Recent approaches to vision-language tasks are built on the remarkable capabilities of large vision-language models (VLMs). These models excel in zero-shot and few-shot learning, enabling them to learn new tasks without parameter updates. However, their primary challenge lies in their design, which primarily accommodates 2D input, thus limiting their effectiveness for medical images, particularly radiological images like MRI and CT, which are typically 3D. To bridge the gap between state-of-the-art 2D VLMs and 3D medical image data, we developed an innovative, one-pass, unsupervised representative slice selection method called Vote-MI, which selects representative 2D slices from 3D medical imaging. To evaluate the effectiveness of Vote-MI when implemented with VLMs, we introduce BrainMD, a robust, multimodal dataset comprising 2,453 annotated 3D MRI brain scans with corresponding textual radiology reports and electronic health records.

Physical models in the form of partial differential equations serve as important priors for many under-constrained problems. One such application is tumor treatment planning, which relies on accurately estimating the spatial distribution of tumor cells within a patient's anatomy. While medical imaging can detect the bulk of a tumor, it cannot capture the full extent of its spread, as low-concentration tumor cells often remain undetectable, particularly in glioblastoma, the most common primary brain tumor. Machine learning approaches struggle to estimate the complete tumor cell distribution due to a lack of appropriate training data. Consequently, most existing methods rely on physics-based simulations to generate anatomically and physiologically plausible estimations. However, these approaches face challenges with complex and unknown initial conditions and are constrained by overly rigid physical models. In this work, we introduce a novel method that integrates data-driven and physics-based cost functions, akin to Physics-Informed Neural Networks (PINNs).

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

Despite being a minor population of cancer cells, the cancer stem cells that are identified in glioblastoma (GSCs) are thought to be the major driving force behind glioblastoma biological heterogeneity and are likely to explain the high rates of glioblastoma recurrence. In the STEMRI clinical trial aiming to study GB heterogeneity and the enrichment of GSC in certain areas defined by multimodal MRI (NCT01872221) [4] different GSC sub-populations extracted from tumor samples obtained by multimodal MRI guided surgery were xenografted into mice brain to study their invasion patterns as well as their aggressiveness. RNA-seq on each tumor bulk samples was also performed. The observed differences in mice survival according to the GSC implanted confirm the heterogeneous nature of tumor cells lineage. In this study, we set out to determine potential genetic markers associated with glioblastoma aggressiveness using multimodal deep learning.

Federated learning (FL) enables collaborative model training across decentralized datasets while preserving data privacy. However, optimally selecting participating collaborators in dynamic FL environments remains challenging. We present RL-HSimAgg, a novel reinforcement learning (RL) and similarity-weighted aggregation (simAgg) algorithm using harmonic mean to manage outlier data points. This paper proposes applying multi-armed bandit algorithms to improve collaborator selection and model generalization. By balancing exploration-exploitation trade-offs, these RL methods can promote resource-efficient training with diverse datasets. We demonstrate the effectiveness of Epsilon-greedy (EG) and upper confidence bound (UCB) algorithms for federated brain lesion segmentation. In simulation experiments on internal and external validation sets, RL-HSimAgg with UCB collaborator outperformed the EG method across all metrics, achieving higher Dice scores for Enhancing Tumor (0.7334 vs 0.6797), Tumor Core (0.7432 vs 0.6821), and Whole Tumor (0.8252 vs 0.7931) segmentation. Therefore, for the Federated Tumor Segmentation Challenge (FeTS 2024), we consider UCB as our primary client selection approach in federated Glioblastoma lesion segmentation of multi-modal MRIs. In conclusion, our research demonstrates that RL-based collaborator management, e.g. using UCB, can potentially improve model robustness and flexibility in distributed learning environments, particularly in domains like brain tumor segmentation.

