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Lanfen Lin

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21 papers

2 author rows

JBHI Journal 2026 Journal Article

Multimodal Graph Learning With Multi-Hypergraph Reasoning Networks for Focal Liver Lesion Classification in Multimodal Magnetic Resonance Imaging

Shaocong Mo
Ming Cai
Lanfen Lin
Ruofeng Tong
Fang Wang
Qingqing Chen
Wenbin Ji
Yinhao Li

Multimodal magnetic resonance imaging (MRI) is instrumental in differentiating liver lesions. The major challenge involves modeling reliable connections and simultaneously learning complementary information across various MRI sequences. While previous studies have primarily focused on multimodal integration in a pair-wise manner using few modalities, our research seeks to advance a more comprehensive understanding of interaction modeling by establishing complex high-order correlations among the diverse modalities in multimodal MRI. In this paper, we introduce a multimodal graph learning with multi-hypergraph reasoning network to capture the full spectrum of both pair-wise and group-wise relationships among different modalities. Specifically, a weight-shared encoder extracts features from regions of interest (ROI) images across all modalities. Subsequently, a collection of uniform hypergraphs are constructed with varying vertex configurations, allowing for the modeling of not only pair-wise correlations but also the high-order collaborations for relational reasoning. Following information propagation through the hypergraph message passing, adaptive intra-modality fusion module is proposed to effectively fuse feature representations from different hypergraphs of the same modality. Finally, all refined features are concatenated to prepare for the classification task. Our experimental evaluations, including focal liver lesions classification using the LLD-MMRI2023 dataset and early recurrence prediction of hepatocellular carcinoma using our internal datasets, demonstrate that our method significantly surpasses the performance of existing approaches, indicating the effectiveness of our model in handling both pair-wise and group-wise interactions across multiple modalities.

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JBHI Journal 2026 Journal Article

SPA: Leveraging the SAM With Spatial Priors Adapter for Enhanced Medical Image Segmentation

Jihong Hu
Yinhao Li
Rahul Kumar Jain
Lanfen Lin
Yen-Wei Chen

The Segment Anything Model (SAM) has gained renown for its success in image segmentation, benefiting significantly from its pretraining on extensive datasets and its interactive prompt-based segmentation approach. Although highly effective in natural (real-world) image segmentation tasks, the SAM model encounters significant challenges in medical imaging due to the inherent differences between these two domains. To address these challenges, we propose the Spatial Prior Adapter (SPA) scheme, a parameter-efficient fine-tuning strategy that enhances SAM's adaptability to medical imaging tasks. SPA introduces two novel modules: the Spatial Prior Module (SPM), which captures localized spatial features through convolutional layers, and the Feature Communication Module (FCM), which integrates these features into SAM's image encoder via cross-attention mechanisms. Furthermore, we develop a Multiscale Feature Fusion Module (MSFFM) to enhance SAM's end-to-end segmentation capabilities by effectively aggregating multiscale contextual information. These lightweight modules require minimal computational resources while significantly boosting segmentation performance. Our approach demonstrates superior performance in both prompt-based and end-to-end segmentation scenarios through extensive experiments on publicly available medical imaging datasets. Performance highlights the potential of the proposed method to bridge the gap between foundation models and domain-specific medical imaging tasks. This advancement paves the way for more effective AI-assisted medical diagnostic systems.

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AAAI Conference 2026 Conference Paper

Taming the Phantom: Token-Asymmetric Filtering for Hallucination Mitigation in Large Vision-Language Models

