Kang Li

Xiaoxiao He, Chaowei Tan, Bo Liu et al.

Federated Learning has gained popularity among medical institutions since it enables collaborative training between clients (e.g., hospitals) without aggregating data. However, due to the high cost associated with creating annotations, especially for large 3D image datasets, clinical institutions do not have enough supervised data for training locally. Thus, the performance of the collaborative model is subpar under limited supervision. On the other hand, large institutions have the resources to compile data repositories with high-resolution images and labels. Therefore, individual clients can utilize the knowledge acquired in the public data repositories to mitigate the shortage of private annotated images. In this paper, we propose a federated few-shot learning method with dual knowledge distillation. This method allows joint training with limited annotations across clients without jeopardizing privacy. The supervised learning of the proposed method extracts features from limited labeled data in each client, while the unsupervised data is used to distill both feature and response-based knowledge from a national data repository to further improve the accuracy of the collaborative model and reduce the communication cost. Extensive evaluations are conducted on 3D magnetic resonance knee images from a private clinical dataset. Our proposed method shows superior performance and less training time than other semi-supervised federated learning methods. Codes and additional visualization results are available at https://github.com/hexiaoxiao-cs/fedml-knee.

Xiaoxiao He, Chaowei Tan, Ligong Han et al.

Accurate 3D cardiac reconstruction from cine magnetic resonance imaging (cMRI) is crucial for improved cardiovascular disease diagnosis and understanding of the heart's motion. However, current cardiac MRI-based reconstruction technology used in clinical settings is 2D with limited through-plane resolution, resulting in low-quality reconstructed cardiac volumes. To better reconstruct 3D cardiac volumes from sparse 2D image stacks, we propose a morphology-guided diffusion model for 3D cardiac volume reconstruction, DMCVR, that synthesizes high-resolution 2D images and corresponding 3D reconstructed volumes. Our method outperforms previous approaches by conditioning the cardiac morphology on the generative model, eliminating the time-consuming iterative optimization process of the latent code, and improving generation quality. The learned latent spaces provide global semantics, local cardiac morphology and details of each 2D cMRI slice with highly interpretable value to reconstruct 3D cardiac shape. Our experiments show that DMCVR is highly effective in several aspects, such as 2D generation and 3D reconstruction performance. With DMCVR, we can produce high-resolution 3D cardiac MRI reconstructions, surpassing current techniques. Our proposed framework has great potential for improving the accuracy of cardiac disease diagnosis and treatment planning. Code can be accessed at https://github.com/hexiaoxiao-cs/DMCVR.

Shurui Gui, Hao Yuan, Jie Wang et al.

We investigate the explainability of graph neural networks (GNNs) as a step toward elucidating their working mechanisms. While most current methods focus on explaining graph nodes, edges, or features, we argue that, as the inherent functional mechanism of GNNs, message flows are more natural for performing explainability. To this end, we propose a novel method here, known as FlowX, to explain GNNs by identifying important message flows. To quantify the importance of flows, we propose to follow the philosophy of Shapley values from cooperative game theory. To tackle the complexity of computing all coalitions' marginal contributions, we propose a flow sampling scheme to compute Shapley value approximations as initial assessments of further training. We then propose an information-controlled learning algorithm to train flow scores toward diverse explanation targets: necessary or sufficient explanations. Experimental studies on both synthetic and real-world datasets demonstrate that our proposed FlowX and its variants lead to improved explainability of GNNs. The code is available at https://github.com/divelab/DIG.

Guotai Wang, Xiangde Luo, Ran Gu et al.

Background and Objective: Open-source deep learning toolkits are one of the driving forces for developing medical image segmentation models. Existing toolkits mainly focus on fully supervised segmentation and require full and accurate pixel-level annotations that are time-consuming and difficult to acquire for segmentation tasks, which makes learning from imperfect labels highly desired for reducing the annotation cost. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation. Methods: Our proposed toolkit named PyMIC is a modular deep learning library for medical image segmentation tasks. In addition to basic components that support development of high-performance models for fully supervised segmentation, it contains several advanced components tailored for learning from imperfect annotations, such as loading annotated and unannounced images, loss functions for unannotated, partially or inaccurately annotated images, and training procedures for co-learning between multiple networks, etc. PyMIC supports development of semi-supervised, weakly supervised and noise-robust learning methods for medical image segmentation. Results: We present several illustrative medical image segmentation tasks based on PyMIC: (1) Achieving competitive performance on fully supervised learning; (2) Semi-supervised cardiac structure segmentation with only 10% training images annotated; (3) Weakly supervised segmentation using scribble annotations; and (4) Learning from noisy labels for chest radiograph segmentation. Conclusions: The PyMIC toolkit is easy to use and facilitates efficient development of medical image segmentation models with imperfect annotations. It is modular and flexible, which enables researchers to develop high-performance models with low annotation cost. The source code is available at: https://github.com/HiLab-git/PyMIC.

Guotai Wang, Jianghao Wu, Xiangde Luo et al.

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.

Junjie Shen, Ningfei Wang, Ziwen Wan et al.

