Nan Yang

Yang Nan, Javier Del Ser, Zeyu Tang et al.

Airway segmentation is crucial for the examination, diagnosis, and prognosis of lung diseases, while its manual delineation is unduly burdensome. To alleviate this time-consuming and potentially subjective manual procedure, researchers have proposed methods to automatically segment airways from computerized tomography (CT) images. However, some small-sized airway branches (e.g., bronchus and terminal bronchioles) significantly aggravate the difficulty of automatic segmentation by machine learning models. In particular, the variance of voxel values and the severe data imbalance in airway branches make the computational module prone to discontinuous and false-negative predictions. especially for cohorts with different lung diseases. Attention mechanism has shown the capacity to segment complex structures, while fuzzy logic can reduce the uncertainty in feature representations. Therefore, the integration of deep attention networks and fuzzy theory, given by the fuzzy attention layer, should be an escalated solution for better generalization and robustness. This paper presents an efficient method for airway segmentation, comprising a novel fuzzy attention neural network and a comprehensive loss function to enhance the spatial continuity of airway segmentation. The deep fuzzy set is formulated by a set of voxels in the feature map and a learnable Gaussian membership function. Different from the existing attention mechanism, the proposed channel-specific fuzzy attention addresses the issue of heterogeneous features in different channels. Furthermore, a novel evaluation metric is proposed to assess both the continuity and completeness of airway structures. The efficiency, generalization and robustness of the proposed method have been proved by training on normal lung disease while testing on datasets of lung cancer, COVID-19 and pulmonary fibrosis.

Nan Yang, Xin Luan, Huidi Jia et al.

Three problems exist in sequential facial image editing: incontinuous editing, inconsistent editing, and irreversible editing. Incontinuous editing is that the current editing can not retain the previously edited attributes. Inconsistent editing is that swapping the attribute editing orders can not yield the same results. Irreversible editing means that operating on a facial image is irreversible, especially in sequential facial image editing. In this work, we put forward three concepts and corresponding definitions: editing continuity, consistency, and reversibility. Then, we propose a novel model to achieve the goal of editing continuity, consistency, and reversibility. A sufficient criterion is defined to determine whether a model is continuous, consistent, and reversible. Extensive qualitative and quantitative experimental results validate our proposed model and show that a continuous, consistent and reversible editing model has a more flexible editing function while preserving facial identity. Furthermore, we think that our proposed definitions and model will have wide and promising applications in multimedia processing. Code and data are available at https://github.com/mickoluan/CCR.

Hao Li, Zeyu Tang, Yang Nan et al.

Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large collections of 2D and 3D images have been made available by medical imaging modalities such as magnetic resonance imaging (MRI), computed tomography (CT), Optical coherence tomography (OCT) and ultrasound in which the spatial arrangement can be observed. Segmentation of these structures in medical imaging is of great importance since the analysis of the structure provides insights into disease diagnosis, treatment planning, and prognosis. Manually labelling extensive data by radiologists is often time-consuming and error-prone. As a result, automated or semi-automated computational models have become a popular research field of medical imaging in the past two decades, and many have been developed to date. In this survey, we aim to provide a comprehensive review of currently publicly available datasets, segmentation algorithms, and evaluation metrics. In addition, current challenges and future research directions are discussed.

Jiahao Huang, Yingying Fang, Yang Nan et al.

Research studies have shown no qualms about using data driven deep learning models for downstream tasks in medical image analysis, e.g., anatomy segmentation and lesion detection, disease diagnosis and prognosis, and treatment planning. However, deep learning models are not the sovereign remedy for medical image analysis when the upstream imaging is not being conducted properly (with artefacts). This has been manifested in MRI studies, where the scanning is typically slow, prone to motion artefacts, with a relatively low signal to noise ratio, and poor spatial and/or temporal resolution. Recent studies have witnessed substantial growth in the development of deep learning techniques for propelling fast MRI. This article aims to (1) introduce the deep learning based data driven techniques for fast MRI including convolutional neural network and generative adversarial network based methods, (2) survey the attention and transformer based models for speeding up MRI reconstruction, and (3) detail the research in coupling physics and data driven models for MRI acceleration. Finally, we will demonstrate through a few clinical applications, explain the importance of data harmonisation and explainable models for such fast MRI techniques in multicentre and multi-scanner studies, and discuss common pitfalls in current research and recommendations for future research directions.

