Magnetic resonance imaging (MRI) is indispensable for diagnosing and planning treatment in various medical conditions due to its ability to produce multi-series images that reveal different tissue characteristics. However, integrating these diverse series to form a coherent analysis presents significant challenges, such as differing spatial resolutions and contrast patterns meanwhile requiring extensive annotated data, which is scarce in clinical practice. Due to these issues, we introduce a novel Cross-Series Masking (CSM) Strategy for effectively learning MRI representation in a self-supervised manner. Specifically, CSM commences by randomly sampling a subset of regions and series, which are then strategically masked. In the training process, the cross-series representation is learned by utilizing the unmasked data to reconstruct the masked portions. This process not only integrates information across different series but also facilitates the ability to model both intra-series and inter-series correlations and complementarities. With the learned representation, the downstream tasks like segmentation and classification are also enhanced. Taking brain tissue segmentation, breast tumor benign/malignant classification, and prostate cancer diagnosis as examples, our method achieves state-of-the-art performance on both public and in-house datasets.

Large Language Models (LLMs) show promise for natural language generation in healthcare, but risk hallucinating factually incorrect information. Deploying LLMs for medical question answering necessitates reliable uncertainty estimation (UE) methods to detect hallucinations. In this work, we benchmark popular UE methods with different model sizes on medical question-answering datasets. Our results show that current approaches generally perform poorly in this domain, highlighting the challenge of UE for medical applications. We also observe that larger models tend to yield better results, suggesting a correlation between model size and the reliability of UE. To address these challenges, we propose Two-phase Verification, a probability-free Uncertainty Estimation approach. First, an LLM generates a step-by-step explanation alongside its initial answer, followed by formulating verification questions to check the factual claims in the explanation. The model then answers these questions twice: first independently, and then referencing the explanation. Inconsistencies between the two sets of answers measure the uncertainty in the original response. We evaluate our approach on three biomedical question-answering datasets using Llama 2 Chat models and compare it against the benchmarked baseline methods. The results show that our Two-phase Verification method achieves the best overall accuracy and stability across various datasets and model sizes, and its performance scales as the model size increases.

Automated classification of liver lesions in multi-phase CT and MR scans is of clinical significance but challenging. This study proposes a novel Siamese Dual-Resolution Transformer (SDR-Former) framework, specifically designed for liver lesion classification in 3D multi-phase CT and MR imaging with varying phase counts. The proposed SDR-Former utilizes a streamlined Siamese Neural Network (SNN) to process multi-phase imaging inputs, possessing robust feature representations while maintaining computational efficiency. The weight-sharing feature of the SNN is further enriched by a hybrid Dual-Resolution Transformer (DR-Former), comprising a 3D Convolutional Neural Network (CNN) and a tailored 3D Transformer for processing high- and low-resolution images, respectively. This hybrid sub-architecture excels in capturing detailed local features and understanding global contextual information, thereby, boosting the SNN's feature extraction capabilities. Additionally, a novel Adaptive Phase Selection Module (APSM) is introduced, promoting phase-specific intercommunication and dynamically adjusting each phase's influence on the diagnostic outcome. The proposed SDR-Former framework has been validated through comprehensive experiments on two clinical datasets: a three-phase CT dataset and an eight-phase MR dataset. The experimental results affirm the efficacy of the proposed framework. To support the scientific community, we are releasing our extensive multi-phase MR dataset for liver lesion analysis to the public. This pioneering dataset, being the first publicly available multi-phase MR dataset in this field, also underpins the MICCAI LLD-MMRI Challenge. The dataset is accessible at:https://bit.ly/3IyYlgN.

Accurate medical image segmentation demands the integration of multi-scale information, spanning from local features to global dependencies. However, it is challenging for existing methods to model long-range global information, where convolutional neural networks (CNNs) are constrained by their local receptive fields, and vision transformers (ViTs) suffer from high quadratic complexity of their attention mechanism. Recently, Mamba-based models have gained great attention for their impressive ability in long sequence modeling. Several studies have demonstrated that these models can outperform popular vision models in various tasks, offering higher accuracy, lower memory consumption, and less computational burden. However, existing Mamba-based models are mostly trained from scratch and do not explore the power of pretraining, which has been proven to be quite effective for data-efficient medical image analysis. This paper introduces a novel Mamba-based model, Swin-UMamba, designed specifically for medical image segmentation tasks, leveraging the advantages of ImageNet-based pretraining. Our experimental results reveal the vital role of ImageNet-based training in enhancing the performance of Mamba-based models. Swin-UMamba demonstrates superior performance with a large margin compared to CNNs, ViTs, and latest Mamba-based models. Notably, on AbdomenMRI, Encoscopy, and Microscopy datasets, Swin-UMamba outperforms its closest counterpart U-Mamba by an average score of 3.58%. The code and models of Swin-UMamba are publicly available at: https://github.com/JiarunLiu/Swin-UMamba

Coronary microvascular disease constitutes a substantial risk to human health. Employing computer-aided analysis and diagnostic systems, medical professionals can intervene early in disease progression, with 3D vessel segmentation serving as a crucial component. Nevertheless, conventional U-Net architectures tend to yield incoherent and imprecise segmentation outcomes, particularly for small vessel structures. While models with attention mechanisms, such as Transformers and large convolutional kernels, demonstrate superior performance, their extensive computational demands during training and inference lead to increased time complexity. In this study, we leverage Fourier domain learning as a substitute for multi-scale convolutional kernels in 3D hierarchical segmentation models, which can reduce computational expenses while preserving global receptive fields within the network. Furthermore, a zero-parameter frequency domain fusion method is designed to improve the skip connections in U-Net architecture. Experimental results on a public dataset and an in-house dataset indicate that our novel Fourier transformation-based network achieves remarkable dice performance (84.37\% on ASACA500 and 80.32\% on ImageCAS) in tubular vessel segmentation tasks and substantially reduces computational requirements without compromising global receptive fields.