Autonomous Driving (AD) systems rely on AI components to make safety and correct driving decisions. Unfortunately, today's AI algorithms are known to be generally vulnerable to adversarial attacks. However, for such AI component-level vulnerabilities to be semantically impactful at the system level, it needs to address non-trivial semantic gaps both (1) from the system-level attack input spaces to those at AI component level, and (2) from AI component-level attack impacts to those at the system level. In this paper, we define such research space as semantic AI security as opposed to generic AI security. Over the past 5 years, increasingly more research works are performed to tackle such semantic AI security challenges in AD context, which has started to show an exponential growth trend. In this paper, we perform the first systematization of knowledge of such growing semantic AD AI security research space. In total, we collect and analyze 53 such papers, and systematically taxonomize them based on research aspects critical for the security field. We summarize 6 most substantial scientific gaps observed based on quantitative comparisons both vertically among existing AD AI security works and horizontally with security works from closely-related domains. With these, we are able to provide insights and potential future directions not only at the design level, but also at the research goal, methodology, and community levels. To address the most critical scientific methodology-level gap, we take the initiative to develop an open-source, uniform, and extensible system-driven evaluation platform, named PASS, for the semantic AD AI security research community. We also use our implemented platform prototype to showcase the capabilities and benefits of such a platform using representative semantic AD AI attacks.

Ran Gu, Guotai Wang, Jiangshan Lu et al.

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

Dongjie Cheng, Ziyuan Qin, Zekun Jiang et al.

The Segment Anything Model (SAM) made an eye-catching debut recently and inspired many researchers to explore its potential and limitation in terms of zero-shot generalization capability. As the first promptable foundation model for segmentation tasks, it was trained on a large dataset with an unprecedented number of images and annotations. This large-scale dataset and its promptable nature endow the model with strong zero-shot generalization. Although the SAM has shown competitive performance on several datasets, we still want to investigate its zero-shot generalization on medical images. As we know, the acquisition of medical image annotation usually requires a lot of effort from professional practitioners. Therefore, if there exists a foundation model that can give high-quality mask prediction simply based on a few point prompts, this model will undoubtedly become the game changer for medical image analysis. To evaluate whether SAM has the potential to become the foundation model for medical image segmentation tasks, we collected more than 12 public medical image datasets that cover various organs and modalities. We also explore what kind of prompt can lead to the best zero-shot performance with different modalities. Furthermore, we find that a pattern shows that the perturbation of the box size will significantly change the prediction accuracy. Finally, Extensive experiments show that the predicted mask quality varied a lot among different datasets. And providing proper prompts, such as bounding boxes, to the SAM will significantly increase its performance.

Ran Gu, Jingyang Zhang, Guotai Wang et al.

Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance for medical image segmentation, yet need plenty of manual annotations for training. Semi-Supervised Learning (SSL) methods are promising to reduce the requirement of annotations, but their performance is still limited when the dataset size and the number of annotated images are small. Leveraging existing annotated datasets with similar anatomical structures to assist training has a potential for improving the model's performance. However, it is further challenged by the cross-anatomy domain shift due to the different appearance and even imaging modalities from the target structure. To solve this problem, we propose Contrastive Semi-supervised learning for Cross Anatomy Domain Adaptation (CS-CADA) that adapts a model to segment similar structures in a target domain, which requires only limited annotations in the target domain by leveraging a set of existing annotated images of similar structures in a source domain. We use Domain-Specific Batch Normalization (DSBN) to individually normalize feature maps for the two anatomical domains, and propose a cross-domain contrastive learning strategy to encourage extracting domain invariant features. They are integrated into a Self-Ensembling Mean-Teacher (SE-MT) framework to exploit unlabeled target domain images with a prediction consistency constraint. Extensive experiments show that our CS-CADA is able to solve the challenging cross-anatomy domain shift problem, achieving accurate segmentation of coronary arteries in X-ray images with the help of retinal vessel images and cardiac MR images with the help of fundus images, respectively, given only a small number of annotations in the target domain.

Shuwei Zhai, Guotai Wang, Xiangde Luo et al.

The success of Convolutional Neural Networks (CNNs) in 3D medical image segmentation relies on massive fully annotated 3D volumes for training that are time-consuming and labor-intensive to acquire. In this paper, we propose to annotate a segmentation target with only seven points in 3D medical images, and design a two-stage weakly supervised learning framework PA-Seg. In the first stage, we employ geodesic distance transform to expand the seed points to provide more supervision signal. To further deal with unannotated image regions during training, we propose two contextual regularization strategies, i.e., multi-view Conditional Random Field (mCRF) loss and Variance Minimization (VM) loss, where the first one encourages pixels with similar features to have consistent labels, and the second one minimizes the intensity variance for the segmented foreground and background, respectively. In the second stage, we use predictions obtained by the model pre-trained in the first stage as pseudo labels. To overcome noises in the pseudo labels, we introduce a Self and Cross Monitoring (SCM) strategy, which combines self-training with Cross Knowledge Distillation (CKD) between a primary model and an auxiliary model that learn from soft labels generated by each other. Experiments on public datasets for Vestibular Schwannoma (VS) segmentation and Brain Tumor Segmentation (BraTS) demonstrated that our model trained in the first stage outperformed existing state-of-the-art weakly supervised approaches by a large margin, and after using SCM for additional training, the model's performance was close to its fully supervised counterpart on the BraTS dataset.

Hao Fu, Guotai Wang, Wenhui Lei et al.