Zeyu Tang, Nan Yang, Simon Walsh et al.

Discontinuity in the delineation of peripheral bronchioles hinders the potential clinical application of automated airway segmentation models. Moreover, the deployment of such models is limited by the data heterogeneity across different centres, and pathological abnormalities also make achieving accurate robust segmentation in distal small airways difficult. Meanwhile, the diagnosis and prognosis of lung diseases often rely on evaluating structural changes in those anatomical regions. To address this gap, this paper presents a patch-scale adversarial-based refinement network that takes in preliminary segmentation along with original CT images and outputs a refined mask of the airway structure. The method is validated on three different datasets encompassing healthy cases, cases with cystic fibrosis and cases with COVID-19. The results are quantitatively evaluated by seven metrics and achieved more than a 15% rise in detected length ratio and detected branch ratio, showing promising performance compared to previously proposed models. The visual illustration also proves our refinement guided by a patch-scale discriminator and centreline objective functions is effective in detecting discontinuities and missing bronchioles. Furthermore, the generalizability of our refinement pipeline is tested on three previous models and improves their segmentation completeness significantly.

Xiaodan Xing, Jiahao Huang, Yang Nan et al.

The destitution of image data and corresponding expert annotations limit the training capacities of AI diagnostic models and potentially inhibit their performance. To address such a problem of data and label scarcity, generative models have been developed to augment the training datasets. Previously proposed generative models usually require manually adjusted annotations (e.g., segmentation masks) or need pre-labeling. However, studies have found that these pre-labeling based methods can induce hallucinating artifacts, which might mislead the downstream clinical tasks, while manual adjustment could be onerous and subjective. To avoid manual adjustment and pre-labeling, we propose a novel controllable and simultaneous synthesizer (dubbed CS$^2$) in this study to generate both realistic images and corresponding annotations at the same time. Our CS$^2$ model is trained and validated using high resolution CT (HRCT) data collected from COVID-19 patients to realize an efficient infections segmentation with minimal human intervention. Our contributions include 1) a conditional image synthesis network that receives both style information from reference CT images and structural information from unsupervised segmentation masks, and 2) a corresponding segmentation mask synthesis network to automatically segment these synthesized images simultaneously. Our experimental studies on HRCT scans collected from COVID-19 patients demonstrate that our CS$^2$ model can lead to realistic synthesized datasets and promising segmentation results of COVID infections compared to the state-of-the-art nnUNet trained and fine-tuned in a fully supervised manner.

Peng Tang, Yang Nan, Tobias Lasser

Many skin lesion analysis (SLA) methods recently focused on developing a multi-modal-based multi-label classification method due to two factors. The first is multi-modal data, i.e., clinical and dermoscopy images, which can provide complementary information to obtain more accurate results than single-modal data. The second one is that multi-label classification, i.e., seven-point checklist (SPC) criteria as an auxiliary classification task can not only boost the diagnostic accuracy of melanoma in the deep learning (DL) pipeline but also provide more useful functions to the clinical doctor as it is commonly used in clinical dermatologist's diagnosis. However, most methods only focus on designing a better module for multi-modal data fusion; few methods explore utilizing the label correlation between SPC and skin disease for performance improvement. This study fills the gap that introduces a Graph Convolution Network (GCN) to exploit prior co-occurrence between each category as a correlation matrix into the DL model for the multi-label classification. However, directly applying GCN degraded the performances in our experiments; we attribute this to the weak generalization ability of GCN in the scenario of insufficient statistical samples of medical data. We tackle this issue by proposing a Graph-Ensemble Learning Model (GELN) that views the prediction from GCN as complementary information of the predictions from the fusion model and adaptively fuses them by a weighted averaging scheme, which can utilize the valuable information from GCN while avoiding its negative influences as much as possible. To evaluate our method, we conduct experiments on public datasets. The results illustrate that our GELN can consistently improve the classification performance on different datasets and that the proposed method can achieve state-of-the-art performance in SPC and diagnosis classification.

Kaiqi Fu, Linkai Peng, Nan Yang et al.

