ResNet101, DenseNet121, Xception, CNN-MRI, and ResNet50 with edge-enhanced images, SVM, and KNN with HOG features. A weighted voting mechanism assigns higher influence to models with better individual accuracy, ensuring robust decision-making. Image processing techniques such as Balance Contrast Enhancement, K-means clustering, and Canny edge detection are applied to enhance feature extraction. Experimental evaluations on the Figshare and Kaggle MRI datasets demonstrate that the proposed method achieves state-of-the-art accuracy, outperforming existing models. These findings highlight the potential of ensemble-based learning for improving brain tumor classification, offering a reliable and scalable framework for medical image analysis.

Deep learning (DL) models have achieved strong performance in an intelligence healthcare setting, yet most existing approaches operate as black boxes and ignore the physical processes that govern tumor growth, limiting interpretability, robustness, and clinical trust. To address this limitation, we propose PhysNet, a physics-embedded DL framework that integrates tumor growth dynamics directly into the feature learning process of a convolutional neural network (CNN). Unlike conventional physics-informed methods that impose physical constraints only at the output level, PhysNet embeds a reaction diffusion model of tumor growth within intermediate feature representations of a ResNet backbone. The architecture jointly performs multi-class tumor classification while learning a latent tumor density field, its temporal evolution, and biologically meaningful physical parameters, including tumor diffusion and growth rates, through end-to-end training. This design is necessary because purely data-driven models, even when highly accurate or ensemble-based, cannot guarantee physically consistent predictions or provide insight into tumor behavior. Experimental results on a large brain MRI dataset demonstrate that PhysNet outperforms multiple state-of-the-art DL baselines, including MobileNetV2, VGG16, VGG19, and ensemble models, achieving superior classification accuracy and F1-score. In addition to improved performance, PhysNet produces interpretable latent representations and learned bio-physical parameters that align with established medical knowledge, highlighting physics-embedded representation learning as a practical pathway toward more trustworthy and clinically meaningful medical AI systems.

MRI-based medical imaging has become indispensable in modern clinical diagnosis, particularly for brain tumor detection. However, the rapid growth in data volume poses challenges for conventional diagnostic approaches. Although deep learning has shown strong performance in automated classification, many existing solutions are confined to closed technical architectures, limiting reproducibility and further academic development. PhyDCM is introduced as an open-source software framework that integrates a hybrid classification architecture based on MedViT with standardized DICOM processing and an interactive desktop visualization interface. The system is designed as a modular digital library that separates computational logic from the graphical interface, allowing independent modification and extension of components. Standardized preprocessing, including intensity rescaling and limited data augmentation, ensures consistency across varying MRI acquisition settings. Experimental evaluation on MRI datasets from BRISC2025 and curated Kaggle collections (FigShare, SARTAJ, and Br35H) demonstrates stable diagnostic performance, achieving over 93% classification accuracy across categories. The framework supports structured, exportable outputs and multi-planar reconstruction of volumetric data. By emphasizing transparency, modularity, and accessibility, PhyDCM provides a practical foundation for reproducible AI-driven medical image analysis, with flexibility for future integration of additional imaging modalities.

The Brain Tumor Reporting and Data System (BT-RADS) standardizes post-treatment MRI response assessment in patients with diffuse gliomas but requires complex integration of imaging trends, medication effects, and radiation timing. This study evaluates an end-to-end multi-agent large language model (LLM) and convolutional neural network (CNN) system for automated BT-RADS classification. A multi-agent LLM system combined with automated CNN-based tumor segmentation was retrospectively evaluated on 509 consecutive post-treatment glioma MRI examinations from a single high-volume center. An extractor agent identified clinical variables (steroid status, bevacizumab status, radiation date) from unstructured clinical notes, while a scorer agent applied BT-RADS decision logic integrating extracted variables with volumetric measurements. Expert reference standard classifications were established by an independent board-certified neuroradiologist. Of 509 examinations, 492 met inclusion criteria. The system achieved 374/492 (76.0%; 95% CI, 72.1%-79.6%) accuracy versus 283/492 (57.5%; 95% CI, 53.1%-61.8%) for initial clinical assessments (+18.5 percentage points; P<.001). Context-dependent categories showed high sensitivity (BT-1b 100%, BT-1a 92.7%, BT-3a 87.5%), while threshold-dependent categories showed moderate sensitivity (BT-3c 74.8%, BT-2 69.2%, BT-4 69.3%, BT-3b 57.1%). For BT-4, positive predictive value was 92.9%. The multi-agent LLM system achieved higher BT-RADS classification agreement with expert reference standard compared to initial clinical scoring, with high accuracy for context-dependent scores and high positive predictive value for BT-4 detection.