Accurate segmentation of Anatomical brain Barriers to Cancer spread (ABCs) plays an important role for automatic delineation of Clinical Target Volume (CTV) of brain tumors in radiotherapy. Despite that variants of U-Net are state-of-the-art segmentation models, they have limited performance when dealing with ABCs structures with various shapes and sizes, especially thin structures (e.g., the falx cerebri) that span only few slices. To deal with this problem, we propose a High and Multi-Resolution Network (HMRNet) that consists of a multi-scale feature learning branch and a high-resolution branch, which can maintain the high-resolution contextual information and extract more robust representations of anatomical structures with various scales. We further design a Bidirectional Feature Calibration (BFC) block to enable the two branches to generate spatial attention maps for mutual feature calibration. Considering the different sizes and positions of ABCs structures, our network was applied after a rough localization of each structure to obtain fine segmentation results. Experiments on the MICCAI 2020 ABCs challenge dataset showed that: 1) Our proposed two-stage segmentation strategy largely outperformed methods segmenting all the structures in just one stage; 2) The proposed HMRNet with two branches can maintain high-resolution representations and is effective to improve the performance on thin structures; 3) The proposed BFC block outperformed existing attention methods using monodirectional feature calibration. Our method won the second place of ABCs 2020 challenge and has a potential for more accurate and reasonable delineation of CTV of brain tumors.

Ziyuan Qin, Huahui Yi, Qicheng Lao et al.

The large-scale pre-trained vision language models (VLM) have shown remarkable domain transfer capability on natural images. However, it remains unknown whether this capability can also apply to the medical image domain. This paper thoroughly studies the knowledge transferability of pre-trained VLMs to the medical domain, where we show that well-designed medical prompts are the key to elicit knowledge from pre-trained VLMs. We demonstrate that by prompting with expressive attributes that are shared between domains, the VLM can carry the knowledge across domains and improve its generalization. This mechanism empowers VLMs to recognize novel objects with fewer or without image samples. Furthermore, to avoid the laborious manual designing process, we develop three approaches for automatic generation of medical prompts, which can inject expert-level medical knowledge and image-specific information into the prompts for fine-grained grounding. We conduct extensive experiments on thirteen different medical datasets across various modalities, showing that our well-designed prompts greatly improve the zero-shot performance compared to the default prompts, and our fine-tuned models surpass the supervised models by a significant margin.

Huahui Yi, Ziyuan Qin, Qicheng Lao et al.

Inevitable domain and task discrepancies in real-world scenarios can impair the generalization performance of the pre-trained deep models for medical data. Therefore, we audaciously propose that we should build a general-purpose medical AI system that can be seamlessly adapted to downstream domains/tasks. Since the domain/task adaption procedures usually involve additional labeling work for the target data, designing a data-efficient adaption algorithm is desired to save the cost of transferring the learned knowledge. Our recent work found that vision-language models (VLMs) are efficient learners with extraordinary cross-domain ability. Therefore, in this work, we further explore the possibility of leveraging pre-trained VLMs as medical foundation models for building general-purpose medical AI, where we thoroughly investigate three machine-learning paradigms, i.e., domain/task-specialized learning, joint learning, and continual learning, for training the VLMs and evaluate their generalization performance on cross-domain and cross-task test sets. To alleviate the catastrophic forgetting during sequential training, we employ rehearsal learning and receive a sharp boost in terms of generalization capability. In a nutshell, our empirical evidence suggests that continual learning may be a practical and efficient learning paradigm for the medical foundation model. And we hope researchers can use our empirical evidence as basement to further explore the path toward medical foundation model.

Shiyi Du, Xiaosong Wang, Yongyi Lu et al.

Image synthesis approaches, e.g., generative adversarial networks, have been popular as a form of data augmentation in medical image analysis tasks. It is primarily beneficial to overcome the shortage of publicly accessible data and associated quality annotations. However, the current techniques often lack control over the detailed contents in generated images, e.g., the type of disease patterns, the location of lesions, and attributes of the diagnosis. In this work, we adapt the latest advance in the generative model, i.e., the diffusion model, with the added control flow using lesion-specific visual and textual prompts for generating dermatoscopic images. We further demonstrate the advantage of our diffusion model-based framework over the classical generation models in both the image quality and boosting the segmentation performance on skin lesions. It can achieve a 9% increase in the SSIM image quality measure and an over 5% increase in Dice coefficients over the prior arts.

Qingbo Kang, Jun Gao, Kang Li et al.

Masked autoencoder (MAE) has attracted unprecedented attention and achieves remarkable performance in many vision tasks. It reconstructs random masked image patches (known as proxy task) during pretraining and learns meaningful semantic representations that can be transferred to downstream tasks. However, MAE has not been thoroughly explored in ultrasound imaging. In this work, we investigate the potential of MAE for ultrasound image recognition. Motivated by the unique property of ultrasound imaging in high noise-to-signal ratio, we propose a novel deblurring MAE approach that incorporates deblurring into the proxy task during pretraining. The addition of deblurring facilitates the pretraining to better recover the subtle details presented in the ultrasound images, thus improving the performance of the downstream classification task. Our experimental results demonstrate the effectiveness of our deblurring MAE, achieving state-of-the-art performance in ultrasound image classification. Overall, our work highlights the potential of MAE for ultrasound image recognition and presents a novel approach that incorporates deblurring to further improve its effectiveness.

Jingxiong Li, Sunyi Zheng, Zhongyi Shui et al.