Shuyi Ouyang
Hongyi Wang
Gongfan Fang
Xinyin Ma
Lanfen Lin
Xinchao Wang

Hallucination in Large Vision-Language Models (LVLMs) remains a critical challenge, undermining their reliability in real-world applications. Existing studies have investigated the causes of hallucination at the modality level and proposed effective strategies. However, interaction patterns beyond the modality level remain insufficiently explored. In this paper, we conduct a token-level analysis and identify two key phenomena: (1) a small subset of textual tokens in LVLMs exert disproportionate influence in the visual-active layers, surpassing that of the visual modality and potentially misleading visual understanding; (2) while LVLMs can correctly identify key visual information, insufficient focus on these cues can sometimes lead to hallucinations. Based on such observation, we attribute hallucinations in LVLMs to two token-level causes: the disproportionate influence of certain textual tokens (phantom tokens) and the underutilization of critical visual cues (anchor tokens). To mitigate these issues, we introduce Token-Asymmetric Filtering (TAF)—a training-free, plug-and-play method that modulates intermediate attention maps in LVLMs. TAF isolates the influence of phantom tokens and emphasizes the influence of anchor tokens in the visual-active layers. Experimental results across multiple benchmarks demonstrate that TAF significantly mitigates hallucinations across a range of state-of-the-art LVLMs.

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JBHI Journal 2026 Journal Article

Topology-aware Diffusion Schrödinger Bridge for Unpaired H&E-to-IHC Stain Translation

Chujie Zhang
Yangyang Xie
Jihong Hu
Xiaoyu Shi
Yinhao Li
Xiao Liang
Lanfen Lin
Yen-Wei Chen

Unpaired H&E-to-IHC Stain Translation aims to generate immunohistochemistry (IHC) staining from Hematoxylin and Eosin (H&E) staining. It offers clearer diagnostic insights and potentially expands access to advanced pathology services in resource-limited areas. This task faces two primary challenges: capturing target domain style characteristics and preserving topological features in histological images. Recently, Schrödinger Bridge (SB)-based methods have offered a solution for unpaired image-to-image translation, addressing the mode collapse and artifact issues in CycleGAN-based approaches, as well as the Gaussian prior assumption limitation in diffusion-based methods. While SB-based methods suffer from the curse of dimensionality with high-resolution images, the Unpaired Neural Schrödinger Bridge (UNSB) overcomes this challenge and achieves state-of-the-art (SOTA) performance on natural images. However, UNSB has two key issues in histological images: (1) loss of topological features and (2) IHC staining representation. UNSB focuses only on the optimal path from source to target domains, ignoring local structure paths. Convolutional neural networks (CNNs) do not perfectly preserve critical anatomical structures due to limitations like receptive field size or model capacity. To address these challenges, we introduce the T opology-aware D iffusion S chrödinger B ridge ( TDSB ), integrating a Topology Guidance (TG) module and Dual-Domain Adaptive Patch-based noise contrastive estimation (DDAP). Experiments on seven translation tasks across three datasets show that our method achieves SOTA performance in unpaired H&E-to-IHC stain translation. Clinical evaluation through pathologists' assessments further validates the effectiveness of our method.

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AAAI Conference 2025 Conference Paper

M2OST: Many-to-one Regression for Predicting Spatial Transcriptomics from Digital Pathology Images

Hongyi Wang
Xiuju Du
Jing Liu
Shuyi Ouyang
Yen-Wei Chen
Lanfen Lin

The advancement of Spatial Transcriptomics (ST) has facilitated the spatially-aware profiling of gene expressions based on histopathology images. Although ST data offers valuable insights into the micro-environment of tumors, its acquisition cost remains expensive. Therefore, directly predicting the ST expressions from digital pathology images is desired. Current methods usually adopt existing regression backbones along with patch-sampling for this task, which ignores the inherent multi-scale information embedded in the pyramidal data structure of digital pathology images, and wastes the inter-spot visual information crucial for accurate gene expression prediction. To address these limitations, we propose M2OST, a many-to-one regression Transformer that can accommodate the hierarchical structure of the pathology images via a decoupled multi-scale feature extractor. Unlike traditional models that are trained with one-to-one image-label pairs, M2OST uses multiple images from different levels of the digital pathology image to jointly predict the gene expressions in their common corresponding spot. Built upon our many-to-one scheme, M2OST can be easily scaled to fit different numbers of inputs, and its network structure inherently incorporates nearby inter-spot features, enhancing regression performance. We have tested M2OST on three public ST datasets and the experimental results show that M2OST can achieve state-of-the-art performance with fewer parameters and floating-point operations (FLOPs).