Accurate classification of brain tumors from magnetic resonance imaging (MRI) plays a critical role in early diagnosis and effective treatment planning. In this study, we propose a deep learning framework based on Vision Transformers (ViT) enhanced with colormap-based feature representation to improve multi-class brain tumor classification performance. The proposed approach leverages the ability of transformer architectures to capture long-range dependencies while incorporating color mapping techniques to emphasize important structural and intensity variations within MRI scans. Experiments are conducted on the BRISC2025 dataset, which includes four classes: glioma, meningioma, pituitary tumor, and non-tumor cases. The model is trained and evaluated using standard performance metrics such as accuracy, precision, recall, F1-score, and area under the receiver operating characteristic curve (AUC). The proposed method achieves a classification accuracy of 98.90%, outperforming baseline convolutional neural network models including ResNet50, ResNet101, and EfficientNetB2. In addition, the model demonstrates strong generalization capability with an AUC of 99.97%, indicating high discriminative performance across all classes. These results highlight the effectiveness of combining Vision Transformers with colormap-based feature enhancement for accurate and robust brain tumor classification and suggest strong potential for clinical decision support applications.

Accurate and interpretable brain tumor classification from medical imaging remains a challenging problem due to the high dimensionality and complex structural patterns present in magnetic resonance imaging (MRI). In this study, we propose a topology-driven framework for brain tumor classification based on Topological Data Analysis (TDA) applied directly to three-dimensional (3D) MRI volumes. Specifically, we analyze 3D Fluid Attenuated Inversion Recovery (FLAIR) images from the BraTS 2020 dataset and extract interpretable topological descriptors using persistent homology. Persistent homology captures intrinsic geometric and structural characteristics of the data through Betti numbers, which describe connected components (Betti-0), loops (Betti-1), and voids (Betti-2). From the 3D MRI volumes, we derive a compact set of 100 topological features that summarize the underlying topology of brain tumor structures. These descriptors represent complex 3D tumor morphology while significantly reducing data dimensionality. Unlike many deep learning approaches that require large-scale training data or complex architectures, the proposed framework relies on computationally efficient topological features extracted directly from the images. These features are used to train classical machine learning classifiers, including Random Forest and XGBoost, for binary classification of high-grade glioma (HGG) and low-grade glioma (LGG). Experimental results on the BraTS 2020 dataset show that the Random Forest classifier combined with selected Betti features achieves an accuracy of 89.19%. These findings highlight the potential of persistent homology as an effective and interpretable approach for analyzing complex 3D medical images and performing brain tumor classification.

Brain tumor classification from magnetic resonance imaging, which is also known as MRI, plays a sensitive role in computer-assisted diagnosis systems. In recent years, deep learning models have achieved high classification accuracy. However, their sensitivity to adversarial perturbations has become an important reliability concern in medical applications. This study suggests a robust brain tumor classification framework that combines Non-Negative Matrix Factorization (NNMF or NMF), lightweight convolutional neural networks (CNNs), and diffusion-based feature purification. Initially, MRI images are preprocessed and converted into a non-negative data matrix, from which compact and interpretable NNMF feature representations are extracted. Statistical metrics, including AUC, Cohen's d, and p-values, are used to rank and choose the most discriminative components. Then, a lightweight CNN classifier is trained directly on the selected feature groups. To improve adversarial robustness, a diffusion-based feature-space purification module is introduced. A forward noise method followed by a learned denoiser network is used before classification. System performance is estimated using both clean accuracy and robust accuracy under powerful adversarial attacks created by AutoAttack. The experimental results show that the proposed framework achieves competitive classification performance while significantly enhancing robustness against adversarial perturbations.The findings presuppose that combining interpretable NNMF-based representations with a lightweight deep approach and diffusion-based defense technique supplies an effective and reliable solution for medical image classification under adversarial conditions.