Karyotyping is of importance for detecting chromosomal aberrations in human disease. However, chromosomes easily appear curved in microscopic images, which prevents cytogeneticists from analyzing chromosome types. To address this issue, we propose a framework for chromosome straightening, which comprises a preliminary processing algorithm and a generative model called masked conditional variational autoencoders (MC-VAE). The processing method utilizes patch rearrangement to address the difficulty in erasing low degrees of curvature, providing reasonable preliminary results for the MC-VAE. The MC-VAE further straightens the results by leveraging chromosome patches conditioned on their curvatures to learn the mapping between banding patterns and conditions. During model training, we apply a masking strategy with a high masking ratio to train the MC-VAE with eliminated redundancy. This yields a non-trivial reconstruction task, allowing the model to effectively preserve chromosome banding patterns and structure details in the reconstructed results. Extensive experiments on three public datasets with two stain styles show that our framework surpasses the performance of state-of-the-art methods in retaining banding patterns and structure details. Compared to using real-world bent chromosomes, the use of high-quality straightened chromosomes generated by our proposed method can improve the performance of various deep learning models for chromosome classification by a large margin. Such a straightening approach has the potential to be combined with other karyotyping systems to assist cytogeneticists in chromosome analysis.

Kien X. Nguyen, Liying Zheng, Ashley L. Hawke et al.

It is necessary to analyze the whole-body kinematics (including joint locations and joint angles) to assess risks of fatal and musculoskeletal injuries in occupational tasks. Human pose estimation has gotten more attention in recent years as a method to minimize the errors in determining joint locations. However, the joint angles are not often estimated, nor is the quality of joint angle estimation assessed. In this paper, we presented an end-to-end approach on direct joint angle estimation from multi-view images. Our method leveraged the volumetric pose representation and mapped the rotation representation to a continuous space where each rotation was uniquely represented. We also presented a new kinematic dataset in the domain of residential roofing with a data processing pipeline to generate necessary annotations for the supervised training procedure on direct joint angle estimation. We achieved a mean angle error of $7.19^\circ$ on the new Roofing dataset and $8.41^\circ$ on the Human3.6M dataset, paving the way for employment of on-site kinematic analysis using multi-view images.

Teng Zhang, Kang Li

Adversarial training and data augmentation with noise are widely adopted techniques to enhance the performance of neural networks. This paper investigates adversarial training and data augmentation with noise in the context of regularized regression in a reproducing kernel Hilbert space (RKHS). We establish the limiting formula for these techniques as the attack and noise size, as well as the regularization parameter, tend to zero. Based on this limiting formula, we analyze specific scenarios and demonstrate that, without appropriate regularization, these two methods may have larger generalization error and Lipschitz constant than standard kernel regression. However, by selecting the appropriate regularization parameter, these two methods can outperform standard kernel regression and achieve smaller generalization error and Lipschitz constant. These findings support the empirical observations that adversarial training can lead to overfitting, and appropriate regularization methods, such as early stopping, can alleviate this issue.

Wenhui Lei, Xu Wei, Xiaofan Zhang et al.

Recent advancements in foundation models have shown significant potential in medical image analysis. However, there is still a gap in models specifically designed for medical image localization. To address this, we introduce MedLAM, a 3D medical foundation localization model that accurately identifies any anatomical part within the body using only a few template scans. MedLAM employs two self-supervision tasks: unified anatomical mapping (UAM) and multi-scale similarity (MSS) across a comprehensive dataset of 14,012 CT scans. Furthermore, we developed MedLSAM by integrating MedLAM with the Segment Anything Model (SAM). This innovative framework requires extreme point annotations across three directions on several templates to enable MedLAM to locate the target anatomical structure in the image, with SAM performing the segmentation. It significantly reduces the amount of manual annotation required by SAM in 3D medical imaging scenarios. We conducted extensive experiments on two 3D datasets covering 38 distinct organs. Our findings are twofold: 1) MedLAM can directly localize anatomical structures using just a few template scans, achieving performance comparable to fully supervised models; 2) MedLSAM closely matches the performance of SAM and its specialized medical adaptations with manual prompts, while minimizing the need for extensive point annotations across the entire dataset. Moreover, MedLAM has the potential to be seamlessly integrated with future 3D SAM models, paving the way for enhanced segmentation performance. Our code is public at \href{https://github.com/openmedlab/MedLSAM}

Xiaoshuang Shi, Zhenhua Guo, Kang Li et al.

Noisy labels composed of correct and corrupted ones are pervasive in practice. They might significantly deteriorate the performance of convolutional neural networks (CNNs), because CNNs are easily overfitted on corrupted labels. To address this issue, inspired by an observation, deep neural networks might first memorize the probably correct-label data and then corrupt-label samples, we propose a novel yet simple self-paced resistance framework to resist corrupted labels, without using any clean validation data. The proposed framework first utilizes the memorization effect of CNNs to learn a curriculum, which contains confident samples and provides meaningful supervision for other training samples. Then it adopts selected confident samples and a proposed resistance loss to update model parameters; the resistance loss tends to smooth model parameters' update or attain equivalent prediction over each class, thereby resisting model overfitting on corrupted labels. Finally, we unify these two modules into a single loss function and optimize it in an alternative learning. Extensive experiments demonstrate the significantly superior performance of the proposed framework over recent state-of-the-art methods on noisy-label data. Source codes of the proposed method are available on https://github.com/xsshi2015/Self-paced-Resistance-Learning.

Rahil Mehrizi, Xi Peng, Shaoting Zhang et al.

