E3D-GPT: Enhanced 3D Visual Foundation for Medical Vision-Language Model

The development of 3D medical vision-language models holds significant potential for disease diagnosis and patient treatment. However, compared to 2D medical images, 3D medical images, such as CT scans, face challenges related to limited training data and high dimension, which severely restrict the progress of 3D medical vision-language models. To address these issues, we collect a large amount of unlabeled 3D CT data and utilize self-supervised learning to construct a 3D visual foundation model for extracting 3D visual features. Then, we apply 3D spatial convolutions to aggregate and project high-level image features, reducing computational complexity while preserving spatial information. We also construct two instruction-tuning datasets based on BIMCV-R and CT-RATE to fine-tune the 3D vision-language model. Our model demonstrates superior performance compared to existing methods in report generation, visual question answering, and disease diagnosis. Code and data will be made publicly available soon.

CARZero: Cross-Attention Alignment for Radiology Zero-Shot Classification

The advancement of Zero-Shot Learning in the medical domain has been driven forward by using pre-trained models on large-scale image-text pairs, focusing on image-text alignment. However, existing methods primarily rely on cosine similarity for alignment, which may not fully capture the complex relationship between medical images and reports. To address this gap, we introduce a novel approach called Cross-Attention Alignment for Radiology Zero-Shot Classification (CARZero). Our approach innovatively leverages cross-attention mechanisms to process image and report features, creating a Similarity Representation that more accurately reflects the intricate relationships in medical semantics. This representation is then linearly projected to form an image-text similarity matrix for cross-modality alignment. Additionally, recognizing the pivotal role of prompt selection in zero-shot learning, CARZero incorporates a Large Language Model-based prompt alignment strategy. This strategy standardizes diverse diagnostic expressions into a unified format for both training and inference phases, overcoming the challenges of manual prompt design. Our approach is simple yet effective, demonstrating state-of-the-art performance in zero-shot classification on five official chest radiograph diagnostic test sets, including remarkable results on datasets with long-tail distributions of rare diseases. This achievement is attributed to our new image-text alignment strategy, which effectively addresses the complex relationship between medical images and reports.

ECAMP: Entity-centered Context-aware Medical Vision Language Pre-training

Despite significant advancements in medical vision-language pre-training, existing methods have largely overlooked the inherent entity-specific context within radiology reports and the complex cross-modality contextual relationships between text and images. To close this gap, we propose a novel Entity-centered Context-aware Medical Vision-language Pre-training (ECAMP) framework, which is designed to enable a more entity-centered and context-sensitive interpretation of medical data. Utilizing the recent powerful large language model, we distill entity-centered context from medical reports, which enables ECAMP to gain more effective supervision from the text modality. By further pre-training our model with carefully designed entity-aware, context-enhanced masked language modeling and context-guided super-resolution tasks, ECAMP significantly refines the interplay between text and image modalities, leading to an enhanced ability to extract entity-centered contextual features. Besides, our proposed multi-scale context fusion design also improves the semantic integration of both coarse and fine-level image representations, prompting better performance for multi-scale downstream applications. Combining these components leads to significant performance leaps over current state-of-the-art methods and establishes a new standard for cross-modality learning in medical imaging, whose effectiveness is demonstrated by our extensive experiments on various tasks including classification, segmentation, and detection across several public datasets. Code and models are available at https://github.com/ToniChopp/ECAMP.

Long-tailed multi-label classification with noisy label of thoracic diseases from chest X-ray

Chest X-rays (CXR) often reveal rare diseases, demanding precise diagnosis. However, current computer-aided diagnosis (CAD) methods focus on common diseases, leading to inadequate detection of rare conditions due to the absence of comprehensive datasets. To overcome this, we present a novel benchmark for long-tailed multi-label classification in CXRs, encapsulating both common and rare thoracic diseases. Our approach includes developing the "LTML-MIMIC-CXR" dataset, an augmentation of MIMIC-CXR with 26 additional rare diseases. We propose a baseline method for this classification challenge, integrating adaptive negative regularization to address negative logits' over-suppression in tail classes, and a large loss reconsideration strategy for correcting noisy labels from automated annotations. Our evaluation on LTML-MIMIC-CXR demonstrates significant advancements in rare disease detection. This work establishes a foundation for robust CAD methods, achieving a balance in identifying a spectrum of thoracic diseases in CXRs. Access to our code and dataset is provided at:https://github.com/laihaoran/LTML-MIMIC-CXR.

DLUNet: Semi-supervised Learning based Dual-Light UNet for Multi-organ Segmentation

The manual ground truth of abdominal multi-organ is labor-intensive. In order to make full use of CT data, we developed a semi-supervised learning based dual-light UNet. In the training phase, it consists of two light UNets, which make full use of label and unlabeled data simultaneously by using consistent-based learning. Moreover, separable convolution and residual concatenation was introduced light UNet to reduce the computational cost. Further, a robust segmentation loss was applied to improve the performance. In the inference phase, only a light UNet is used, which required low time cost and less GPU memory utilization. The average DSC of this method in the validation set is 0.8718. The code is available in https://github.com/laihaoran/Semi-SupervisednnUNet.

Semi-Supervised Hybrid Spine Network for Segmentation of Spine MR Images

Automatic segmentation of vertebral bodies (VBs) and intervertebral discs (IVDs) in 3D magnetic resonance (MR) images is vital in diagnosing and treating spinal diseases. However, segmenting the VBs and IVDs simultaneously is not trivial. Moreover, problems exist, including blurry segmentation caused by anisotropy resolution, high computational cost, inter-class similarity and intra-class variability, and data imbalances. We proposed a two-stage algorithm, named semi-supervised hybrid spine network (SSHSNet), to address these problems by achieving accurate simultaneous VB and IVD segmentation. In the first stage, we constructed a 2D semi-supervised DeepLabv3+ by using cross pseudo supervision to obtain intra-slice features and coarse segmentation. In the second stage, a 3D full-resolution patch-based DeepLabv3+ was built. This model can be used to extract inter-slice information and combine the coarse segmentation and intra-slice features provided from the first stage. Moreover, a cross tri-attention module was applied to compensate for the loss of inter-slice and intra-slice information separately generated from 2D and 3D networks, thereby improving feature representation ability and achieving satisfactory segmentation results. The proposed SSHSNet was validated on a publicly available spine MR image dataset, and remarkable segmentation performance was achieved. Moreover, results show that the proposed method has great potential in dealing with the data imbalance problem. Based on previous reports, few studies have incorporated a semi-supervised learning strategy with a cross attention mechanism for spine segmentation. Therefore, the proposed method may provide a useful tool for spine segmentation and aid clinically in spinal disease diagnoses and treatments. Codes are publicly available at: https://github.com/Meiyan88/SSHSNet.