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JBHI Journal 2025 Journal Article

S 2 Match: Revisiting Weak-to-Strong Consistency from a Semantic Similarity Perspective for Semi-supervised Medical Image Segmentation

Shiao Xie
Hongyi Wang
Ziwei Niu
Hao Sun
Shuyi Ouyang
Yen-Wei Chen
Lanfen Lin

Semi-supervised learning (SSL) for medical image segmentation is a challenging yet highly practical task, which reduces reliance on large-scale labeled datasets by leveraging unlabeled samples. Among SSL techniques, the weak-to-strong consistency framework, popularized by FixMatch, has emerged as a state-of-the-art method in classification tasks. Notably, such a simple pipeline has also shown competitive performance in medical image segmentation. However, two key limitations still persist, impeding its efficient adaptation: (1) the neglect of contextual dependencies results in inconsistent predictions for similar semantic features, leading to incomplete object segmentation; (2) the lack of exploitation on semantic similarity between labeled and unlabeled data induces considerable class-distribution discrepancy. To address these limitations, we propose a novel SSL framework for medical image segmentation, named S 2 Match, powered by two appealing designs from a semantic similarity perspective: (1) rectifying pixel-wise prediction by reasoning about the intra-image pair-wise affinity map, thus integrating contextual dependencies explicitly into the final prediction; (2) bridging labeled and unlabeled data via a feature querying mechanism for compact class representation learning, which fully considers cross-image anatomical similarities. As the reliable semantic similarity extraction depends on robust features, we further introduce an effective Spatial-aware Fusion Module (SFM) to explore distinctive information from multiple scales. Experiments show that S 2 Match yields consistent improvements over the state-of-the-art methods across five public medical image segmentation benchmarks, exhibiting competitive performance on both 2D and 3D tasks.

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JBHI Journal 2025 Journal Article

SAMA: A Self-and-Mutual Attention Network for Accurate Recurrence Prediction of Non-Small Cell Lung Cancer Using Genetic and CT Data

Yang Ai
Jing Liu
Yinhao Li
Fang Wang
Xiuju Du
Rahul Kumar Jain
Lanfen Lin
Yen-Wei Chen

Accurate preoperative recurrence prediction for non-small cell lung cancer (NSCLC) is a challenging issue in the medical field. Existing studies primarily conduct image and molecular analyses independently or directly fuse multimodal information through radiomics and genomics, which fail to fully exploit and effectively utilize the highly heterogeneous cross-modal information at different levels and model the complex relationships between modalities, resulting in poor fusion performance and becoming the bottleneck of precise recurrence prediction. To address these limitations, we propose a novel unified framework, the Self-and-Mutual Attention (SAMA) Network, designed to efficiently fuse and utilize macroscopic CT images and microscopic gene data for precise NSCLC recurrence prediction, integrating handcrafted features, deep features, and gene features. Specifically, we design a Self-and-Mutual Attention Module that performs three-stage fusion: the self-enhancement stage enhances modality-specific features; the gene-guided and CT-guided cross-modality fusion stages perform bidirectional cross-guidance on the self-enhanced features, complementing and refining each modality, enhancing heterogeneous feature expression; and the optimized feature aggregation stage ensures the refined interactive features for precise prediction. Extensive experiments on both publicly available datasets from The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA) demonstrate that our method achieves state-of-the-art performance and exhibits broad applicability to various cancers.

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ECAI Conference 2025 Conference Paper

Triple-Prompt Controllable Diffusion for Universal Data Augmentation in Medical Image Segmentation

Shiao Xie
Ke Meng
Hongyi Wang 0002
Liangjun Zhang
Ziwei Niu
Yen-Wei Chen 0001
Lanfen Lin