The differentiation between tumor recurrence and radiation-induced contrast enhancements in post-treatment glioblastoma patients remains a major clinical challenge. Existing approaches rely on clinically sparsely available diffusion MRI or do not consider radiation maps, which are gaining increasing interest in the tumor board for this differentiation. We introduce RICE-NET, a multimodal 3D deep learning model that integrates longitudinal MRI data with radiotherapy dose distributions for automated lesion classification using conventional T1-weighted MRI data. Using a cohort of 92 patients, the model achieved an F1 score of 0.92 on an independent test set. During extensive ablation experiments, we quantified the contribution of each timepoint and modality and showed that reliable classification largely depends on the radiation map. Occlusion-based interpretability analyses further confirmed the model's focus on clinically relevant regions. These findings highlight the potential of multimodal deep learning to enhance diagnostic accuracy and support clinical decision-making in neuro-oncology.

Segmentation is crucial for brain gliomas as it delineates the glioma s extent and location, aiding in precise treatment planning and monitoring, thus improving patient outcomes. Accurate segmentation ensures proper identification of the glioma s size and position, transforming images into applicable data for analysis. Classification of brain gliomas is also essential because different types require different treatment approaches. Accurately classifying brain gliomas by size, location, and aggressiveness is essential for personalized prognosis prediction, follow-up care, and monitoring disease progression, ensuring effective diagnosis, treatment, and management. In glioma research, irregular tissues are often observable, but error free and reproducible segmentation is challenging. Many researchers have surveyed brain glioma segmentation, proposing both fully automatic and semi-automatic techniques. The adoption of these methods by radiologists depends on ease of use and supervision, with semi-automatic techniques preferred due to the need for accurate evaluations. This review evaluates effective segmentation and classification techniques post magnetic resonance imaging acquisition, highlighting that convolutional neural network architectures outperform traditional techniques in these tasks.

Accurate brain tumor typing requires integrating heterogeneous clinical evidence, including magnetic resonance imaging (MRI), histopathology, and pathology reports, which are often incomplete at the time of diagnosis. We introduce CoRe-BT, a cross-modal radiology-pathology-text benchmark for brain tumor typing, designed to study robust multimodal learning under missing modality conditions. The dataset comprises 310 patients with multi-sequence brain MRI (T1, T1c, T2, FLAIR), including 95 cases with paired H&E-stained whole-slide pathology images and pathology reports. All cases are annotated with tumor type and grade, and MRI volumes include expert-annotated tumor masks, enabling both region-aware modeling and auxiliary learning tasks. Tumors are categorized into six clinically relevant classes capturing the heterogeneity of common and rare glioma subtypes. We evaluate tumor typing under variable modality availability by comparing MRI-only models with multimodal approaches that incorporate pathology information when present. Baseline experiments demonstrate the feasibility of multimodal fusion and highlight complementary modality contributions across clinically relevant typing tasks. CoRe-BT provides a grounded testbed for advancing multimodal glioma typing and representation learning in realistic scenarios with incomplete clinical data.

Accurate classification of pediatric central nervous system tumors remains challenging due to histological complexity and limited training data. While pathology foundation models have advanced whole-slide image (WSI) analysis, they often fail to leverage the rich, complementary information found in clinical text and tissue microarchitecture. To this end, we propose PathMoE, an interpretable multimodal framework that integrates H&E slides, pathology reports, and nuclei-level cell graphs via an interaction-aware mixture-of-experts architecture built on state-of-the-art foundation models for each modality. By training specialized experts to capture modality uniqueness, redundancy, and synergy, PathMoE employs an input-dependent gating mechanism that dynamically weights these interactions, providing sample-level interpretability. We evaluate our framework on two dataset-specific classification tasks on an internal pediatric brain tumor dataset (PBT) and external TCGA datasets. PathMoE improves macro-F1 from 0.762 to 0.799 (+0.037) on PBT when integrating WSI, text, and graph modalities; on TCGA, augmenting WSI with graph knowledge improves macro-F1 from 0.668 to 0.709 (+0.041). These results demonstrate significant performance gains over state-of-the-art image-only baselines while revealing the specific modality interactions driving individual predictions. This interpretability is particularly critical for rare tumor subtypes, where transparent model reasoning is essential for clinical trust and diagnostic validation.