Large language models (LLMs), renowned for their powerful conversational abilities, are widely recognized as exceptional tools in the field of education, particularly in the context of automated intelligent instruction systems for language learning. In this paper, we propose a scoring system based on LLMs, motivated by their positive impact on text-related scoring tasks. Specifically, the speech encoder first maps the learner's speech into contextual features. The adapter layer then transforms these features to align with the text embedding in latent space. The assessment task-specific prefix and prompt text are embedded and concatenated with the features generated by the modality adapter layer, enabling the LLMs to predict accuracy and fluency scores. Our experiments demonstrate that the proposed scoring systems achieve competitive results compared to the baselines on the Speechocean762 datasets. Moreover, we also conducted an ablation study to better understand the contributions of the prompt text and training strategy in the proposed scoring system.

Yanli Li, Zhongliang Guo, Nan Yang et al.

Federated Learning (FL) offers innovative solutions for privacy-preserving collaborative machine learning (ML). Despite its promising potential, FL is vulnerable to various attacks due to its distributed nature, affecting the entire life cycle of FL services. These threats can harm the model's utility or compromise participants' privacy, either directly or indirectly. In response, numerous defense frameworks have been proposed, demonstrating effectiveness in specific settings and scenarios. To provide a clear understanding of the current research landscape, this paper reviews the most representative and state-of-the-art threats and defense frameworks throughout the FL service life cycle. We start by identifying FL threats that harm utility and privacy, including those with potential or direct impacts. Then, we dive into the defense frameworks, analyze the relationship between threats and defenses, and compare the trade-offs among different defense strategies. Finally, we summarize current research bottlenecks and offer insights into future research directions to conclude this survey. We hope this survey sheds light on trustworthy FL research and contributes to the FL community.

Shiyi Wang, Yang Nan, Simon Walsh et al.

We propose a novel Deep Active Learning (DeepAL) model-3D Wasserstein Discriminative UNet (WD-UNet) for reducing the annotation effort of medical 3D Computed Tomography (CT) segmentation. The proposed WD-UNet learns in a semi-supervised way and accelerates learning convergence to meet or exceed the prediction metrics of supervised learning models. Our method can be embedded with different Active Learning (AL) strategies and different network structures. The model is evaluated on 3D lung airway CT scans for medical segmentation and show that the use of uncertainty metric, which is parametrized as an input of query strategy, leads to more accurate prediction results than some state-of-the-art Deep Learning (DL) supervised models, e.g.,3DUNet and 3D CEUNet. Compared to the above supervised DL methods, our WD-UNet not only saves the cost of annotation for radiologists but also saves computational resources. WD-UNet uses a limited amount of annotated data (35% of the total) to achieve better predictive metrics with a more efficient deep learning model algorithm.

Xiaodan Xing, Junzhi Ning, Yang Nan et al.

Deep generative models have significantly advanced medical imaging analysis by enhancing dataset size and quality. Beyond mere data augmentation, our research in this paper highlights an additional, significant capacity of deep generative models: their ability to reveal and demonstrate patterns in medical images. We employ a generative structure with hybrid conditions, combining clinical data and segmentation masks to guide the image synthesis process. Furthermore, we innovatively transformed the tabular clinical data into textual descriptions. This approach simplifies the handling of missing values and also enables us to leverage large pre-trained vision-language models that investigate the relations between independent clinical entries and comprehend general terms, such as gender and smoking status. Our approach differs from and presents a more challenging task than traditional medical report-guided synthesis due to the less visual correlation of our clinical information with the images. To overcome this, we introduce a text-visual embedding mechanism that strengthens the conditions, ensuring the network effectively utilizes the provided information. Our pipeline is generalizable to both GAN-based and diffusion models. Experiments on chest CT, particularly focusing on the smoking status, demonstrated a consistent intensity shift in the lungs which is in agreement with clinical observations, indicating the effectiveness of our method in capturing and visualizing the impact of specific attributes on medical image patterns. Our methods offer a new avenue for the early detection and precise visualization of complex clinical conditions with deep generative models. All codes are https://github.com/junzhin/DGM-VLC.

Yang Nan, Xiaodan Xing, Shiyi Wang et al.

Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.

Peng Tang, Xintong Yan, Yang Nan et al.