Medical image segmentation is a crucial yet challenging task in image analysis across diverse anatomical structures. Current segmentation models heavily depend on large-scale datasets, which are laborious to collect and annotate. While generative models offer a promising alternative for data augmentation, most existing approaches are limited to single-modality outputs, either synthetic images or segmentation masks. Moreover, these methods often lack flexible conditioning mechanisms and struggle to capture the rich contextual dependencies inherent in anatomical structures. To address these challenges, in this paper, we propose TPCDM, a novel framework that co-synthesizes high-fidelity paired medical images and segmentation masks through a unified Triple-Prompt Conditional Diffusion Model. At the heart of TPCDM lies a newly defined joint image-label generation paradigm, termed Coordinated Distribution Learning, governed by three synergistic prompts: (1) a text prompt encoding global anatomical semantics; (2) a spatial prompt enforcing pixel-wise spatial coherence; (3) a task prompt dynamically adapting to diverse distributions. Furthermore, TPCDM disentangles instance-wise annotations into semantic masks and distance maps, enabling seamless extension to instance segmentation tasks. Extensive experiments on four benchmarks demonstrate that TPCDM achieves superior synthesis quality. Besides, incorporating the synthesized samples leads to state-of-the-art performance in both downstream semantic and instance segmentation tasks, while also delivering significant improvements under limited labeled data.

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AAAI Conference 2024 Conference Paper

Combinatorial CNN-Transformer Learning with Manifold Constraints for Semi-supervised Medical Image Segmentation

Huimin Huang
Yawen Huang
Shiao Xie
Lanfen Lin
Ruofeng Tong
Yen-Wei Chen
Yuexiang Li
Yefeng Zheng

Semi-supervised learning (SSL), as one of the dominant methods, aims at leveraging the unlabeled data to deal with the annotation dilemma of supervised learning, which has attracted much attentions in the medical image segmentation. Most of the existing approaches leverage a unitary network by convolutional neural networks (CNNs) with compulsory consistency of the predictions through small perturbations applied to inputs or models. The penalties of such a learning paradigm are that (1) CNN-based models place severe limitations on global learning; (2) rich and diverse class-level distributions are inhibited. In this paper, we present a novel CNN-Transformer learning framework in the manifold space for semi-supervised medical image segmentation. First, at intra-student level, we propose a novel class-wise consistency loss to facilitate the learning of both discriminative and compact target feature representations. Then, at inter-student level, we align the CNN and Transformer features using a prototype-based optimal transport method. Extensive experiments show that our method outperforms previous state-of-the-art methods on three public medical image segmentation benchmarks.

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JBHI Journal 2024 Journal Article

Segmentation Guided Crossing Dual Decoding Generative Adversarial Network for Synthesizing Contrast-Enhanced Computed Tomography Images

Yulin Yang
Qingqing Chen
Yinhao Li
Fang Wang
Xian-Hua Han
Yutaro Iwamoto
Jing Liu
Lanfen Lin

Although contrast-enhanced computed tomography (CE-CT) images significantly improve the accuracy of diagnosing focal liver lesions (FLLs), the administration of contrast agents imposes a considerable physical burden on patients. The utilization of generative models to synthesize CE-CT images from non-contrasted CT images offers a promising solution. However, existing image synthesis models tend to overlook the importance of critical regions, inevitably reducing their effectiveness in downstream tasks. To overcome this challenge, we propose an innovative CE-CT image synthesis model called Segmentation Guided Crossing Dual Decoding Generative Adversarial Network (SGCDD-GAN). Specifically, the SGCDD-GAN involves a crossing dual decoding generator including an attention decoder and an improved transformation decoder. The attention decoder is designed to highlight some critical regions within the abdominal cavity, while the improved transformation decoder is responsible for synthesizing CE-CT images. These two decoders are interconnected using a crossing technique to enhance each other's capabilities. Furthermore, we employ a multi-task learning strategy to guide the generator to focus more on the lesion area. To evaluate the performance of proposed SGCDD-GAN, we test it on an in-house CE-CT dataset. In both CE-CT image synthesis tasks–namely, synthesizing ART images and synthesizing PV images–the proposed SGCDD-GAN demonstrates superior performance metrics across the entire image and liver region, including SSIM, PSNR, MSE, and PCC scores. Furthermore, CE-CT images synthetized from our SGCDD-GAN achieve remarkable accuracy rates of 82. 68%, 94. 11%, and 94. 11% in a deep learning-based FLLs classification task, along with a pilot assessment conducted by two radiologists.