Accurate brain tumor diagnosis requires models to not only detect lesions but also generate clinically interpretable reasoning grounded in imaging manifestations, yet existing public datasets remain limited in annotation richness and diagnostic semantics. To bridge this gap, we introduce MM-NeuroOnco, a large-scale multimodal benchmark and instruction-tuning dataset for brain tumor MRI understanding, consisting of 24,726 MRI slices from 20 data sources paired with approximately 200,000 semantically enriched multimodal instructions spanning diverse tumor subtypes and imaging modalities. To mitigate the scarcity and high cost of diagnostic semantic annotations, we develop a multi-model collaborative pipeline for automated medical information completion and quality control, enabling the generation of diagnosis-related semantics beyond mask-only annotations. Building upon this dataset, we further construct MM-NeuroOnco-Bench, a manually annotated evaluation benchmark with a rejection-aware setting to reduce biases inherent in closed-ended question formats. Evaluation across ten representative models shows that even the strongest baseline, Gemini 3 Flash, achieves only 41.88% accuracy on diagnosis-related questions, highlighting the substantial challenges of multimodal brain tumor diagnostic understanding. Leveraging MM-NeuroOnco, we further propose NeuroOnco-GPT, which achieves a 27% absolute accuracy improvement on diagnostic questions following fine-tuning. This result demonstrates the effectiveness of our dataset and benchmark in advancing clinically grounded multimodal diagnostic reasoning. Code and dataset are publicly available at: https://github.com/gfnnnb/MM-NeuroOnco

Deep intracranial tumors situated in eloquent brain regions controlling vital functions present critical diagnostic challenges. Clinical practice has shifted toward stereotactic biopsy for pathological confirmation before treatment. Yet biopsy carries inherent risks of hemorrhage and neurological deficits and struggles with sampling bias due to tumor spatial heterogeneity, because pathological changes are typically region-selective rather than tumor-wide. Therefore, advancing non-invasive MRI-based pathology prediction is essential for holistic tumor assessment and modern clinical decision-making. The primary challenge lies in data scarcity: low tumor incidence requires long collection cycles, and annotation demands biopsy-verified pathology from neurosurgical experts. Additionally, tiny lesion volumes lacking segmentation masks cause critical features to be overwhelmed by background noise. To address these challenges, we construct the ICT-MRI dataset - the first public biopsy-verified benchmark with 249 cases across four categories. We propose a Virtual Biopsy framework comprising: MRI-Processor for standardization; Tumor-Localizer employing vision-language models for coarse-to-fine localization via weak supervision; and Adaptive-Diagnoser with a Masked Channel Attention mechanism fusing local discriminative features with global contexts. Experiments demonstrate over 90% accuracy, outperforming baselines by more than 20%.

Deep learning has significantly advanced automated brain tumor diagnosis, yet clinical adoption remains limited by interpretability and computational constraints. Conventional models often act as opaque ''black boxes'' and fail to quantify the complex, irregular tumor boundaries that characterize malignant growth. To address these challenges, we present XMorph, an explainable and computationally efficient framework for fine-grained classification of three prominent brain tumor types: glioma, meningioma, and pituitary tumors. We propose an Information-Weighted Boundary Normalization (IWBN) mechanism that emphasizes diagnostically relevant boundary regions alongside nonlinear chaotic and clinically validated features, enabling a richer morphological representation of tumor growth. A dual-channel explainable AI module combines GradCAM++ visual cues with LLM-generated textual rationales, translating model reasoning into clinically interpretable insights. The proposed framework achieves a classification accuracy of 96.0%, demonstrating that explainability and high performance can co-exist in AI-based medical imaging systems. The source code and materials for XMorph are all publicly available at: https://github.com/ALSER-Lab/XMorph.

Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a predefined size and necessitating pre-processing steps like resizing, padding, or cropping. This poses challenges in medical imaging, particularly with irregularly shaped structures like tumors. A fixed bounding box crop size produces input images with highly variable foreground-to-background ratios. Resizing medical images can degrade information and introduce artefacts, impacting diagnosis. Hence, tailoring variable-sized crops to regions of interest can enhance feature representation capabilities. Moreover, large images are computationally expensive, and smaller sizes risk information loss, presenting a computation-accuracy tradeoff. We propose VariViT, an improved ViT model crafted to handle variable image sizes while maintaining a consistent patch size. VariViT employs a novel positional embedding resizing scheme for a variable number of patches. We also implement a new batching strategy within VariViT to reduce computational complexity, resulting in faster training and inference times. In our evaluations on two 3D brain MRI datasets, VariViT surpasses vanilla ViTs and ResNet in glioma genotype prediction and brain tumor classification. It achieves F1-scores of 75.5% and 76.3%, respectively, learning more discriminative features. Our proposed batching strategy reduces computation time by up to 30% compared to conventional architectures. These findings underscore the efficacy of VariViT in image representation learning. Our code can be found here: https://github.com/Aswathi-Varma/varivit