WSI-LLaVA: A Multimodal Large Language Model for Whole Slide Image

Recent advancements in computational pathology have produced patch-level Multi-modal Large Language Models (MLLMs), but these models are limited by their inability to analyze whole slide images (WSIs) comprehensively and their tendency to bypass crucial morphological features that pathologists rely on for diagnosis. To address these challenges, we first introduce WSI-Bench, a large-scale morphology-aware benchmark containing 180k VQA pairs from 9,850 WSIs across 30 cancer types, designed to evaluate MLLMs' understanding of morphological characteristics crucial for accurate diagnosis. Building upon this benchmark, we present WSI-LLaVA, a novel framework for gigapixel WSI understanding that employs a three-stage training approach: WSI-text alignment, feature space alignment, and task-specific instruction tuning. To better assess model performance in pathological contexts, we develop two specialized WSI metrics: WSI-Precision and WSI-Relevance. Experimental results demonstrate that WSI-LLaVA outperforms existing models across all capability dimensions, with a significant improvement in morphological analysis, establishing a clear correlation between morphological understanding and diagnostic accuracy.

Artificial Intelligence-Enhanced Couinaud Segmentation for Precision Liver Cancer Therapy

Precision therapy for liver cancer necessitates accurately delineating liver sub-regions to protect healthy tissue while targeting tumors, which is essential for reducing recurrence and improving survival rates. However, the segmentation of hepatic segments, known as Couinaud segmentation, is challenging due to indistinct sub-region boundaries and the need for extensive annotated datasets. This study introduces LiverFormer, a novel Couinaud segmentation model that effectively integrates global context with low-level local features based on a 3D hybrid CNN-Transformer architecture. Additionally, a registration-based data augmentation strategy is equipped to enhance the segmentation performance with limited labeled data. Evaluated on CT images from 123 patients, LiverFormer demonstrated high accuracy and strong concordance with expert annotations across various metrics, allowing for enhanced treatment planning for surgery and radiation therapy. It has great potential to reduces complications and minimizes potential damages to surrounding tissue, leading to improved outcomes for patients undergoing complex liver cancer treatments.

Accelerated Multi-Contrast MRI Reconstruction via Frequency and Spatial Mutual Learning

To accelerate Magnetic Resonance (MR) imaging procedures, Multi-Contrast MR Reconstruction (MCMR) has become a prevalent trend that utilizes an easily obtainable modality as an auxiliary to support high-quality reconstruction of the target modality with under-sampled k-space measurements. The exploration of global dependency and complementary information across different modalities is essential for MCMR. However, existing methods either struggle to capture global dependency due to the limited receptive field or suffer from quadratic computational complexity. To tackle this dilemma, we propose a novel Frequency and Spatial Mutual Learning Network (FSMNet), which efficiently explores global dependencies across different modalities. Specifically, the features for each modality are extracted by the Frequency-Spatial Feature Extraction (FSFE) module, featuring a frequency branch and a spatial branch. Benefiting from the global property of the Fourier transform, the frequency branch can efficiently capture global dependency with an image-size receptive field, while the spatial branch can extract local features. To exploit complementary information from the auxiliary modality, we propose a Cross-Modal Selective fusion (CMS-fusion) module that selectively incorporate the frequency and spatial features from the auxiliary modality to enhance the corresponding branch of the target modality. To further integrate the enhanced global features from the frequency branch and the enhanced local features from the spatial branch, we develop a Frequency-Spatial fusion (FS-fusion) module, resulting in a comprehensive feature representation for the target modality. Extensive experiments on the BraTS and fastMRI datasets demonstrate that the proposed FSMNet achieves state-of-the-art performance for the MCMR task with different acceleration factors. The code is available at: https://github.com/qic999/FSMNet.