The aim of this study is developing an automatic system for detection of gait-related health problems using Deep Neural Networks (DNNs). The proposed system takes a video of patients as the input and estimates their 3D body pose using a DNN based method. Our code is publicly available at https://github.com/rmehrizi/multi-view-pose-estimation. The resulting 3D body pose time series are then analyzed in a classifier, which classifies input gait videos into four different groups including Healthy, with Parkinsons disease, Post Stroke patient, and with orthopedic problems. The proposed system removes the requirement of complex and heavy equipment and large laboratory space, and makes the system practical for home use. Moreover, it does not need domain knowledge for feature engineering since it is capable of extracting semantic and high level features from the input data. The experimental results showed the classification accuracy of 56% to 96% for different groups. Furthermore, only 1 out of 25 healthy subjects were misclassified (False positive), and only 1 out of 70 patients were classified as a healthy subject (False negative). This study presents a starting point toward a powerful tool for automatic classification of gait disorders and can be used as a basis for future applications of Deep Learning in clinical gait analysis. Since the system uses digital cameras as the only required equipment, it can be employed in domestic environment of patients and elderly people for consistent gait monitoring and early detection of gait alterations.

Jiajia Liu, Mengyuan Yang, Yankai Yu et al.

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of unlabeled input using self-supervised or semi-supervised learning. However, their potential for solving bioinformatics problems may even exceed their proficiency in modeling human language. In this review, we will provide a comprehensive overview of the essential components of large language models (LLMs) in bioinformatics, spanning genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis. Key aspects covered include tokenization methods for diverse data types, the architecture of transformer models, the core attention mechanism, and the pre-training processes underlying these models. Additionally, we will introduce currently available foundation models and highlight their downstream applications across various bioinformatics domains. Finally, drawing from our experience, we will offer practical guidance for both LLM users and developers, emphasizing strategies to optimize their use and foster further innovation in the field.

Jianghao Wu, Dong Guo, Guotai Wang et al.

Adapting a medical image segmentation model to a new domain is important for improving its cross-domain transferability, and due to the expensive annotation process, Unsupervised Domain Adaptation (UDA) is appealing where only unlabeled images are needed for the adaptation. Existing UDA methods are mainly based on image or feature alignment with adversarial training for regularization, and they are limited by insufficient supervision in the target domain. In this paper, we propose an enhanced Filtered Pseudo Label (FPL+)-based UDA method for 3D medical image segmentation. It first uses cross-domain data augmentation to translate labeled images in the source domain to a dual-domain training set consisting of a pseudo source-domain set and a pseudo target-domain set. To leverage the dual-domain augmented images to train a pseudo label generator, domain-specific batch normalization layers are used to deal with the domain shift while learning the domain-invariant structure features, generating high-quality pseudo labels for target-domain images. We then combine labeled source-domain images and target-domain images with pseudo labels to train a final segmentor, where image-level weighting based on uncertainty estimation and pixel-level weighting based on dual-domain consensus are proposed to mitigate the adverse effect of noisy pseudo labels. Experiments on three public multi-modal datasets for Vestibular Schwannoma, brain tumor and whole heart segmentation show that our method surpassed ten state-of-the-art UDA methods, and it even achieved better results than fully supervised learning in the target domain in some cases.

Ziyuan Qin, Dongjie Cheng, Haoyu Wang et al.

Contemporary Text-to-Image (T2I) models frequently depend on qualitative human evaluations to assess the consistency between synthesized images and the text prompts. There is a demand for quantitative and automatic evaluation tools, given that human evaluation lacks reproducibility. We believe that an effective T2I evaluation metric should accomplish the following: detect instances where the generated images do not align with the textual prompts, a discrepancy we define as the `hallucination problem' in T2I tasks; record the types and frequency of hallucination issues, aiding users in understanding the causes of errors; and provide a comprehensive and intuitive scoring that close to human standard. To achieve these objectives, we propose a method based on large language models (LLMs) for conducting question-answering with an extracted scene-graph and created a dataset with human-rated scores for generated images. From the methodology perspective, we combine knowledge-enhanced question-answering tasks with image evaluation tasks, making the evaluation metrics more controllable and easier to interpret. For the contribution on the dataset side, we generated 12,000 synthesized images based on 1,000 composited prompts using three advanced T2I models. Subsequently, we conduct human scoring on all synthesized images and prompt pairs to validate the accuracy and effectiveness of our method as an evaluation metric. All generated images and the human-labeled scores will be made publicly available in the future to facilitate ongoing research on this crucial issue. Extensive experiments show that our method aligns more closely with human scoring patterns than other evaluation metrics.

Kangyu Zhu, Ziyuan Qin, Huahui Yi et al.

While mainstream vision-language models (VLMs) have advanced rapidly in understanding image level information, they still lack the ability to focus on specific areas designated by humans. Rather, they typically rely on large volumes of high-quality image-text paired data to learn and generate posterior attention maps. To address this critical issue, we propose leveraging visual prompts:simple visual markers in various forms to guide and enhance the formation of region-specific attention. Thus, we introduce MedVP, a pioneering framework that integrates medical entity extraction, visual prompt generation, and dataset adaptation for visual prompt guided fine-tuning. We successfully outperform recent state-of-the-art large models across multiple medical VQA datasets. Extensive experiments and Human evaluation are conducted to analyze the impact of different visual prompt forms and how they contribute to performance improvement. The results demonstrate both the effectiveness and clinical significance of our approach.

Xiaoxiao He, Haizhou Shi, Ligong Han et al.