This study presents a robust and efficient client selection protocol designed to optimize the Federated Learning (FL) process for the Federated Tumor Segmentation Challenge (FeTS 2024). In the evolving landscape of FL, the judicious selection of collaborators emerges as a critical determinant for the success and efficiency of collective learning endeavors, particularly in domains requiring high precision. This work introduces a recommender engine framework based on non-negative matrix factorization (NNMF) and a hybrid aggregation approach that blends content-based and collaborative filtering. This method intelligently analyzes historical performance, expertise, and other relevant metrics to identify the most suitable collaborators. This approach not only addresses the cold start problem where new or inactive collaborators pose selection challenges due to limited data but also significantly improves the precision and efficiency of the FL process. Additionally, we propose harmonic similarity weight aggregation (HSimAgg) for adaptive aggregation of model parameters. We utilized a dataset comprising 1,251 multi-parametric magnetic resonance imaging (mpMRI) scans from individuals diagnosed with glioblastoma (GBM) for training purposes and an additional 219 mpMRI scans for external evaluations. Our federated tumor segmentation approach achieved dice scores of 0.7298, 0.7424, and 0.8218 for enhancing tumor (ET), tumor core (TC), and whole tumor (WT) segmentation tasks respectively on the external validation set. In conclusion, this research demonstrates that selecting collaborators with expertise aligned to specific tasks, like brain tumor segmentation, improves the effectiveness of FL networks.

Spinal cord tumors significantly contribute to neurological morbidity and mortality. Precise morphometric quantification, encompassing the size, location, and type of such tumors, holds promise for optimizing treatment planning strategies. Although recent methods have demonstrated excellent performance in medical image segmentation, they primarily focus on discerning shapes with relatively large morphology such as brain tumors, ignoring the challenging problem of identifying spinal cord tumors which tend to have tiny sizes, diverse locations, and shapes. To tackle this hard problem of multiclass spinal cord tumor segmentation, we propose a new method, called BATseg, to learn a tumor surface distance field by applying our new multiclass boundary-aware loss function. To verify the effectiveness of our approach, we also introduce the first and large-scale spinal cord tumor dataset. It comprises gadolinium-enhanced T1-weighted 3D MRI scans from 653 patients and contains the four most common spinal cord tumor types: astrocytomas, ependymomas, hemangioblastomas, and spinal meningiomas. Extensive experiments on our dataset and another public kidney tumor segmentation dataset show that our proposed method achieves superior performance for multiclass tumor segmentation.

Glioblastoma (GBL) is one of the deadliest brain cancers in adults. The GBL cells invade the physical structures within the brain extracellular environment with patient-specific features. In this work, we propose a proof-of-concept for mathematical framework of precision oncology enabling rapid parameter estimation from neuroimaging data in clinical settings. The proposed diffuse interface model of GBL growth is informed by neuroimaging data, periodically collected in a clinical study from diagnosis to surgery and adjuvant treatment. We build a robust and efficient computational pipeline to aid clinical decision-making based on integrating model reduction techniques and neural networks. Patient specificity is captured through the segmentation of the magnetic resonance imaging into a computational replica of the patient brain, mimicking the brain microstructure by incorporating also the diffusion tensor imaging data. The full order model (FOM) is first discretized using the finite element method and later approximated by a reduced order model (ROM) adopting proper orthogonal decomposition (POD). Trained by clinical data, we finally use neural networks to map the parameter space of GBL evolution over time and to predict the patient-specific model parameters from the observed clinical evolution of the tumor mass.

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation.

Early and accurate diagnosis of brain tumors is crucial for improving patient survival rates. However, the detection and classification of brain tumors are challenging due to their diverse types and complex morphological characteristics. This study investigates the application of pre-trained models for brain tumor classification, with a particular focus on deploying the Mamba model. We fine-tuned several mainstream transfer learning models and applied them to the multi-class classification of brain tumors. By comparing these models to those trained from scratch, we demonstrated the significant advantages of transfer learning, especially in the medical imaging field, where annotated data is often limited. Notably, we introduced the Vision Mamba (Vim), a novel network architecture, and applied it for the first time in brain tumor classification, achieving exceptional classification accuracy. Experimental results indicate that the Vim model achieved 100% classification accuracy on an independent test set, emphasizing its potential for tumor classification tasks. These findings underscore the effectiveness of transfer learning in brain tumor classification and reveal that, compared to existing state-of-the-art models, the Vim model is lightweight, efficient, and highly accurate, offering a new perspective for clinical applications. Furthermore, the framework proposed in this study for brain tumor classification, based on transfer learning and the Vision Mamba model, is broadly applicable to other medical imaging classification problems.