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We present a framework that combines Large Language Models with computational image analytics for non-invasive, zero-shot prediction of IDH mutation status in brain gliomas. For each subject, coregistered multi-parametric MRI scans and multi-class tumor segmentation maps were processed to extract interpretable semantic (visual) attributes and quantitative features, serialized in a standardized JSON file, and used to query GPT 4o and GPT 5 without fine-tuning. We evaluated this framework on six publicly available datasets (N = 1427) and results showcased high accuracy and balanced classification performance across heterogeneous cohorts, even in the absence of manual annotations. GPT 5 outperformed GPT 4o in context-driven phenotype interpretation. Volumetric features emerged as the most important predictors, supplemented by subtype-specific imaging markers and clinical information. Our results demonstrate the potential of integrating LLM-based reasoning with computational image analytics for precise, non-invasive tumor genotyping, advancing diagnostic strategies in neuro-oncology. The code is available at https://github.com/ATPLab-LUMS/CIM-LLM.

DSC-MRI perfusion is a medical imaging technique for diagnosing and prognosing brain tumors and strokes. Its analysis relies on mathematical deconvolution, but noise or motion artifacts in a clinical environment can disrupt this process, leading to incorrect estimate of perfusion parameters. Although deep learning approaches have shown promising results, their calibration typically rely on third-party deconvolution algorithms to generate reference outputs and are bound to reproduce their limitations. To adress this problem, we propose a physics-informed autoencoder that leverages an analytical model to decode the perfusion parameters and guide the learning of the encoding network. This autoencoder is trained in a self-supervised fashion without any third-party software and its performance is evaluated on a database with glioma patients. Our method shows reliable results for glioma grading in accordance with other well-known deconvolution algorithms despite a lower computation time. It also achieved competitive performance even in the presence of high noise which is critical in a medical environment.

Accurate, noninvasive detection of isocitrate dehydrogenase (IDH) mutation is essential for effective glioma management. Traditional methods rely on invasive tissue sampling, which may fail to capture a tumor's spatial heterogeneity. While deep learning models have shown promise in molecular profiling, their performance is often limited by scarce annotated data. In contrast, foundation deep learning models offer a more generalizable approach for glioma imaging biomarkers. We propose a Foundation-based Biomarker Network (FoundBioNet) that utilizes a SWIN-UNETR-based architecture to noninvasively predict IDH mutation status from multi-parametric MRI. Two key modules are incorporated: Tumor-Aware Feature Encoding (TAFE) for extracting multi-scale, tumor-focused features, and Cross-Modality Differential (CMD) for highlighting subtle T2-FLAIR mismatch signals associated with IDH mutation. The model was trained and validated on a diverse, multi-center cohort of 1705 glioma patients from six public datasets. Our model achieved AUCs of 90.58%, 88.08%, 65.41%, and 80.31% on independent test sets from EGD, TCGA, Ivy GAP, RHUH, and UPenn, consistently outperforming baseline approaches (p <= 0.05). Ablation studies confirmed that both the TAFE and CMD modules are essential for improving predictive accuracy. By integrating large-scale pretraining and task-specific fine-tuning, FoundBioNet enables generalizable glioma characterization. This approach enhances diagnostic accuracy and interpretability, with the potential to enable more personalized patient care.

Large Language Models (LLMs) have shown strong performance in text-based healthcare tasks. However, their utility in image-based applications remains unexplored. We investigate the effectiveness of LLMs for medical imaging tasks, specifically glioma classification and segmentation, and compare their performance to that of traditional convolutional neural networks (CNNs). Using the BraTS 2020 dataset of multi-modal brain MRIs, we evaluated a general-purpose vision-language LLM (LLaMA 3.2 Instruct) both before and after fine-tuning, and benchmarked its performance against custom 3D CNNs. For glioma classification (Low-Grade vs. High-Grade), the CNN achieved 80% accuracy and balanced precision and recall. The general LLM reached 76% accuracy but suffered from a specificity of only 18%, often misclassifying Low-Grade tumors. Fine-tuning improved specificity to 55%, but overall performance declined (e.g., accuracy dropped to 72%). For segmentation, three methods - center point, bounding box, and polygon extraction, were implemented. CNNs accurately localized gliomas, though small tumors were sometimes missed. In contrast, LLMs consistently clustered predictions near the image center, with no distinction of glioma size, location, or placement. Fine-tuning improved output formatting but failed to meaningfully enhance spatial accuracy. The bounding polygon method yielded random, unstructured outputs. Overall, CNNs outperformed LLMs in both tasks. LLMs showed limited spatial understanding and minimal improvement from fine-tuning, indicating that, in their current form, they are not well-suited for image-based tasks. More rigorous fine-tuning or alternative training strategies may be needed for LLMs to achieve better performance, robustness, and utility in the medical space.