Cardiovascular disease (CVD) and cardiac dyssynchrony are major public health problems in the United States. Precise cardiac image segmentation is crucial for extracting quantitative measures that help categorize cardiac dyssynchrony. However, achieving high accuracy often depends on centralizing large datasets from different hospitals, which can be challenging due to privacy concerns. To solve this problem, Federated Learning (FL) is proposed to enable decentralized model training on such data without exchanging sensitive information. However, bandwidth limitations and data heterogeneity remain as significant challenges in conventional FL algorithms. In this paper, we propose a novel efficient and adaptive federate learning method for cardiac segmentation that improves model performance while reducing the bandwidth requirement. Our method leverages the low-rank adaptation (LoRA) to regularize model weight update and reduce communication overhead. We also propose a \mymethod{} aggregation technique to address data heterogeneity among clients. This technique adaptively penalizes the aggregated weights from different clients by comparing the validation accuracy in each client, allowing better generalization performance and fast local adaptation. In-client and cross-client evaluations on public cardiac MR datasets demonstrate the superiority of our method over other LoRA-based federate learning approaches.

Anyang Ji, Qingbo Kang, Wei Xu et al.

The emergence of large-scale pre-trained vision foundation models has greatly advanced the medical imaging field through the pre-training and fine-tuning paradigm. However, selecting appropriate medical data for downstream fine-tuning remains a significant challenge considering its annotation cost, privacy concerns, and the detrimental effects of confounding variables. In this work, we present a confounder-aware medical data selection approach for medical dataset curation aiming to select minimal representative data by strategically mitigating the undesirable impact of confounding variables while preserving the natural distribution of the dataset. Our approach first identifies confounding variables within data and then develops a distance-based data selection strategy for confounder-aware sampling with a constrained budget in the data size. We validate the superiority of our approach through extensive experiments across diverse medical imaging modalities, highlighting its effectiveness in addressing the substantial impact of confounding variables and enhancing the fine-tuning efficiency in the medical imaging domain, compared to other data selection approaches.

Xi Chen, MingKe You, Li Wang et al.

The efficacy of large language models (LLMs) in domain-specific medicine, particularly for managing complex diseases such as osteoarthritis (OA), remains largely unexplored. This study focused on evaluating and enhancing the clinical capabilities of LLMs in specific domains, using osteoarthritis (OA) management as a case study. A domain specific benchmark framework was developed, which evaluate LLMs across a spectrum from domain-specific knowledge to clinical applications in real-world clinical scenarios. DocOA, a specialized LLM tailored for OA management that integrates retrieval-augmented generation (RAG) and instruction prompts, was developed. The study compared the performance of GPT-3.5, GPT-4, and a specialized assistant, DocOA, using objective and human evaluations. Results showed that general LLMs like GPT-3.5 and GPT-4 were less effective in the specialized domain of OA management, particularly in providing personalized treatment recommendations. However, DocOA showed significant improvements. This study introduces a novel benchmark framework which assesses the domain-specific abilities of LLMs in multiple aspects, highlights the limitations of generalized LLMs in clinical contexts, and demonstrates the potential of tailored approaches for developing domain-specific medical LLMs.

Huahui Yi, Ziyuan Qin, Wei Xu et al.

Large pre-trained vision-language models have shown great prominence in transferring pre-acquired knowledge to various domains and downstream tasks with appropriate prompting or tuning. Existing prevalent tuning methods can be generally categorized into three genres: 1) prompt engineering by creating suitable prompt texts, which is time-consuming and requires domain expertise; 2) or simply fine-tuning the whole model, which is extremely inefficient; 3) prompt tuning through parameterized prompt embeddings with the text encoder. Nevertheless, all methods rely on the text encoder for bridging the modality gap between vision and language. In this work, we question the necessity of the cumbersome text encoder for a more lightweight and efficient tuning paradigm as well as more representative prompt embeddings closer to the image representations. To achieve this, we propose a Concept Embedding Search (ConES) approach by optimizing prompt embeddings -- without the need of the text encoder -- to capture the 'concept' of the image modality through a variety of task objectives. By dropping the text encoder, we are able to significantly speed up the learning process, \eg, from about an hour to just ten minutes in our experiments for personalized text-to-image generation without impairing the generation quality. Moreover, our proposed approach is orthogonal to current existing tuning methods since the searched concept embeddings can be further utilized in the next stage of fine-tuning the pre-trained large models for boosting performance. Extensive experiments show that our approach can beat the prompt tuning and textual inversion methods in a variety of downstream tasks including objection detection, instance segmentation, and image generation. Our approach also shows better generalization capability for unseen concepts in specialized domains, such as the medical domain.

Jie Xu, Lu Lu, Sen Yang et al.

METHODS: First, a set of evaluation criteria is designed based on a comprehensive literature review. Second, existing candidate criteria are optimized for using a Delphi method by five experts in medicine and engineering. Third, three clinical experts design a set of medical datasets to interact with LLMs. Finally, benchmarking experiments are conducted on the datasets. The responses generated by chatbots based on LLMs are recorded for blind evaluations by five licensed medical experts. RESULTS: The obtained evaluation criteria cover medical professional capabilities, social comprehensive capabilities, contextual capabilities, and computational robustness, with sixteen detailed indicators. The medical datasets include twenty-seven medical dialogues and seven case reports in Chinese. Three chatbots are evaluated, ChatGPT by OpenAI, ERNIE Bot by Baidu Inc., and Doctor PuJiang (Dr. PJ) by Shanghai Artificial Intelligence Laboratory. Experimental results show that Dr. PJ outperforms ChatGPT and ERNIE Bot in both multiple-turn medical dialogue and case report scenarios.

Xiangde Luo, Wenjun Liao, Jianghong Xiao et al.