OccMamba: Semantic Occupancy Prediction with State Space Models

Training deep learning models for semantic occupancy prediction is challenging due to factors such as a large number of occupancy cells, severe occlusion, limited visual cues, complicated driving scenarios, etc. Recent methods often adopt transformer-based architectures given their strong capability in learning input-conditioned weights and long-range relationships. However, transformer-based networks are notorious for their quadratic computation complexity, seriously undermining their efficacy and deployment in semantic occupancy prediction. Inspired by the global modeling and linear computation complexity of the Mamba architecture, we present the first Mamba-based network for semantic occupancy prediction, termed OccMamba. However, directly applying the Mamba architecture to the occupancy prediction task yields unsatisfactory performance due to the inherent domain gap between the linguistic and 3D domains. To relieve this problem, we present a simple yet effective 3D-to-1D reordering operation, i.e., height-prioritized 2D Hilbert expansion. It can maximally retain the spatial structure of point clouds as well as facilitate the processing of Mamba blocks. Our OccMamba achieves state-of-the-art performance on three prevalent occupancy prediction benchmarks, including OpenOccupancy, SemanticKITTI and SemanticPOSS. Notably, on OpenOccupancy, our OccMamba outperforms the previous state-of-the-art Co-Occ by 3.1% IoU and 3.2% mIoU, respectively. Codes will be released upon publication.

Focus on Focus: Focus-oriented Representation Learning and Multi-view Cross-modal Alignment for Glioma Grading

Recently, multimodal deep learning, which integrates histopathology slides and molecular biomarkers, has achieved a promising performance in glioma grading. Despite great progress, due to the intra-modality complexity and inter-modality heterogeneity, existing studies suffer from inadequate histopathology representation learning and inefficient molecular-pathology knowledge alignment. These two issues hinder existing methods to precisely interpret diagnostic molecular-pathology features, thereby limiting their grading performance. Moreover, the real-world applicability of existing multimodal approaches is significantly restricted as molecular biomarkers are not always available during clinical deployment. To address these problems, we introduce a novel Focus on Focus (FoF) framework with paired pathology-genomic training and applicable pathology-only inference, enhancing molecular-pathology representation effectively. Specifically, we propose a Focus-oriented Representation Learning (FRL) module to encourage the model to identify regions positively or negatively related to glioma grading and guide it to focus on the diagnostic areas with a consistency constraint. To effectively link the molecular biomarkers to morphological features, we propose a Multi-view Cross-modal Alignment (MCA) module that projects histopathology representations into molecular subspaces, aligning morphological features with corresponding molecular biomarker status by supervised contrastive learning. Experiments on the TCGA GBM-LGG dataset demonstrate that our FoF framework significantly improves the glioma grading. Remarkably, our FoF achieves superior performance using only histopathology slides compared to existing multimodal methods. The source code is available at https://github.com/peterlipan/FoF.

MMR-Mamba: Multi-Modal MRI Reconstruction with Mamba and Spatial-Frequency Information Fusion

Multi-modal MRI offers valuable complementary information for diagnosis and treatment; however, its utility is limited by prolonged scanning times. To accelerate the acquisition process, a practical approach is to reconstruct images of the target modality, which requires longer scanning times, from under-sampled k-space data using the fully-sampled reference modality with shorter scanning times as guidance. The primary challenge of this task is comprehensively and efficiently integrating complementary information from different modalities to achieve high-quality reconstruction. Existing methods struggle with this: 1) convolution-based models fail to capture long-range dependencies; 2) transformer-based models, while excelling in global feature modeling, struggle with quadratic computational complexity. To address this, we propose MMR-Mamba, a novel framework that thoroughly and efficiently integrates multi-modal features for MRI reconstruction, leveraging Mamba's capability to capture long-range dependencies with linear computational complexity while exploiting global properties of the Fourier domain. Specifically, we first design a Target modality-guided Cross Mamba (TCM) module in the spatial domain, which maximally restores the target modality information by selectively incorporating relevant information from the reference modality. Then, we introduce a Selective Frequency Fusion (SFF) module to efficiently integrate global information in the Fourier domain and recover high-frequency signals for the reconstruction of structural details. Furthermore, we devise an Adaptive Spatial-Frequency Fusion (ASFF) module, which mutually enhances the spatial and frequency domains by supplementing less informative channels from one domain with corresponding channels from the other.