Brain tumors are serious health problems that require early diagnosis due to their high mortality rates. Diagnosing tumors by examining Magnetic Resonance Imaging (MRI) images is a process that requires expertise and is prone to error. Therefore, the need for automated diagnosis systems is increasing day by day. In this context, a robust and explainable Deep Learning (DL) model for the classification of brain tumors is proposed. In this study, a publicly available Figshare dataset containing 3,064 T1-weighted contrast-enhanced brain MRI images of three tumor types was used. First, the classification performance of nine well-known CNN architectures was evaluated to determine the most effective backbone. Among these, EfficientNetV2 demonstrated the best performance and was selected as the backbone for further development. Subsequently, an attention-based MLP-Mixer architecture was integrated into EfficientNetV2 to enhance its classification capability. The performance of the final model was comprehensively compared with basic CNNs and the methods in the literature. Additionally, Grad-CAM visualization was used to interpret and validate the decision-making process of the proposed model. The proposed model's performance was evaluated using the five-fold cross-validation method. The proposed model demonstrated superior performance with 99.50% accuracy, 99.47% precision, 99.52% recall and 99.49% F1 score. The results obtained show that the model outperforms the studies in the literature. Moreover, Grad-CAM visualizations demonstrate that the model effectively focuses on relevant regions of MRI images, thus improving interpretability and clinical reliability. A robust deep learning model for clinical decision support systems has been obtained by combining EfficientNetV2 and attention-based MLP-Mixer, providing high accuracy and interpretability in brain tumor classification.

Glioma, the prevalent primary brain tumor, exhibits diverse aggressiveness levels and prognoses. Precise classification of glioma is paramount for treatment planning and predicting prognosis. This study aims to develop an algorithm to fuse the MRI images from T1, T2, T1ce, and fluid-attenuated inversion recovery (FLAIR) sequences to enhance the efficacy of glioma subclass classification as no tumor, necrotic core, peritumoral edema, and enhancing tumor. The MRI images from BraTS datasets were used in this work. The images were pre-processed using max-min normalization to ensure consistency in pixel intensity values across different images. The segmentation of the necrotic core, peritumoral edema, and enhancing tumor was performed on 2D and 3D images separately using UNET architecture. Further, the segmented regions from multimodal MRI images were fused using the weighted averaging technique. Integrating 2D and 3D segmented outputs enhances classification accuracy by capturing detailed features like tumor shape, boundaries, and intensity distribution in slices, while also providing a comprehensive view of spatial extent, shape, texture, and localization within the brain volume. The fused images were used as input to the pre-trained ResNet50 model for glioma subclass classification. The network is trained on 80% and validated on 20% of the data. The proposed method achieved a classification of accuracy of 99.25%, precision of 99.30%, recall of 99.10, F1 score of 99.19%, Intersection Over Union of 84.49%, and specificity of 99.76, which showed a significantly higher performance than existing techniques. These findings emphasize the significance of glioma segmentation and classification in aiding accurate diagnosis.

Missing data imputation is a critical challenge in various domains, such as healthcare and finance, where data completeness is vital for accurate analysis. Large language models (LLMs), trained on vast corpora, have shown strong potential in data generation, making them a promising tool for data imputation. However, challenges persist in designing effective prompts for a finetuning-free process and in mitigating the risk of LLM hallucinations. To address these issues, we propose a novel framework, LLM-Forest, which introduces a "forest" of few-shot learning LLM "trees" with confidence-based weighted voting, inspired by ensemble learning (Random Forest). This framework is established on a new concept of bipartite information graphs to identify high-quality relevant neighboring entries with both feature and value granularity. Extensive experiments on 9 real-world datasets demonstrate the effectiveness and efficiency of LLM-Forest.

Brain tumor detection and classification are critical tasks in medical image analysis, particularly in early-stage diagnosis, where accurate and timely detection can significantly improve treatment outcomes. In this study, we apply various statistical and machine learning models to detect and classify brain tumors using brain MRI images. We explore a variety of statistical models including linear, logistic, and Bayesian regressions, and the machine learning models including decision tree, random forest, single-layer perceptron, multi-layer perceptron, convolutional neural network (CNN), recurrent neural network, and long short-term memory. Our findings show that CNN outperforms other models, achieving the best performance. Additionally, we confirm that the CNN model can also work for multi-class classification, distinguishing between four categories of brain MRI images such as normal, glioma, meningioma, and pituitary tumor images. This study demonstrates that machine learning approaches are suitable for brain tumor detection and classification, facilitating real-world medical applications in assisting radiologists with early and accurate diagnosis.

Gliomas, the most common primary brain tumors, show high heterogeneity in histological and molecular characteristics. Accurate molecular profiling, like isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion, is critical for diagnosis, treatment, and prognosis. This review evaluates MRI-based deep learning (DL) models' efficacy in predicting these biomarkers. Following PRISMA guidelines, we systematically searched major databases (PubMed, Scopus, Ovid, and Web of Science) up to February 2024, screening studies that utilized DL to predict IDH and 1p/19q codeletion status from MRI data of glioma patients. We assessed the quality and risk of bias using the radiomics quality score and QUADAS-2 tool. Our meta-analysis used a bivariate model to compute pooled sensitivity, specificity, and meta-regression to assess inter-study heterogeneity. Of the 565 articles, 57 were selected for qualitative synthesis, and 52 underwent meta-analysis. The pooled estimates showed high diagnostic performance, with validation sensitivity, specificity, and area under the curve (AUC) of 0.84 [prediction interval (PI): 0.67-0.93, I2=51.10%, p < 0.05], 0.87 [PI: 0.49-0.98, I2=82.30%, p < 0.05], and 0.89 for IDH prediction, and 0.76 [PI: 0.28-0.96, I2=77.60%, p < 0.05], 0.85 [PI: 0.49-0.97, I2=80.30%, p < 0.05], and 0.90 for 1p/19q prediction, respectively. Meta-regression analyses revealed significant heterogeneity influenced by glioma grade, data source, inclusion of non-radiomics data, MRI sequences, segmentation and feature extraction methods, and validation techniques. DL models demonstrate strong potential in predicting molecular biomarkers from MRI scans, with significant variability influenced by technical and clinical factors. Thorough external validation is necessary to increase clinical utility.