Whole abdominal organ segmentation is important in diagnosing abdomen lesions, radiotherapy, and follow-up. However, oncologists' delineating all abdominal organs from 3D volumes is time-consuming and very expensive. Deep learning-based medical image segmentation has shown the potential to reduce manual delineation efforts, but it still requires a large-scale fine annotated dataset for training, and there is a lack of large-scale datasets covering the whole abdomen region with accurate and detailed annotations for the whole abdominal organ segmentation. In this work, we establish a new large-scale \textit{W}hole abdominal \textit{OR}gan \textit{D}ataset (\textit{WORD}) for algorithm research and clinical application development. This dataset contains 150 abdominal CT volumes (30495 slices). Each volume has 16 organs with fine pixel-level annotations and scribble-based sparse annotations, which may be the largest dataset with whole abdominal organ annotation. Several state-of-the-art segmentation methods are evaluated on this dataset. And we also invited three experienced oncologists to revise the model predictions to measure the gap between the deep learning method and oncologists. Afterwards, we investigate the inference-efficient learning on the WORD, as the high-resolution image requires large GPU memory and a long inference time in the test stage. We further evaluate the scribble-based annotation-efficient learning on this dataset, as the pixel-wise manual annotation is time-consuming and expensive. The work provided a new benchmark for the abdominal multi-organ segmentation task, and these experiments can serve as the baseline for future research and clinical application development.

Zhi Zhang, Yueqiang Cheng, Minghua Wang et al.

Rowhammer attacks that corrupt level-1 page tables to gain kernel privilege are the most detrimental to system security and hard to mitigate. However, recently proposed software-only mitigations are not effective against such kernel privilege escalation attacks. In this paper, we propose an effective and practical software-only defense, called SoftTRR, to protect page tables from all existing rowhammer attacks on x86. The key idea of SoftTRR is to refresh the rows occupied by page tables when a suspicious rowhammer activity is detected. SoftTRR is motivated by DRAM-chip-based target row refresh (ChipTRR) but eliminates its main security limitation (i.e., ChipTRR tracks a limited number of rows and thus can be bypassed by many-sided hammer). Specifically, SoftTRR protects an unlimited number of page tables by tracking memory accesses to the rows that are in close proximity to page-table rows and refreshing the page-table rows once the tracked access count exceeds a pre-defined threshold. We implement a prototype of SoftTRR as a loadable kernel module, and evaluate its security effectiveness, performance overhead, and memory consumption. The experimental results show that SoftTRR protects page tables from real-world rowhammer attacks and incurs small performance overhead as well as memory cost.

Fengting Li, Xuankai Liu, Xiaoli Zhang et al.

Deep neural networks (DNNs) have been applied in a wide range of applications,e.g.,face recognition and image classification; however,they are vulnerable to adversarial examples. By adding a small amount of imperceptible perturbations,an attacker can easily manipulate the outputs of a DNN. Particularly,the localized adversarial examples only perturb a small and contiguous region of the target object,so that they are robust and effective in both digital and physical worlds. Although the localized adversarial examples have more severe real-world impacts than traditional pixel attacks,they have not been well addressed in the literature. In this paper,we propose a generic defense system called TaintRadar to accurately detect localized adversarial examples via analyzing critical regions that have been manipulated by attackers. The main idea is that when removing critical regions from input images,the ranking changes of adversarial labels will be larger than those of benign labels. Compared with existing defense solutions,TaintRadar can effectively capture sophisticated localized partial attacks, e.g.,the eye-glasses attack,while not requiring additional training or fine-tuning of the original model's structure. Comprehensive experiments have been conducted in both digital and physical worlds to verify the effectiveness and robustness of our defense.

Hao Yuan, Haiyang Yu, Jie Wang et al.

We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.

Tianlu Wang, Xuezhi Wang, Yao Qin et al.

NLP models are shown to suffer from robustness issues, i.e., a model's prediction can be easily changed under small perturbations to the input. In this work, we present a Controlled Adversarial Text Generation (CAT-Gen) model that, given an input text, generates adversarial texts through controllable attributes that are known to be invariant to task labels. For example, in order to attack a model for sentiment classification over product reviews, we can use the product categories as the controllable attribute which would not change the sentiment of the reviews. Experiments on real-world NLP datasets demonstrate that our method can generate more diverse and fluent adversarial texts, compared to many existing adversarial text generation approaches. We further use our generated adversarial examples to improve models through adversarial training, and we demonstrate that our generated attacks are more robust against model re-training and different model architectures.

Kang Li, Lequan Yu, Shujun Wang et al.

The success of deep convolutional neural networks is partially attributed to the massive amount of annotated training data. However, in practice, medical data annotations are usually expensive and time-consuming to be obtained. Considering multi-modality data with the same anatomic structures are widely available in clinic routine, in this paper, we aim to exploit the prior knowledge (e.g., shape priors) learned from one modality (aka., assistant modality) to improve the segmentation performance on another modality (aka., target modality) to make up annotation scarcity. To alleviate the learning difficulties caused by modality-specific appearance discrepancy, we first present an Image Alignment Module (IAM) to narrow the appearance gap between assistant and target modality data.We then propose a novel Mutual Knowledge Distillation (MKD) scheme to thoroughly exploit the modality-shared knowledge to facilitate the target-modality segmentation. To be specific, we formulate our framework as an integration of two individual segmentors. Each segmentor not only explicitly extracts one modality knowledge from corresponding annotations, but also implicitly explores another modality knowledge from its counterpart in mutual-guided manner. The ensemble of two segmentors would further integrate the knowledge from both modalities and generate reliable segmentation results on target modality. Experimental results on the public multi-class cardiac segmentation data, i.e., MMWHS 2017, show that our method achieves large improvements on CT segmentation by utilizing additional MRI data and outperforms other state-of-the-art multi-modality learning methods.

