Yong Liang

Weijian Huang, Cheng Li, Hong-Yu Zhou et al.

Recently, multi-modal vision-language foundation models have gained significant attention in the medical field. While these models offer great opportunities, they still face crucial challenges, such as the requirement for fine-grained knowledge understanding in computer-aided diagnosis and the capability of utilizing very limited or even no task-specific labeled data in real-world clinical applications. In this study, we present MaCo, a masked contrastive chest X-ray foundation model that tackles these challenges. MaCo explores masked contrastive learning to simultaneously achieve fine-grained image understanding and zero-shot learning for a variety of medical imaging tasks. It designs a correlation weighting mechanism to adjust the correlation between masked chest X-ray image patches and their corresponding reports, thereby enhancing the model's representation learning capabilities. To evaluate the performance of MaCo, we conducted extensive experiments using 6 well-known open-source X-ray datasets. The experimental results demonstrate the superiority of MaCo over 10 state-of-the-art approaches across tasks such as classification, segmentation, detection, and phrase grounding. These findings highlight the significant potential of MaCo in advancing a wide range of medical image analysis tasks.

Yong Liang, Xiaojie Mao, Shiyuan Wang

We study an online joint assortment-inventory optimization problem, in which we assume that the choice behavior of each customer follows the Multinomial Logit (MNL) choice model, and the attraction parameters are unknown a priori. The retailer makes periodic assortment and inventory decisions to dynamically learn from the customer choice observations about the attraction parameters while maximizing the expected total profit over time. In this paper, we propose a novel algorithm that can effectively balance exploration and exploitation in the online decision-making of assortment and inventory. Our algorithm builds on a new estimator for the MNL attraction parameters, an innovative approach to incentivize exploration by adaptively tuning certain known and unknown parameters, and an optimization oracle to static single-cycle assortment-inventory planning problems with given parameters. We establish a regret upper bound for our algorithm and a lower bound for the online joint assortment-inventory optimization problem, suggesting that our algorithm achieves nearly optimal regret rate, provided that the static optimization oracle is exact. Then we incorporate more practical approximate static optimization oracles into our algorithm, and bound from above the impact of static optimization errors on the regret of our algorithm. We perform numerical studies to demonstrate the effectiveness of our proposed algorithm. At last, we extend our study by incorporating inventory carryover and the learning of customer arrival distribution.

Weijian Huang, Cheng Li, Hong-Yu Zhou et al.

The development of medical vision-language foundation models has attracted significant attention in the field of medicine and healthcare due to their promising prospect in various clinical applications. While previous studies have commonly focused on feature learning at a single learning scale, investigation on integrating multi-scale information is lacking, which may hinder the potential for mutual reinforcement among these features. This paper aims to bridge this gap by proposing a method that effectively exploits multi-scale information to enhance the performance of medical foundation models. The proposed method simultaneously exploits features at the local, instance, modality and global aspects, facilitating comprehensive representation learning within the models. We evaluate the effectiveness of the proposed method on six open-source datasets across different clinical tasks, demonstrating its ability to enhance the performance of medical foundation models.

Jiarun Liu, Hao Yang, Hong-Yu Zhou et al.

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_Enc by an average score of 2.72%.

Hong Wang, Qi Xie, Qian Zhao et al.

As a common weather, rain streaks adversely degrade the image quality. Hence, removing rains from an image has become an important issue in the field. To handle such an ill-posed single image deraining task, in this paper, we specifically build a novel deep architecture, called rain convolutional dictionary network (RCDNet), which embeds the intrinsic priors of rain streaks and has clear interpretability. In specific, we first establish a RCD model for representing rain streaks and utilize the proximal gradient descent technique to design an iterative algorithm only containing simple operators for solving the model. By unfolding it, we then build the RCDNet in which every network module has clear physical meanings and corresponds to each operation involved in the algorithm. This good interpretability greatly facilitates an easy visualization and analysis on what happens inside the network and why it works well in inference process. Moreover, taking into account the domain gap issue in real scenarios, we further design a novel dynamic RCDNet, where the rain kernels can be dynamically inferred corresponding to input rainy images and then help shrink the space for rain layer estimation with few rain maps so as to ensure a fine generalization performance in the inconsistent scenarios of rain types between training and testing data. By end-to-end training such an interpretable network, all involved rain kernels and proximal operators can be automatically extracted, faithfully characterizing the features of both rain and clean background layers, and thus naturally lead to better deraining performance. Comprehensive experiments substantiate the superiority of our method, especially on its well generality to diverse testing scenarios and good interpretability for all its modules. Code is available in \emph{\url{https://github.com/hongwang01/DRCDNet}}.

Jiarun Liu, Hong-Yu Zhou, Cheng Li et al.

