arXiv:2502.18775v1 Announce Type: cross Abstract: 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.

arXiv:2502.19760v1 Announce Type: cross Abstract: Brain tumor diagnosis is a challenging task for clinicians in the modern world. Among the major reasons for cancer-related death is the brain tumor. Gliomas, a category of central nervous system (CNS) tumors, encompass diverse subregions. For accurate diagnosis of brain tumors, precise segmentation of brain images and quantitative analysis are required. A fully automatic approach to glioma segmentation is required because the manual segmentation process is laborious, prone to mistakes, as well as time-consuming. Modern techniques for segmenting gliomas are based on fully convolutional neural networks (FCNs), which can either use two-dimensional (2D) or three-dimensional (3D) convolutions. Nevertheless, 3D convolutions suffer from computational costs and memory demand, while 2D convolutions cannot fully utilize the spatial insights of volumetric clinical imaging data. To obtain an optimal solution, it is vital to balance the computational efficiency of 2D convolutions along with the spatial accuracy of 3D convolutions. This balance can potentially be realized by developing an advanced model to overcome these challenges. The 2D and 3D models implemented here are based on UNET architecture, Inception, and ResNet models. The research work has been implemented on the BraTS 2018, 2019, and 2020 datasets. The best performer of all the models' evaluations metrics for proposed methodologies offer superior potential in terms of the effective segmentation of gliomas. The ResNet model has resulted in 98.91% accuracy for 3D segmentation and 99.77 for 2D segmentations. The dice scores for 2D and 3D segmentations are 0.8312 and 0.9888, respectively. This model can be applied to various other medical applications with fine-tuning, thereby aiding clinicians in brain tumor analysis and improving the diagnosis process effectively.

arXiv:2409.18901v2 Announce Type: replace-cross Abstract: Learning a discriminative model that distinguishes the specified target from surrounding distractors across frames is essential for generic object tracking (GOT). Dynamic adaptation of target representation against distractors remains challenging because prevailing trackers exhibit limited discriminative capability. To address this issue, we present a new visual prompting mechanism for generic object tracking, termed PiVOT. PiVOT introduces mechanisms that leverage the pretrained foundation model (CLIP) to automatically generate and refine visual prompts online, thereby enabling the tracker to suppress distractors through contrastive guidance. To transfer contrastive knowledge from the foundation model to the tracker, PiVOT automatically propagates this knowledge online and dynamically generates and updates visual prompts. Specifically, it proposes a prompt initialization mechanism that produces an initial visual prompt highlighting potential target locations. The foundation model is then used to refine the prompt based on appearance similarities between candidate objects and reference templates across potential targets. After refinement, the visual prompt better highlights potential target locations and reduces irrelevant prompt information. With the proposed prompting mechanism, the tracker can generate instance-aware feature maps guided by the visual prompts, which are incrementally and automatically updated during tracking, thereby effectively suppressing distractors. Extensive experiments across multiple benchmarks indicate that PiVOT, with the proposed prompting mechanism, can suppress distracting objects and improve tracking performance.

arXiv:2503.05031v2 Announce Type: replace-cross Abstract: Alzheimer's disease (AD) is a major neurodegenerative condition that affects millions around the world. As one of the main biomarkers in the AD diagnosis procedure, brain amyloid positivity is typically identified by positron emission tomography (PET), which is costly and invasive. Brain structural magnetic resonance imaging (sMRI) may provide a safer and more convenient solution for the AD diagnosis. Recent advances in geometric deep learning have facilitated sMRI analysis and early diagnosis of AD. However, determining AD pathology, such as brain amyloid deposition, in preclinical stage remains challenging, as less significant morphological changes can be observed. As a result, few AD classification models are generalizable to the brain amyloid positivity classification task. Blood-based biomarkers (BBBMs), on the other hand, have recently achieved remarkable success in predicting brain amyloid positivity and identifying individuals with high risk of being brain amyloid positive. However, individuals in medium risk group still require gold standard tests such as Amyloid PET for further evaluation. Inspired by the recent success of transformer architectures, we propose a geometric deep learning model based on transformer that is both scalable and robust to variations in input volumetric mesh size. Our work introduced a novel tokenization scheme for tetrahedral meshes, incorporating anatomical landmarks generated by a pre-trained Gaussian process model. Our model achieved superior classification performance in AD classification task. In addition, we showed that the model was also generalizable to the brain amyloid positivity prediction with individuals in the medium risk class, where BM alone cannot achieve a clear classification. Our work may enrich geometric deep learning research and improve AD diagnosis accuracy without using expensive and invasive PET scans.

arXiv:2602.22263v2 Announce Type: replace-cross Abstract: High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta are computationally expensive, demand extensive manual tuning, and present a significant bottleneck for researchers. We present CryoNet.Refine, an end-to-end deep learning framework that automates and accelerates molecular structure refinement. Our approach utilizes a one-step diffusion model that integrates a density-aware loss function with robust stereochemical restraints, enabling rapid optimization of a structure against experimental data. CryoNet.Refine provides a unified and versatile solution capable of refining protein complexes as well as DNA/RNA-protein complexes. In benchmarks against Phenix.real_space_refine, CryoNet.Refine consistently achieves substantial improvements in both model-map correlation and overall geometric quality metrics. By offering a scalable, automated, and powerful alternative, CryoNet.Refine aims to serve as an essential tool for next-generation cryo-EM structure refinement. Web server: https://cryonet.ai/refine; Source code: https://github.com/kuixu/cryonet.refine.