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JBHI Journal 2023 Journal Article

Adaptive Decomposition and Shared Weight Volumetric Transformer Blocks for Efficient Patch-Free 3D Medical Image Segmentation

Hongyi Wang
Yingying Xu
Qingqing Chen
Ruofeng Tong
Yen-Wei Chen
Hongjie Hu
Lanfen Lin

High resolution (HR) 3D medical image segmentation is vital for an accurate diagnosis. However, in the field of medical imaging, it is still a challenging task to achieve a high segmentation performance with cost-effective and feasible computation resources. Previous methods commonly use patch-sampling to reduce the input size, but this inevitably harms the global context and decreases the model's performance. In recent years, a few patch-free strategies have been presented to deal with this issue, but either they have limited performance due to their over-simplified model structures or they follow a complicated training process. In this study, to effectively address these issues, we present Adaptive Decomposition (A-Decomp) and Shared Weight Volumetric Transformer Blocks (SW-VTB). A-Decomp can adaptively decompose features and reduce their spatial size, which greatly lowers GPU memory consumption. SW-VTB is able to capture long-range dependencies at a low cost with its lightweight design and cross-scale weight-sharing mechanism. Our proposed cross-scale weight-sharing approach enhances the network's ability to capture scale-invariant core semantic information in addition to reducing parameter numbers. By combining these two designs together, we present a novel patch-free segmentation framework named VolumeFormer. Experimental results on two datasets show that VolumeFormer outperforms existing patch-based and patch-free methods with a comparatively fast inference speed and relatively compact design.

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AAAI Conference 2023 Conference Paper

ClassFormer: Exploring Class-Aware Dependency with Transformer for Medical Image Segmentation

Huimin Huang
Shiao Xie
Lanfen Lin
Ruofeng Tong
Yen-Wei Chen
Hong Wang
Yuexiang Li
Yawen Huang

Vision Transformers have recently shown impressive performances on medical image segmentation. Despite their strong capability of modeling long-range dependencies, the current methods still give rise to two main concerns in a class-level perspective: (1) intra-class problem: the existing methods lacked in extracting class-specific correspondences of different pixels, which may lead to poor object coverage and/or boundary prediction; (2) inter-class problem: the existing methods failed to model explicit category-dependencies among various objects, which may result in inaccurate localization. In light of these two issues, we propose a novel transformer, called ClassFormer, powered by two appealing transformers, i.e., intra-class dynamic transformer and inter-class interactive transformer, to address the challenge of fully exploration on compactness and discrepancy. Technically, the intra-class dynamic transformer is first designed to decouple representations of different categories with an adaptive selection mechanism for compact learning, which optimally highlights the informative features to reflect the salient keys/values from multiple scales. We further introduce the inter-class interactive transformer to capture the category dependency among different objects, and model class tokens as the representative class centers to guide a global semantic reasoning. As a consequence, the feature consistency is ensured with the expense of intra-class penalization, while inter-class constraint strengthens the feature discriminability between different categories. Extensive empirical evidence shows that ClassFormer can be easily plugged into any architecture, and yields improvements over the state-of-the-art methods in three public benchmarks.

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NeurIPS Conference 2023 Conference Paper

HAP: Structure-Aware Masked Image Modeling for Human-Centric Perception

Junkun Yuan
Xinyu Zhang
Hao Zhou
Jian Wang
Zhongwei Qiu
Zhiyin Shao
Shaofeng Zhang
Sifan Long

Model pre-training is essential in human-centric perception. In this paper, we first introduce masked image modeling (MIM) as a pre-training approach for this task. Upon revisiting the MIM training strategy, we reveal that human structure priors offer significant potential. Motivated by this insight, we further incorporate an intuitive human structure prior - human parts - into pre-training. Specifically, we employ this prior to guide the mask sampling process. Image patches, corresponding to human part regions, have high priority to be masked out. This encourages the model to concentrate more on body structure information during pre-training, yielding substantial benefits across a range of human-centric perception tasks. To further capture human characteristics, we propose a structure-invariant alignment loss that enforces different masked views, guided by the human part prior, to be closely aligned for the same image. We term the entire method as HAP. HAP simply uses a plain ViT as the encoder yet establishes new state-of-the-art performance on 11 human-centric benchmarks, and on-par result on one dataset. For example, HAP achieves 78. 1% mAP on MSMT17 for person re-identification, 86. 54% mA on PA-100K for pedestrian attribute recognition, 78. 2% AP on MS COCO for 2D pose estimation, and 56. 0 PA-MPJPE on 3DPW for 3D pose and shape estimation.