Albeit the notable performance on in-domain test points, it is non-trivial for deep neural networks to attain satisfactory accuracy when deploying in the open world, where novel domains and object classes often occur. In this paper, we study a practical problem of Domain Generalization under Category Shift (DGCS), which aims to simultaneously detect unknown-class samples and classify known-class samples in the target domains. Compared to prior DG works, we face two new challenges: 1) how to learn the concept of ``unknown'' during training with only source known-class samples, and 2) how to adapt the source-trained model to unseen environments for safe model deployment. To this end, we propose a novel Activate and Reject (ART) framework to reshape the model's decision boundary to accommodate unknown classes and conduct post hoc modification to further discriminate known and unknown classes using unlabeled test data. Specifically, during training, we promote the response to the unknown by optimizing the unknown probability and then smoothing the overall output to mitigate the overconfidence issue. At test time, we introduce a step-wise online adaptation method that predicts the label by virtue of the cross-domain nearest neighbor and class prototype information without updating the network's parameters or using threshold-based mechanisms. Experiments reveal that ART consistently improves the generalization capability of deep networks on different vision tasks. For image classification, ART improves the H-score by 6.1% on average compared to the previous best method. For object detection and semantic segmentation, we establish new benchmarks and achieve competitive performance.

Dataset Condensation aims to condense a large dataset into a smaller one while maintaining its ability to train a well-performing model, thus reducing the storage cost and training effort in deep learning applications. However, conventional dataset condensation methods are optimization-oriented and condense the dataset by performing gradient or parameter matching during model optimization, which is computationally intensive even on small datasets and models. In this paper, we propose a novel dataset condensation method based on distribution matching, which is more efficient and promising. Specifically, we identify two important shortcomings of naive distribution matching (i.e., imbalanced feature numbers and unvalidated embeddings for distance computation) and address them with three novel techniques (i.e., partitioning and expansion augmentation, efficient and enriched model sampling, and class-aware distribution regularization). Our simple yet effective method outperforms most previous optimization-oriented methods with much fewer computational resources, thereby scaling data condensation to larger datasets and models. Extensive experiments demonstrate the effectiveness of our method. Codes are available at https://github.com/uitrbn/IDM

During the diagnostic process, clinicians leverage multimodal information, such as chief complaints, medical images, and laboratory-test results. Deep-learning models for aiding diagnosis have yet to meet this requirement. Here we report a Transformer-based representation-learning model as a clinical diagnostic aid that processes multimodal input in a unified manner. Rather than learning modality-specific features, the model uses embedding layers to convert images and unstructured and structured text into visual tokens and text tokens, and bidirectional blocks with intramodal and intermodal attention to learn a holistic representation of radiographs, the unstructured chief complaint and clinical history, structured clinical information such as laboratory-test results and patient demographic information. The unified model outperformed an image-only model and non-unified multimodal diagnosis models in the identification of pulmonary diseases (by 12% and 9%, respectively) and in the prediction of adverse clinical outcomes in patients with COVID-19 (by 29% and 7%, respectively). Leveraging unified multimodal Transformer-based models may help streamline triage of patients and facilitate the clinical decision process.

Learning image classification and image generation using the same set of network parameters is a challenging problem. Recent advanced approaches perform well in one task often exhibit poor performance in the other. This work introduces an energy-based classifier and generator, namely EGC, which can achieve superior performance in both tasks using a single neural network. Unlike a conventional classifier that outputs a label given an image (i.e., a conditional distribution $p(y|\mathbf{x})$), the forward pass in EGC is a classifier that outputs a joint distribution $p(\mathbf{x},y)$, enabling an image generator in its backward pass by marginalizing out the label $y$. This is done by estimating the energy and classification probability given a noisy image in the forward pass, while denoising it using the score function estimated in the backward pass. EGC achieves competitive generation results compared with state-of-the-art approaches on ImageNet-1k, CelebA-HQ and LSUN Church, while achieving superior classification accuracy and robustness against adversarial attacks on CIFAR-10. This work represents the first successful attempt to simultaneously excel in both tasks using a single set of network parameters. We believe that EGC bridges the gap between discriminative and generative learning.

In this work, we present Multi-Level Contrastive Learning for Dense Prediction Task (MCL), an efficient self-supervised method for learning region-level feature representation for dense prediction tasks. Our method is motivated by the three key factors in detection: localization, scale consistency and recognition. To explicitly encode absolute position and scale information, we propose a novel pretext task that assembles multi-scale images in a montage manner to mimic multi-object scenarios. Unlike the existing image-level self-supervised methods, our method constructs a multi-level contrastive loss that considers each sub-region of the montage image as a singleton. Our method enables the neural network to learn regional semantic representations for translation and scale consistency while reducing pre-training epochs to the same as supervised pre-training. Extensive experiments demonstrate that MCL consistently outperforms the recent state-of-the-art methods on various datasets with significant margins. In particular, MCL obtains 42.5 AP$^\mathrm{bb}$ and 38.3 AP$^\mathrm{mk}$ on COCO with the 1x schedule fintuning, when using Mask R-CNN with R50-FPN backbone pre-trained with 100 epochs. In comparison to MoCo, our method surpasses their performance by 4.0 AP$^\mathrm{bb}$ and 3.1 AP$^\mathrm{mk}$. Furthermore, we explore the alignment between pretext task and downstream tasks. We extend our pretext task to supervised pre-training, which achieves a similar performance to self-supervised learning. This result demonstrates the importance of the alignment between pretext task and downstream tasks, indicating the potential for wider applicability of our method beyond self-supervised settings.