Brain tumor segmentation is crucial for diagnosis and treatment planning, yet challenges such as class imbalance and limited model generalization continue to hinder progress. This work presents a reproducible evaluation of U-Net segmentation performance on brain tumor MRI using focal loss and basic data augmentation strategies. Experiments were conducted on a publicly available MRI dataset, focusing on focal loss parameter tuning and assessing the impact of three data augmentation techniques: horizontal flip, rotation, and scaling. The U-Net with focal loss achieved a precision of 90%, comparable to state-of-the-art results. By making all code and results publicly available, this study establishes a transparent, reproducible baseline to guide future research on augmentation strategies and loss function design in brain tumor segmentation.

Contrast-enhanced computed tomography (CECT) is the primary imaging technique that provides valuable spatial-temporal information about lesions, enabling the accurate diagnosis and subclassification of pancreatic tumors. However, the high heterogeneity and variability of pancreatic tumors still pose substantial challenges for precise subtyping diagnosis. Previous methods fail to effectively explore the contextual information across multiple CECT phases commonly used in radiologists' diagnostic workflows, thereby limiting their performance. In this paper, we introduce, for the first time, an automatic way to combine the multi-phase CECT data to discriminate between pancreatic tumor subtypes, among which the key is using Mamba with promising learnability and simplicity to encourage both temporal and spatial modeling from multi-phase CECT. Specifically, we propose a dual hierarchical contrast-enhanced-aware Mamba module incorporating two novel spatial and temporal sampling sequences to explore intra and inter-phase contrast variations of lesions. A similarity-guided refinement module is also imposed into the temporal scanning modeling to emphasize the learning on local tumor regions with more obvious temporal variations. Moreover, we design the space complementary integrator and multi-granularity fusion module to encode and aggregate the semantics across different scales, achieving more efficient learning for subtyping pancreatic tumors. The experimental results on an in-house dataset of 270 clinical cases achieve an accuracy of 97.4% and an AUC of 98.6% in distinguishing between pancreatic ductal adenocarcinoma (PDAC) and pancreatic neuroendocrine tumors (PNETs), demonstrating its potential as a more accurate and efficient tool.

Deep generative models and synthetic medical data have shown significant promise in addressing key challenges in healthcare, such as privacy concerns, data bias, and the scarcity of realistic datasets. While research in this area has grown rapidly and demonstrated substantial theoretical potential, its practical adoption in clinical settings remains limited. Despite the benefits synthetic data offers, questions surrounding its reliability and credibility persist, leading to a lack of trust among clinicians. This position paper argues that fostering trust in synthetic medical data is crucial for its clinical adoption. It aims to spark a discussion on the viability of synthetic medical data in clinical practice, particularly in the context of current advancements in AI. We present empirical evidence from brain tumor segmentation to demonstrate that the quality, diversity, and proportion of synthetic data directly impact trust in clinical AI models. Our findings provide insights to improve the deployment and acceptance of synthetic data-driven AI systems in real-world clinical workflows.

Multiple Instance Learning (MIL) methods allow for gigapixel Whole-Slide Image (WSI) analysis with only slide-level annotations. Interpretability is crucial for safely deploying such algorithms in high-stakes medical domains. Traditional MIL methods offer explanations by highlighting salient regions. However, such spatial heatmaps provide limited insights for end users. To address this, we propose a novel inherently interpretable WSI-classification approach that uses human-understandable pathology concepts to generate explanations. Our proposed Concept MIL model leverages recent advances in vision-language models to directly predict pathology concepts based on image features. The model's predictions are obtained through a linear combination of the concepts identified on the top-K patches of a WSI, enabling inherent explanations by tracing each concept's influence on the prediction. In contrast to traditional concept-based interpretable models, our approach eliminates the need for costly human annotations by leveraging the vision-language model. We validate our method on two widely used pathology datasets: Camelyon16 and PANDA. On both datasets, Concept MIL achieves AUC and accuracy scores over 0.9, putting it on par with state-of-the-art models. We further find that 87.1\% (Camelyon16) and 85.3\% (PANDA) of the top 20 patches fall within the tumor region. A user study shows that the concepts identified by our model align with the concepts used by pathologists, making it a promising strategy for human-interpretable WSI classification.