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IJCAI Conference 2023 Conference Paper

SLViT: Scale-Wise Language-Guided Vision Transformer for Referring Image Segmentation

Shuyi Ouyang
Hongyi Wang
Shiao Xie
Ziwei Niu
Ruofeng Tong
Yen-Wei Chen
Lanfen Lin

Referring image segmentation aims to segment an object out of an image via a specific language expression. The main concept is establishing global visual-linguistic relationships to locate the object and identify boundaries using details of the image. Recently, various Transformer-based techniques have been proposed to efficiently leverage long-range cross-modal dependencies, enhancing performance for referring segmentation. However, existing methods consider visual feature extraction and cross-modal fusion separately, resulting in insufficient visual-linguistic alignment in semantic space. In addition, they employ sequential structures and hence lack multi-scale information interaction. To address these limitations, we propose a Scale-Wise Language-Guided Vision Transformer (SLViT) with two appealing designs: (1) Language-Guided Multi-Scale Fusion Attention, a novel attention mechanism module for extracting rich local visual information and modeling global visual-linguistic relationships in an integrated manner. (2) An Uncertain Region Cross-Scale Enhancement module that can identify regions of high uncertainty using linguistic features and refine them via aggregated multi-scale features. We have evaluated our method on three benchmark datasets. The experimental results demonstrate that SLViT surpasses state-of-the-art methods with lower computational cost. The code is publicly available at: https: //github. com/NaturalKnight/SLViT.

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JBHI Journal 2022 Journal Article

DeepRecS: From RECIST Diameters to Precise Liver Tumor Segmentation

Yue Zhang
Chengtao Peng
Liying Peng
Yingying Xu
Lanfen Lin
Ruofeng Tong
Zhiyi Peng
Xiongwei Mao

Liver tumor segmentation (LiTS) is of primary importance in diagnosis and treatment of hepatocellular carcinoma. Known automated LiTS methods could not yield satisfactory results for clinical use since they were hard to model flexible tumor shapes and locations. In clinical practice, radiologists usually estimate tumor shape and size by a Response Evaluation Criteria in Solid Tumor (RECIST) mark. Inspired by this, in this paper, we explore a deep learning (DL) based interactive LiTS method, which incorporates guidance from user-provided RECIST marks. Our method takes a three-step framework to predict liver tumor boundaries. Under this architecture, we develop a RECIST mark propagation network (RMP-Net) to estimate RECIST-like marks in off-RECIST slices. We also devise a context-guided boundary-sensitive network (CGBS-Net) to distill tumors’ contextual and boundary information from corresponding RECIST(-like) marks, and then predict tumor maps. To further refine the segmentation results, we process the tumor maps using a 3D conditional random field (CRF) algorithm and a morphology hole-filling operation. Verified on two clinical contrast-enhanced abdomen computed tomography (CT) image datasets, our proposed approach can produce promising segmentation results, and outperforms the state-of-the-art interactive segmentation methods.

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JBHI Journal 2022 Journal Article

MTL-ABS 3 Net: Atlas-Based Semi-Supervised Organ Segmentation Network With Multi-Task Learning for Medical Images

Huimin Huang
Qingqing Chen
Lanfen Lin
Ming Cai
Qiaowei Zhang
Yutaro Iwamoto
Xianhua Han
Akira Furukawa