Most convolutional neural network (CNN) based methods for skin cancer classification obtain their results using only dermatological images. Although good classification results have been shown, more accurate results can be achieved by considering the patient's metadata, which is valuable clinical information for dermatologists. Current methods only use the simple joint fusion structure (FS) and fusion modules (FMs) for the multi-modal classification methods, there still is room to increase the accuracy by exploring more advanced FS and FM. Therefore, in this paper, we design a new fusion method that combines dermatological images (dermoscopy images or clinical images) and patient metadata for skin cancer classification from the perspectives of FS and FM. First, we propose a joint-individual fusion (JIF) structure that learns the shared features of multi-modality data and preserves specific features simultaneously. Second, we introduce a fusion attention (FA) module that enhances the most relevant image and metadata features based on both the self and mutual attention mechanism to support the decision-making pipeline. We compare the proposed JIF-MMFA method with other state-of-the-art fusion methods on three different public datasets. The results show that our JIF-MMFA method improves the classification results for all tested CNN backbones and performs better than the other fusion methods on the three public datasets, demonstrating our method's effectiveness and robustness

Yang Nan, Huichi Zhou, Xiaodan Xing et al.

As artificial intelligence and digital medicine increasingly permeate healthcare systems, robust governance frameworks are essential to ensure ethical, secure, and effective implementation. In this context, medical image retrieval becomes a critical component of clinical data management, playing a vital role in decision-making and safeguarding patient information. Existing methods usually learn hash functions using bottleneck features, which fail to produce representative hash codes from blended embeddings. Although contrastive hashing has shown superior performance, current approaches often treat image retrieval as a classification task, using category labels to create positive/negative pairs. Moreover, many methods fail to address the out-of-distribution (OOD) issue when models encounter external OOD queries or adversarial attacks. In this work, we propose a novel method to consolidate knowledge of hierarchical features and optimisation functions. We formulate the knowledge consolidation by introducing Depth-aware Representation Fusion (DaRF) and Structure-aware Contrastive Hashing (SCH). DaRF adaptively integrates shallow and deep representations into blended features, and SCH incorporates image fingerprints to enhance the adaptability of positive/negative pairings. These blended features further facilitate OOD detection and content-based recommendation, contributing to a secure AI-driven healthcare environment. Moreover, we present a content-guided ranking to improve the robustness and reproducibility of retrieval results. Our comprehensive assessments demonstrate that the proposed method could effectively recognise OOD samples and significantly outperform existing approaches in medical image retrieval (p<0.05). In particular, our method achieves a 5.6-38.9% improvement in mean Average Precision on the anatomical radiology dataset.

Yang Nan, Guang Yang

Automated cell segmentation has become increasingly crucial for disease diagnosis and drug discovery, as manual delineation is excessively laborious and subjective. To address this issue with limited manual annotation, researchers have developed semi/unsupervised segmentation approaches. Among these approaches, the Deep Gaussian mixture model plays a vital role due to its capacity to facilitate complex data distributions. However, these models assume that the data follows symmetric normal distributions, which is inapplicable for data that is asymmetrically distributed. These models also obstacles weak generalization capacity and are sensitive to outliers. To address these issues, this paper presents a novel asymmetric mixture model for unsupervised cell segmentation. This asymmetric mixture model is built by aggregating certain multivariate Gaussian mixture models with log-likelihood and self-supervised-based optimization functions. The proposed asymmetric mixture model outperforms (nearly 2-30% gain in dice coefficient, p<0.05) the existing state-of-the-art unsupervised models on cell segmentation including the segment anything.

Yang Nan, Gianmarc Coppola, Qiaokang Liang et al.

Gastric cancer is the second leading cause of cancer-related deaths worldwide, and the major hurdle in biomedical image analysis is the determination of the cancer extent. This assignment has high clinical relevance and would generally require vast microscopic assessment by pathologists. Recent advances in deep learning have produced inspiring results on biomedical image segmentation, while its outcome is reliant on comprehensive annotation. This requires plenty of labor costs, for the ground truth must be annotated meticulously by pathologists. In this paper, a reiterative learning framework was presented to train our network on partial annotated biomedical images, and superior performance was achieved without any pre-trained or further manual annotation. We eliminate the boundary error of patch-based model through our overlapped region forecast algorithm. Through these advisable methods, a mean intersection over union coefficient (IOU) of 0.883 and mean accuracy of 91.09% on the partial labeled dataset was achieved, which made us win the 2017 China Big Data & Artificial Intelligence Innovation and Entrepreneurship Competitions.