Lei Fan

Dr. Lei Fan


Research Focus & Metrics

Academic Career Length

9Years (2018-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
12 December 2022 in IEEE Transactions on Medical Imaging
Verified
Journal Article
Closed access
LFLei Fan
Lei Fan
ASArcot Sowmya
Arcot Sowmya
EMErik Meijering
Erik Meijering
YSYang Song
Yang Song
Histopathological Whole Slide Images (WSIs) at giga-pixel resolution are the gold standard for cancer analysis and prognosis. Due to the scarcity of pixel- or patch-level annotations of WSIs, many existing methods attempt to predict survival outcomes based on a three-stage strategy that includes patch selection, patch-level feature extraction and aggregation. However, the patch features are usually extracted by using truncated models ( e.g . ResNet) pretrained on ImageNet without fine-tuning on WSI tasks, and the aggregation stage does not consider the many-to-one relationship between multiple WSIs and the patient. In this paper, we propose a novel survival prediction framework that consists of patch sampling, feature extraction and patient-level survival prediction. Specifically, we employ two kinds of self-supervised learning methods, i.e . colorization and cross-channel, as pretext tasks to train convnet-based models that are tailored for extracting features from WSIs. Then, at the patient-level survival prediction we explicitly aggregate features from multiple WSIs, using consistency and contrastive losses to normalize slide-level features at the patient level. We conduct extensive experiments on three large-scale datasets: TCGA-GBM, TCGA-LUSC and NLST. Experimental results demonstrate the effectiveness of our proposed framework, as it achieves state-of-the-art performance in comparison with previous studies, with concordance index of 0.670, 0.679 and 0.711 on TCGA-GBM, TCGA-LUSC and NLST, respectively.

1 September 2025
Verified
Conference Paper
Open access
PDF file
MQMingcheng Qu
Mingcheng Qu
GYGuang Yang
Guang Yang
DDDonglin Di
Donglin Di
TSTonghua Su
Tonghua Su
YGYue Gao
Yue Gao
LFLei Fan
Lei Fan
Multimodal pathology-genomic analysis has become increasingly prominent in cancer survival prediction. However, existing studies mainly utilize multi-instance learning to aggregate patch-level features, neglecting the information loss of contextual and hierarchical details within pathology images. Furthermore, the disparity in data granularity and dimensionality between pathology and genomics leads to a significant modality imbalance. The high spatial resolution inherent in pathology data renders it a dominant role while overshadowing genomics in multimodal integration. In this paper, we propose a multimodal survival prediction framework that incorporates hypergraph learning to effectively capture both contextual and hierarchical details from pathology images. Moreover, it employs a modality rebalance mechanism and an interactive alignment fusion strategy to dynamically reweight the contributions of the two modalities, thereby mitigating the pathology-genomics imbalance. Quantitative and qualitative experiments are conducted on five TCGA datasets, demonstrating that our model outperforms advanced methods by over 3.4% in C-Index performance. Code: https://github.com/MCPathology/MRePath.

16 September 2022
Verified
Book Chapter
Closed access
PDF file
LFLei Fan
Lei Fan
ASArcot Sowmya
Arcot Sowmya
EMErik Meijering
Erik Meijering
YSYang Song
Yang Song

26 February 2025 in IEEE Transactions on Instrumentation and Measurement
Verified
Journal Article
Closed access
YLYun Liang
Yun Liang
ZHZhiguang Hu
Zhiguang Hu
JHJunjie Huang
Junjie Huang
DDDonglin Di
Donglin Di
ASAnyang Su
Anyang Su
LFLei Fan
Lei Fan
Unsupervised industrial anomaly detection methods can identify product defects in industrial images using only normal samples for training. Existing approaches perform well on public industrial image datasets but struggle with specific anomaly types due to the domain gap between pre-trained feature extractors and target-specific domains. To tackle this issue, this paper presents a two-stage training strategy, called ToCoAD. In the first stage, a discriminative network is trained by using synthetic anomalies in a self-supervised learning manner. This network is then utilized in the second stage to provide a negative feature guide, aiding in the training of the feature extractor through bootstrap contrastive learning. This approach enables the model to progressively learn the distribution of anomalies specific to industrial datasets, effectively enhancing its generalizability to various types of anomalies. Extensive experiments are conducted to demonstrate the effectiveness of our proposed two-stage training strategy, and our model produces competitive performance, achieving pixel-level AUROC scores of 98.21%, 98.43% and 97.70% on MVTec AD, VisA and BTAD respectively.

30 January 2025 in IEEE Transactions on Industrial Informatics
Verified
Journal Article
Closed access
LFLei Fan
Lei Fan
DFDongdong Fan
Dongdong Fan
YDYiwen Ding
Yiwen Ding
YWYong Wu
Yong Wu
DDDonglin Di
Donglin Di
YSYang Song
Yang Song
Grain appearance inspection is crucial for evaluating grain quality and determining seed stratification. Typically, trained inspectors manually examine each grain kernel to identify and remove defective ones, which is time-consuming and error-prone. In this article, we present GrainBrain, a robotic vision-based system comprising a hardware prototype (A100) and a deep learning model (GrainAD). A100 is equipped with five cameras to capture high-quality, multiview images of each kernel. The identification of defective kernels is treated as an unsupervised anomaly detection task. GrainAD trains a classifier to distinguish between healthy and pseudoanomaly samples generated at both image and feature levels, and a supervised contrastive learning loss is employed to obtain compact feature representations of healthy kernels. In addition, we release a large-scale dataset containing over 100K annotated images of four types of cereal grains. Extensive experiments were conducted to verify the superiority of our system, achieving an average AUROC of 94.4/90.4% at the image/pixel level. Our system excelled in both efficiency and consistency, as demonstrated by experiments comparing human experts to the system.

12 November 2018 in IEEE Access
Verified
Journal Article
Open access
LFLei Fan
Lei Fan
WWWei-Chien Wang
Wei-Chien Wang
FZFuyuan Zha
Fuyuan Zha
JYJiapeng Yan
Jiapeng Yan
Semantic segmentation, as dense pixel-wise classification task, played an important tache in scene understanding. There are two main challenges in many state-of-the-art works: 1) most backbone of segmentation models that often were extracted from pretrained classification models generated poor performance in small categories because they were lacking in spatial information. 2) the gap of combination between high-level and low-level features in segmentation models has led to inaccurate predictions. To handle these challenges, in this paper, we proposed a new tailored backbone and Attention Select Module for segmentation tasks. Specifically, our new backbone was modified from the original Resnet, which can yield better segmentation performance. Attention Select Module employed spatial and channel self-attention mechanism to reinforce the propagation of contextual features, which can aggregate semantic and spatial information simultaneously. In addition, based on our new backbone and Attention Select Module, we further proposed our segmentation model for street scenes understanding. We conducted a series of ablation studies on two public benchmarks including Cityscapes and CamVid dataset to demonstrate the effectiveness of our proposals. Our model achieved a mIoU score of 71.5% on the Cityscapes test set with only fine annotation data and 60.1% on the CamVid test set.