Accurate segmentation of brain tumors from 3D multimodal MRI is vital for diagnosis and treatment planning across diverse brain tumors. This paper addresses the challenges posed by the BraTS 2023, presenting a unified transfer learning approach that applies to a broader spectrum of brain tumors. We introduce HT-CNNs, an ensemble of Hybrid Transformers and Convolutional Neural Networks optimized through transfer learning for varied brain tumor segmentation. This method captures spatial and contextual details from MRI data, fine-tuned on diverse datasets representing common tumor types. Through transfer learning, HT-CNNs utilize the learned representations from one task to improve generalization in another, harnessing the power of pre-trained models on large datasets and fine-tuning them on specific tumor types. We preprocess diverse datasets from multiple international distributions, ensuring representativeness for the most common brain tumors. Our rigorous evaluation employs standardized quantitative metrics across all tumor types, ensuring robustness and generalizability. The proposed ensemble model achieves superior segmentation results across the BraTS validation datasets over the previous winning methods. Comprehensive quantitative evaluations using the DSC and HD95 demonstrate the effectiveness of our approach. Qualitative segmentation predictions further validate the high-quality outputs produced by our model. Our findings underscore the potential of transfer learning and ensemble approaches in medical image segmentation, indicating a substantial enhancement in clinical decision-making and patient care. Despite facing challenges related to post-processing and domain gaps, our study sets a new precedent for future research for brain tumor segmentation. The docker image for the code and models has been made publicly available, https://hub.docker.com/r/razeineldin/ht-cnns.

Tumors in the brain result from abnormal cell growth within the brain tissue, arising from various types of brain cells. When left undiagnosed, they lead to severe neurological deficits such as cognitive impairment, motor dysfunction, and sensory loss. As the tumor grows, it causes an increase in intracranial pressure, potentially leading to life-threatening complications such as brain herniation. Therefore, early detection and treatment are necessary to manage the complications caused by such tumors to slow down their growth. Numerous works involving deep learning (DL) and artificial intelligence (AI) are being carried out to assist physicians in early diagnosis by utilizing the scans obtained through Magnetic Resonance Imaging (MRI). Our research proposes DL frameworks for localizing, segmenting, and classifying the grade of these gliomas from MRI images to solve this critical issue. In our localization framework, we enhance the LinkNet framework with a VGG19- inspired encoder architecture for improved multimodal tumor feature extraction, along with spatial and graph attention mechanisms to refine feature focus and inter-feature relationships. Following this, we integrated the SeResNet101 CNN model as the encoder backbone into the LinkNet framework for tumor segmentation, which achieved an IoU Score of 96%. To classify the segmented tumors, we combined the SeResNet152 feature extractor with an Adaptive Boosting classifier, which yielded an accuracy of 98.53%. Our proposed models demonstrated promising results, with the potential to advance medical AI by enabling early diagnosis and providing more accurate treatment options for patients.

Objective: Gadolinium-based contrast agents (GBCAs) are commonly used in MRI scans of patients with gliomas to enhance brain tumor characterization using T1-weighted (T1W) MRI. However, there is growing concern about GBCA toxicity. This study develops a deep-learning framework to generate T1-postcontrast (T1C) from pre-contrast multiparametric MRI. Approach: We propose the tumor-aware vision transformer (TA-ViT) model that predicts high-quality T1C images. The predicted tumor region is significantly improved (P < .001) by conditioning the transformer layers from predicted segmentation maps through adaptive layer norm zero mechanism. The predicted segmentation maps were generated with the multi-parametric residual (MPR) ViT model and transformed into a latent space to produce compressed, feature-rich representations. The TA-ViT model predicted T1C MRI images of 501 glioma cases. Selected patients were split into training (N=400), validation (N=50), and test (N=51) sets. Main Results: Both qualitative and quantitative results demonstrate that the TA-ViT model performs superior against the benchmark MRP-ViT model. Our method produces synthetic T1C MRI with high soft tissue contrast and more accurately reconstructs both the tumor and whole brain volumes. The synthesized T1C images achieved remarkable improvements in both tumor and healthy tissue regions compared to the MRP-ViT model. For healthy tissue and tumor regions, the results were as follows: NMSE: 8.53 +/- 4.61E-4; PSNR: 31.2 +/- 2.2; NCC: 0.908 +/- .041 and NMSE: 1.22 +/- 1.27E-4, PSNR: 41.3 +/- 4.7, and NCC: 0.879 +/- 0.042, respectively. Significance: The proposed method generates synthetic T1C images that closely resemble real T1C images. Future development and application of this approach may enable contrast-agent-free MRI for brain tumor patients, eliminating the risk of GBCA toxicity and simplifying the MRI scan protocol.