Chaowei Tan, Zhennan Yan, Shaoting Zhang et al.

The 3D morphology and quantitative assessment of knee articular cartilages (i.e., femoral, tibial, and patellar cartilage) in magnetic resonance (MR) imaging is of great importance for knee radiographic osteoarthritis (OA) diagnostic decision making. However, effective and efficient delineation of all the knee articular cartilages in large-sized and high-resolution 3D MR knee data is still an open challenge. In this paper, we propose a novel framework to solve the MR knee cartilage segmentation task. The key contribution is the adversarial learning based collaborative multi-agent segmentation network. In the proposed network, we use three parallel segmentation agents to label cartilages in their respective region of interest (ROI), and then fuse the three cartilages by a novel ROI-fusion layer. The collaborative learning is driven by an adversarial sub-network. The ROI-fusion layer not only fuses the individual cartilages from multiple agents, but also backpropagates the training loss from the adversarial sub-network to each agent to enable joint learning of shape and spatial constraints. Extensive evaluations are conducted on a dataset including hundreds of MR knee volumes with diverse populations, and the proposed method shows superior performance.

Xiaoxiao He, Chaowei Tan, Yuting Qiao et al.

For the initial shoulder preoperative diagnosis, it is essential to obtain a three-dimensional (3D) bone mask from medical images, e.g., magnetic resonance (MR). However, obtaining high-resolution and dense medical scans is both costly and time-consuming. In addition, the imaging parameters for each 3D scan may vary from time to time and thus increase the variance between images. Therefore, it is practical to consider the bone extraction on low-resolution data which may influence imaging contrast and make the segmentation work difficult. In this paper, we present a joint segmentation for the humerus and scapula bones on a small dataset with low-contrast and high-shape-variability 3D MR images. The proposed network has a deep end-to-end architecture to obtain the initial 3D bone masks. Because the existing scarce and inaccurate human-labeled ground truth, we design a self-reinforced learning strategy to increase performance. By comparing with the non-reinforced segmentation and a classical multi-atlas method with joint label fusion, the proposed approach obtains better results.

Rahil Mehrizi, Xi Peng, Zhiqiang Tang et al.

Lifting is a common manual material handling task performed in the workplaces. It is considered as one of the main risk factors for Work-related Musculoskeletal Disorders. To improve work place safety, it is necessary to assess musculoskeletal and biomechanical risk exposures associated with these tasks, which requires very accurate 3D pose. Existing approaches mainly utilize marker-based sensors to collect 3D information. However, these methods are usually expensive to setup, time-consuming in process, and sensitive to the surrounding environment. In this study, we propose a multi-view based deep perceptron approach to address aforementioned limitations. Our approach consists of two modules: a "view-specific perceptron" network extracts rich information independently from the image of view, which includes both 2D shape and hierarchical texture information; while a "multi-view integration" network synthesizes information from all available views to predict accurate 3D pose. To fully evaluate our approach, we carried out comprehensive experiments to compare different variants of our design. The results prove that our approach achieves comparable performance with former marker-based methods, i.e. an average error of $14.72 \pm 2.96$ mm on the lifting dataset. The results are also compared with state-of-the-art methods on HumanEva-I dataset, which demonstrates the superior performance of our approach.

Kang Li, Xiaoguang Zhao, Jiang Bian et al.

Surveillance is essential for the safety of power substation. The detection of whether wearing safety helmets or not for perambulatory workers is the key component of overall intelligent surveillance system in power substation. In this paper, a novel and practical safety helmet detection framework based on computer vision, machine learning and image processing is proposed. In order to ascertain motion objects in power substation, the ViBe background modelling algorithm is employed. Moreover, based on the result of motion objects segmentation, real-time human classification framework C4 is applied to locate pedestrian in power substation accurately and quickly. Finally, according to the result of pedestrian detection, the safety helmet wearing detection is implemented using the head location, the color space transformation and the color feature discrimination. Extensive compelling experimental results in power substation illustrate the efficiency and effectiveness of the proposed framework.

Qixue Xiao, Kang Li, Deyue Zhang et al.

This paper considers security risks buried in the data processing pipeline in common deep learning applications. Deep learning models usually assume a fixed scale for their training and input data. To allow deep learning applications to handle a wide range of input data, popular frameworks, such as Caffe, TensorFlow, and Torch, all provide data scaling functions to resize input to the dimensions used by deep learning models. Image scaling algorithms are intended to preserve the visual features of an image after scaling. However, common image scaling algorithms are not designed to handle human crafted images. Attackers can make the scaling outputs look dramatically different from the corresponding input images. This paper presents a downscaling attack that targets the data scaling process in deep learning applications. By carefully crafting input data that mismatches with the dimension used by deep learning models, attackers can create deceiving effects. A deep learning application effectively consumes data that are not the same as those presented to users. The visual inconsistency enables practical evasion and data poisoning attacks to deep learning applications. This paper presents proof-of-concept attack samples to popular deep-learning-based image classification applications. To address the downscaling attacks, the paper also suggests multiple potential mitigation strategies.