MMR-Mamba: Multi-Contrast MRI Reconstruction with Mamba and Spatial-Frequency Information Fusion

Multi-contrast MRI acceleration has become prevalent in MR imaging, enabling the reconstruction of high-quality MR images from under-sampled k-space data of the target modality, using guidance from a fully-sampled auxiliary modality. The main crux lies in efficiently and comprehensively integrating complementary information from the auxiliary modality. Existing methods either suffer from quadratic computational complexity or fail to capture long-range correlated features comprehensively. In this work, we propose MMR-Mamba, a novel framework that achieves comprehensive integration of multi-contrast features through Mamba and spatial-frequency information fusion. Firstly, we design the \textit{Target modality-guided Cross Mamba} (TCM) module in the spatial domain, which maximally restores the target modality information by selectively absorbing useful information from the auxiliary modality. Secondly, leveraging global properties of the Fourier domain, we introduce the \textit{Selective Frequency Fusion} (SFF) module to efficiently integrate global information in the frequency domain and recover high-frequency signals for the reconstruction of structure details. Additionally, we present the \textit{Adaptive Spatial-Frequency Fusion} (ASFF) module, which enhances fused features by supplementing less informative features from one domain with corresponding features from the other domain. These innovative strategies ensure efficient feature fusion across spatial and frequency domains, avoiding the introduction of redundant information and facilitating the reconstruction of high-quality target images. Extensive experiments on the BraTS and fastMRI knee datasets demonstrate the superiority of the proposed MMR-Mamba over state-of-the-art MRI reconstruction methods.

Discrepancy-based Active Learning for Weakly Supervised Bleeding Segmentation in Wireless Capsule Endoscopy Images

Weakly supervised methods, such as class activation maps (CAM) based, have been applied to achieve bleeding segmentation with low annotation efforts in Wireless Capsule Endoscopy (WCE) images. However, the CAM labels tend to be extremely noisy, and there is an irreparable gap between CAM labels and ground truths for medical images. This paper proposes a new Discrepancy-basEd Active Learning (DEAL) approach to bridge the gap between CAMs and ground truths with a few annotations. Specifically, to liberate labor, we design a novel discrepancy decoder model and a CAMPUS (CAM, Pseudo-label and groUnd-truth Selection) criterion to replace the noisy CAMs with accurate model predictions and a few human labels. The discrepancy decoder model is trained with a unique scheme to generate standard, coarse and fine predictions. And the CAMPUS criterion is proposed to predict the gaps between CAMs and ground truths based on model divergence and CAM divergence. We evaluate our method on the WCE dataset and results show that our method outperforms the state-of-the-art active learning methods and reaches comparable performance to those trained with full annotated datasets with only 10% of the training data labeled.

Categorical Relation-Preserving Contrastive Knowledge Distillation for Medical Image Classification

The amount of medical images for training deep classification models is typically very scarce, making these deep models prone to overfit the training data. Studies showed that knowledge distillation (KD), especially the mean-teacher framework which is more robust to perturbations, can help mitigate the over-fitting effect. However, directly transferring KD from computer vision to medical image classification yields inferior performance as medical images suffer from higher intra-class variance and class imbalance. To address these issues, we propose a novel Categorical Relation-preserving Contrastive Knowledge Distillation (CRCKD) algorithm, which takes the commonly used mean-teacher model as the supervisor. Specifically, we propose a novel Class-guided Contrastive Distillation (CCD) module to pull closer positive image pairs from the same class in the teacher and student models, while pushing apart negative image pairs from different classes. With this regularization, the feature distribution of the student model shows higher intra-class similarity and inter-class variance. Besides, we propose a Categorical Relation Preserving (CRP) loss to distill the teacher's relational knowledge in a robust and class-balanced manner. With the contribution of the CCD and CRP, our CRCKD algorithm can distill the relational knowledge more comprehensively. Extensive experiments on the HAM10000 and APTOS datasets demonstrate the superiority of the proposed CRCKD method.