Existing contrastive language-image pre-training aims to learn a joint representation by matching abundant image-text pairs. However, the number of image-text pairs in medical datasets is usually orders of magnitude smaller than that in natural datasets. Besides, medical image-text pairs often involve numerous complex fine-grained correspondences. This paper aims to enhance the data efficiency by introducing multiple-to-multiple local relationship modeling to capture denser supervisions. More specifically, we propose a Medical Language-Image Pre-training (MLIP) framework, which exploits the limited image-text medical data more efficiently through patch-sentence matching. Furthermore, we introduce a masked contrastive learning strategy with semantic integrity estimation to reduce redundancy in images while preserving the underlying semantics. Our evaluation results show that MLIP outperforms previous work in zero/few-shot classification and few-shot segmentation tasks by a large margin.

Hao Yang, Hong-Yu Zhou, Cheng Li et al.

Multimodal deep learning utilizing imaging and diagnostic reports has made impressive progress in the field of medical imaging diagnostics, demonstrating a particularly strong capability for auxiliary diagnosis in cases where sufficient annotation information is lacking. Nonetheless, localizing diseases accurately without detailed positional annotations remains a challenge. Although existing methods have attempted to utilize local information to achieve fine-grained semantic alignment, their capability in extracting the fine-grained semantics of the comprehensive context within reports is limited. To address this problem, a new method is introduced that takes full sentences from textual reports as the basic units for local semantic alignment. This approach combines chest X-ray images with their corresponding textual reports, performing contrastive learning at both global and local levels. The leading results obtained by this method on multiple datasets confirm its efficacy in the task of lesion localization.

Yishen Liu, Shengda Luo, Zishao Zhong et al.

Large language models (LLMs) primarily trained on English texts, often face biases and inaccuracies in Chinese contexts. Their limitations are pronounced in fields like Traditional Chinese Medicine (TCM), where cultural and clinical subtleties are vital, further hindered by a lack of domain-specific data, such as rheumatoid arthritis (RA). To address these issues, this paper introduces Hengqin-RA-v1, the first large language model specifically tailored for TCM with a focus on diagnosing and treating RA. We also present HQ-GCM-RA-C1, a comprehensive RA-specific dataset curated from ancient Chinese medical literature, classical texts, and modern clinical studies. This dataset empowers Hengqin-RA-v1 to deliver accurate and culturally informed responses, effectively bridging the gaps left by general-purpose models. Extensive experiments demonstrate that Hengqin-RA-v1 outperforms state-of-the-art models, even surpassing the diagnostic accuracy of TCM practitioners in certain cases.

Hao Yang, Hong-Yu Zhou, Jiarun Liu et al.

Existing deep learning models for defining pathology from clinical imaging data rely on expert annotations and lack generalization capabilities in open clinical environments. Here, we present a generalizable vision-language model for Annotation-Free pathology Localization (AFLoc). The core strength of AFLoc is extensive multi-level semantic structure-based contrastive learning, which comprehensively aligns multi-granularity medical concepts with abundant image features to adapt to the diverse expressions of pathologies without the reliance on expert image annotations. We conduct primary experiments on a dataset of 220K pairs of image-report chest X-ray images and perform validation across eight external datasets encompassing 34 types of chest pathologies. The results demonstrate that AFLoc outperforms state-of-the-art methods in both annotation-free localization and classification tasks. Additionally, we assess the generalizability of AFLoc on other modalities, including histopathology and retinal fundus images. We show that AFLoc exhibits robust generalization capabilities, even surpassing human benchmarks in localizing five different types of pathological images. These results highlight the potential of AFLoc in reducing annotation requirements and its applicability in complex clinical environments.

Jiarun Liu, Hong-Yu Zhou, Weijian Huang et al.

Scaling up model and data size have demonstrated impressive performance improvement over a wide range of tasks. Despite extensive studies on scaling behaviors for general-purpose tasks, medical images exhibit substantial differences from natural data. It remains unclear the key factors in developing medical vision foundation models at scale due to the absence of an extensive understanding of scaling behavior in the medical domain. In this paper, we explored the scaling behavior across model sizes, training algorithms, data sizes, and imaging modalities in developing scalable medical vision foundation models by self-supervised learning. To support scalable pretraining, we introduce BioVFM-21M, a large-scale biomedical image dataset encompassing a wide range of biomedical image modalities and anatomies. We observed that scaling up does provide benefits but varies across tasks. Additional analysis reveals several factors correlated with scaling benefits. Finally, we propose BioVFM, a large-scale medical vision foundation model pretrained on 21 million biomedical images, which outperforms the previous state-of-the-art foundation models across 12 medical benchmarks. Our results highlight that while scaling up is beneficial for pursuing better performance, task characteristics, data diversity, pretraining methods, and computational efficiency remain critical considerations for developing scalable medical foundation models.