Organ segmentation is one of the most important step for various medical image analysis tasks. Recently, semi-supervised learning (SSL) has attracted much attentions by reducing labeling cost. However, most of the existing SSLs neglected the prior shape and position information specialized in the medical images, leading to unsatisfactory localization and non-smooth of objects. In this paper, we propose a novel atlas-based semi-supervised segmentation network with multi-task learning for medical organs, named MTL-ABS 3 Net, which incorporates the anatomical priors and makes full use of unlabeled data in a self-training and multi-task learning manner. The MTL-ABS 3 Net consists of two components: an Atlas-Based Semi-Supervised Segmentation Network (ABS 3 Net) and Reconstruction-Assisted Module (RAM). Specifically, the ABS 3 Net improves the existing SSLs by utilizing atlas prior, which generates credible pseudo labels in a self-training manner; while the RAM further assists the segmentation network by capturing the anatomical structures from the original images in a multi-task learning manner. Better reconstruction quality is achieved by using MS-SSIM loss function, which further improves the segmentation accuracy. Experimental results from the liver and spleen datasets demonstrated that the performance of our method was significantly improved compared to existing state-of-the-art methods.

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IJCAI Conference 2022 Conference Paper

ScaleFormer: Revisiting the Transformer-based Backbones from a Scale-wise Perspective for Medical Image Segmentation

Huimin Huang
Shiao Xie
Lanfen Lin
Yutaro Iwamoto
Xian-Hua Han
Yen-Wei Chen
Ruofeng Tong

Recently, a variety of vision transformers have been developed as their capability of modeling long-range dependency. In current transformer-based backbones for medical image segmentation, convolutional layers were replaced with pure transformers, or transformers were added to the deepest encoder to learn global context. However, there are mainly two challenges in a scale-wise perspective: (1) intra-scale problem: the existing methods lacked in extracting local-global cues in each scale, which may impact the signal propagation of small objects; (2) inter-scale problem: the existing methods failed to explore distinctive information from multiple scales, which may hinder the representation learning from objects with widely variable size, shape and location. To address these limitations, we propose a novel backbone, namely ScaleFormer, with two appealing designs: (1) A scale-wise intra-scale transformer is designed to couple the CNN-based local features with the transformer-based global cues in each scale, where the row-wise and column-wise global dependencies can be extracted by a lightweight Dual-Axis MSA. (2) A simple and effective spatial-aware inter-scale transformer is designed to interact among consensual regions in multiple scales, which can highlight the cross-scale dependency and resolve the complex scale variations. Experimental results on different benchmarks demonstrate that our Scale-Former outperforms the current state-of-the-art methods. The code is publicly available at: https: //github. com/ZJUGiveLab/ScaleFormer.

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JBHI Journal 2021 Journal Article

Attention-RefNet: Interactive Attention Refinement Network for Infected Area Segmentation of COVID-19

Titinunt Kitrungrotsakul
Qingqing Chen
Huitao Wu
Yutaro Iwamoto
Hongjie Hu
Wenchao Zhu
Chao Chen
Fangyi Xu

COVID-19 pneumonia is a disease that causes an existential health crisis in many people by directly affecting and damaging lung cells. The segmentation of infected areas from computed tomography (CT) images can be used to assist and provide useful information for COVID-19 diagnosis. Although several deep learning-based segmentation methods have been proposed for COVID-19 segmentation and have achieved state-of-the-art results, the segmentation accuracy is still not high enough (approximately 85%) due to the variations of COVID-19 infected areas (such as shape and size variations) and the similarities between COVID-19 and non-COVID-infected areas. To improve the segmentation accuracy of COVID-19 infected areas, we propose an interactive attention refinement network (Attention RefNet). The interactive attention refinement network can be connected with any segmentation network and trained with the segmentation network in an end-to-end fashion. We propose a skip connection attention module to improve the important features in both segmentation and refinement networks and a seed point module to enhance the important seeds (positions) for interactive refinement. The effectiveness of the proposed method was demonstrated on public datasets (COVID-19CTSeg and MICCAI) and our private multicenter dataset. The segmentation accuracy was improved to more than 90%. We also confirmed the generalizability of the proposed network on our multicenter dataset. The proposed method can still achieve high segmentation accuracy.