Brain tumors in magnetic resonance imaging (MR) are difficult, time-consuming, and prone to human error. These challenges can be resolved by developing automatic brain tumor segmentation methods from MR images. Various deep-learning models based on the U-Net have been proposed for the task. These deep-learning models are trained on a dataset of tumor images and then used for segmenting the masks. Mini-batch training is a widely used method in deep learning for training. However, one of the significant challenges associated with this approach is that if the training dataset has under-represented samples or samples with complex latent representations, the model may not generalize well to these samples. The issue leads to skewed learning of the data, where the model learns to fit towards the majority representations while underestimating the under-represented samples. The proposed dynamic batch training method addresses the challenges posed by under-represented data points, data points with complex latent representation, and imbalances within the class, where some samples may be harder to learn than others. Poor performance of such samples can be identified only after the completion of the training, leading to the wastage of computational resources. Also, training easy samples after each epoch is an inefficient utilization of computation resources. To overcome these challenges, the proposed method identifies hard samples and trains such samples for more iterations compared to easier samples on the BraTS2020 dataset. Additionally, the samples trained multiple times are identified and it provides a way to identify hard samples in the BraTS2020 dataset. The comparison of the proposed training approach with U-Net and other models in the literature highlights the capabilities of the proposed training approach.

Breast cancer poses a profound threat to lives globally, claiming numerous lives each year. Therefore, timely detection is crucial for early intervention and improved chances of survival. Accurately diagnosing and classifying breast tumors using ultrasound images is a persistent challenge in medicine, demanding cutting-edge solutions for improved treatment strategies. This research introduces multiattention-enhanced deep learning (DL) frameworks designed for the classification and segmentation of breast cancer tumors from ultrasound images. A spatial channel attention mechanism is proposed for segmenting tumors from ultrasound images, utilizing a novel LinkNet DL framework with an InceptionResNet backbone. Following this, the paper proposes a deep convolutional neural network with an integrated multi-attention framework (DCNNIMAF) to classify the segmented tumor as benign, malignant, or normal. From experimental results, it is observed that the segmentation model has recorded an accuracy of 98.1%, with a minimal loss of 0.6%. It has also achieved high Intersection over Union (IoU) and Dice Coefficient scores of 96.9% and 97.2%, respectively. Similarly, the classification model has attained an accuracy of 99.2%, with a low loss of 0.31%. Furthermore, the classification framework has achieved outstanding F1-Score, precision, and recall values of 99.1%, 99.3%, and 99.1%, respectively. By offering a robust framework for early detection and accurate classification of breast cancer, this proposed work significantly advances the field of medical image analysis, potentially improving diagnostic precision and patient outcomes.

Accurate segmentation of tumors in PET/CT images is important in computer-aided diagnosis and treatment of cancer. The key issue of such a segmentation problem lies in the effective integration of complementary information from PET and CT images. However, the quality of PET and CT images varies widely in clinical settings, which leads to uncertainty in the modality information extracted by networks. To take the uncertainty into account in multi-modal information fusion, this paper proposes a novel Multi-modal Evidential Fusion Network (MEFN) comprising a Cross-Modal Feature Learning (CFL) module and a Multi-modal Trusted Fusion (MTF) module. The CFL module reduces the domain gap upon modality conversion and highlights common tumor features, thereby alleviating the needs of the segmentation module to handle modality specificity. The MTF module utilizes mutual attention mechanisms and an uncertainty calibrator to fuse modality features based on modality uncertainty and then fuse the segmentation results under the guidance of Dempster-Shafer Theory. Besides, a new uncertainty perceptual loss is introduced to force the model focusing on uncertain features and hence improve its ability to extract trusted modality information. Extensive comparative experiments are conducted on two publicly available PET/CT datasets to evaluate the performance of our proposed method whose results demonstrate that our MEFN significantly outperforms state-of-the-art methods with improvements of 2.15% and 3.23% in DSC scores on the AutoPET dataset and the Hecktor dataset, respectively. More importantly, our model can provide radiologists with credible uncertainty of the segmentation results for their decision in accepting or rejecting the automatic segmentation results, which is particularly important for clinical applications. Our code will be available at https://github.com/QPaws/MEFN.