Xin Dong, Rui Miao, Suyan Zhang et al.

Repositioning drug-disease relationships has always been a hot field of research. However, actual cases of biologically validated drug relocation remain very limited, and existing models have not yet fully utilized the structural information of the drug. Furthermore, most repositioning models are only used to complete the relationship matrix, and their practicality is poor when dealing with drug cold start problems. This paper proposes a structure-enhanced multimodal relationship prediction model (SMRP). SMPR is based on the SMILE structure of the drug, using the Mol2VEC method to generate drug embedded representations, and learn disease embedded representations through heterogeneous network graph neural networks. Ultimately, a drug-disease relationship matrix is constructed. In addition, to reduce the difficulty of users' use, SMPR also provides a cold start interface based on structural similarity based on reposition results to simply and quickly predict drug-related diseases. The repositioning ability and cold start capability of the model are verified from multiple perspectives. While the AUC and ACUPR scores of repositioning reach 99% and 61% respectively, the AUC of cold start achieve 80%. In particular, the cold start Recall indicator can reach more than 70%, which means that SMPR is more sensitive to positive samples. Finally, case analysis is used to verify the practical value of the model and visual analysis directly demonstrates the improvement of the structure to the model. For quick use, we also provide local deployment of the model and package it into an executable program.

Weijian Huang, Cheng Li, Hao Yang et al.

Recently, vision-language representation learning has made remarkable advancements in building up medical foundation models, holding immense potential for transforming the landscape of clinical research and medical care. The underlying hypothesis is that the rich knowledge embedded in radiology reports can effectively assist and guide the learning process, reducing the need for additional labels. However, these reports tend to be complex and sometimes even consist of redundant descriptions that make the representation learning too challenging to capture the key semantic information. This paper develops a novel iterative vision-language representation learning framework by proposing a key semantic knowledge-emphasized report refinement method. Particularly, raw radiology reports are refined to highlight the key information according to a constructed clinical dictionary and two model-optimized knowledge-enhancement metrics. The iterative framework is designed to progressively learn, starting from gaining a general understanding of the patient's condition based on raw reports and gradually refines and extracts critical information essential to the fine-grained analysis tasks. The effectiveness of the proposed framework is validated on various downstream medical image analysis tasks, including disease classification, region-of-interest segmentation, and phrase grounding. Our framework surpasses seven state-of-the-art methods in both fine-tuning and zero-shot settings, demonstrating its encouraging potential for different clinical applications.

Ziyi Yang, Jun Shu, Yong Liang et al.

Current machine learning has made great progress on computer vision and many other fields attributed to the large amount of high-quality training samples, while it does not work very well on genomic data analysis, since they are notoriously known as small data. In our work, we focus on few-shot disease subtype prediction problem, identifying subgroups of similar patients that can guide treatment decisions for a specific individual through training on small data. In fact, doctors and clinicians always address this problem by studying several interrelated clinical variables simultaneously. We attempt to simulate such clinical perspective, and introduce meta learning techniques to develop a new model, which can extract the common experience or knowledge from interrelated clinical tasks and transfer it to help address new tasks. Our new model is built upon a carefully designed meta-learner, called Prototypical Network, that is a simple yet effective meta learning machine for few-shot image classification. Observing that gene expression data have specifically high dimensionality and high noise properties compared with image data, we proposed a new extension of it by appending two modules to address these issues. Concretely, we append a feature selection layer to automatically filter out the disease-irrelated genes and incorporate a sample reweighting strategy to adaptively remove noisy data, and meanwhile the extended model is capable of learning from a limited number of training examples and generalize well. Simulations and real gene expression data experiments substantiate the superiority of the proposed method for predicting the subtypes of disease and identifying potential disease-related genes.

Hong Wang, Yichen Wu, Qi Xie et al.

To alleviate the adverse effect of rain streaks in image processing tasks, CNN-based single image rain removal methods have been recently proposed. However, the performance of these deep learning methods largely relies on the covering range of rain shapes contained in the pre-collected training rainy-clean image pairs. This makes them easily trapped into the overfitting-to-the-training-samples issue and cannot finely generalize to practical rainy images with complex and diverse rain streaks. Against this generalization issue, this study proposes a new network architecture by enforcing the output residual of the network possess intrinsic rain structures. Such a structural residual setting guarantees the rain layer extracted by the network finely comply with the prior knowledge of general rain streaks, and thus regulates sound rain shapes capable of being well extracted from rainy images in both training and predicting stages. Such a general regularization function naturally leads to both its better training accuracy and testing generalization capability even for those non-seen rain configurations. Such superiority is comprehensively substantiated by experiments implemented on synthetic and real datasets both visually and quantitatively as compared with current state-of-the-art methods.