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ECAI Conference 2020 Conference Paper

Black-Box Adversarial Attacks Against Deep Learning Based Malware Binaries Detection with GAN

Junkun Yuan
Shaofang Zhou
Lanfen Lin
Feng Wang
Jia Cui

For efficient malware detection, there are more and more deep learning methods based on raw software binaries. Recent studies show that deep learning models can easily be fooled to make a wrong decision by introducing subtle perturbations to inputs, which attracts a large influx of work in adversarial attacks. However, most of the existing attack methods are based on manual features (e. g. , API calls) or in the white-box setting, making the attacks impractical in current real-world scenarios. In this work, we propose a novel attack framework called GAPGAN, which generates adversarial payloads (padding bytes) with generative adversarial networks (GANs). To the best of our knowledge, it is the first work that performs end-to-end black-box attacks at the byte-level against deep learning based malware binaries detection. In our attack framework, we map input discrete malware binaries to continuous space, then feed it to the generator of GAPGAN to generate adversarial payloads. We append payloads to the original binaries to craft an adversarial sample while preserving its functionality. We propose to use a dynamic threshold for reducing the loss of the effectiveness of the payloads when mapping it from continuous format back to the original discrete format. For balancing the attention of the generator to the payloads and the adversarial samples, we use an automatic weight tuning strategy. We train GAPGAN with both malicious and benign software. Once the training is finished, the generator can generate an adversarial sample with only the input malware in less than twenty milliseconds. We apply GAPGAN to attack the state-of-the-art detector MalConv and achieve 100% attack success rate with only appending payloads of 2. 5% of the total length of the data for detection. We also attack deep learning models with different structures under different defense methods. The experiments show that GAPGAN outperforms other state-of-the-art attack models in efficiency and effectiveness.

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JBHI Journal 2020 Journal Article

Semi-Supervised Learning for Semantic Segmentation of Emphysema With Partial Annotations

Liying Peng
Lanfen Lin
Hongjie Hu
Yue Zhang
Huali Li
Yutaro Iwamoto
Xian-Hua Han
Yen-Wei Chen

Segmentation and quantification of each subtype of emphysema is helpful to monitor chronic obstructive pulmonary disease. Due to the nature of emphysema (diffuse pulmonary disease), it is very difficult for experts to allocate semantic labels to every pixel in the CT images. In practice, partially annotating is a better choice for the radiologists to reduce their workloads. In this paper, we propose a new end-to-end trainable semi-supervised framework for semantic segmentation of emphysema with partial annotations, in which a segmentation network is trained from both annotated and unannotated areas. In addition, we present a new loss function, referred to as Fisher loss, to enhance the discriminative power of the model and successfully integrate it into our proposed framework. Our experimental results show that the proposed methods have superior performance over the baseline supervised approach (trained with only annotated areas) and outperform the state-of-the-art methods for emphysema segmentation.

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JBHI Journal 2019 Journal Article

Classification and Quantification of Emphysema Using a Multi-Scale Residual Network

Liying Peng
Yen-Wei Chen
Lanfen Lin
Hongjie Hu
Huali Li
Qingqing Chen
Xiaoli Ling
Dan Wang

Automated tissue classification is an essential step for quantitative analysis and treatment of emphysema. Although many studies have been conducted in this area, there still remain two major challenges. First, different emphysematous tissue appears in different scales, which we call “inter-class variations. ” Second, the intensities of CT images acquired from different patients, scanners or scanning protocols may vary, which we call “intra-class variations”. In this paper, we present a novel multi-scale residual network with two channels of raw CT image and its differential excitation component. We incorporate multi-scale information into our networks to address the challenge of inter-class variations. In addition to the conventional raw CT image, we use its differential excitation component as a pair of inputs to handle intra-class variations. Experimental results show that our approach has superior performance over the state-of-theart methods, achieving a classification accuracy of 93. 74% on our original emphysema database. Based on the classification results, we also perform the quantitative analysis of emphysema in 50 subjects by correlating the quantitative results (the area percentage of each class) with pulmonary functions. We show that centrilobular emphysema (CLE) and panlobular emphysema (PLE) have strong correlation with the pulmonary functions and the sum of CLE and PLE can be used as a new and accurate measure of emphysema severity instead of the conventional measure (sum of all subtypes of emphysema). The correlations between the new measure and various pulmonary functions are up to |r| = 0. 922 (ris correlation coefficient).

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