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2021 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2021

作者： Deng, Chao Lin, Cui-Xiang Li, Hong-Dong Central South University Human Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Changsha China

ISBN: (纸本)9781665401265

Identifying disease-associated genes is key to studying the pathogenic mechanism of complex diseases. Existing methods for predicting disease genes are dominantly based on molecular networks or omics data, including gene expression, protein expression, co-expression networks, protein-protein interaction, etc. The annotated gene sets such as Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes pathways represent knowledge about the functional association between genes, which may be of predictive value for disease gene identification. However, the knowledge is barely explored in existing approaches. In this study, we propose a new method for predicting disease-associated genes by integrating annotated gene sets. It first constructs a signal matrix by integrating annotated gene sets in the MSigDB data, a comprehensive database of curated gene sets. Then it uses the signal matrix as input features to build a prediction model with machine learning approaches. We compared our method with existing disease gene prediction methods on five complex diseases. The results showed that our method is superior to other methods. © 2021 IEEE.

关键词： Gene Ontology

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A Fully Automated CT-Guided Learning for Survival Prediction of Esophageal Cancer

A Fully Automated CT-Guided Learning for Survival Prediction...

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2023 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2023

作者： Yue, Hailin Liu, Jin Kuang, Hulin Cheng, Jianhong Li, Junjian Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha China Institute of Guizhou Aerospace Measuring and Testing Technology Guiyang China

ISBN: (纸本)9798350337488

Accurately predicting survival of esophageal cancer is essential for clinical precision treatment. However, the existing region of interest (ROI) based methods not only require prior medical knowledge to complete the delineation of tumor, but may also lead to excessive sensitivity of the model towards ROI. To address these challenges, we design a fully automated CT-guided learning that combines a CNN-Transformer size aware U-Net and a ranked survival prediction network together to automatically predict the survival of patients with esophageal cancer. Specifically, we first incorporate the Transformer with shifted windowing multi-head self-attention mechanism into the base of the encoder in the U-Net to capture the long-range dependency in the 3D CT images. Then, to alleviate the imbalance between the ROI and the background in CT images, we design a size-aware coefficient for the segmentation loss. Finally, we design a ranked pair sorting loss to learn more fully the ranked information hidden in esophageal cancer patients. To validate the effectiveness of our method, we conduct extensive experiments on a dataset containing 759 esophageal cancer samples. The experimental results demonstrate that our proposed method can still achieve the best performance in survival prediction without ROI ground truth. © 2023 IEEE.

关键词： CT-Guided Esophageal Cancer Survival Prediction Transformer

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MTFIL-Net: Automated Alzheimer's disease detection and MMSE score prediction based on feature interactive learning

MTFIL-Net: Automated Alzheimer's disease detection and MMSE ...

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2021 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2021

作者： Liu, Jin Tian, Xu Wang, Jianxin Guo, Rui Kuang, Hulin Central South University Hunan Province Key Lab on Bioinformatics School of Computer Science and Engineering Changsha China

ISBN: (纸本)9781665401265

Automatic detection of Alzheimer's disease (AD) is conducive to intervention in the disease progression. MMSE score prediction can reveal the development of AD. In recent years, some studies have designed multi-task methods for AD detection and MMSE score prediction to take advantage of the correlation between them. However, how to use the correlation between the two task features is still a problem. To address this challenge, we propose a multi-task feature interactive leanrning network (MTFIL-Net) to perform AD detection and MMSE score prediction. First, we interact the features acquired by CNNs corresponding to the two tasks to take advantage of the feature correlation between the two tasks. The interaction module extracts the shared features of the two tasks and concatenate them with the features of the two task. Then, we design a joint loss based on cross entropy and smooth L1 function. We use the distribution of MMSE scores to dynamically adjust the relationship between the two tasks. We validate our method with subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI). We use the ADNI1 dataset for training and testing, and used the ADNI2 dataset as an external validation set. Our proposed MTFIL-Net reached an ACC of 0.86 for AD detection and a correlation coefficient of 0.67 for MMSE score prediction on the ADNI1 dataset, and reached an ACC of 0.85 for AD detection and a correlation coefficient of 0.66 for MMSE score prediction on the ADNI2 dataset. Experiment results show that MTFIL-Net effectively utilizes the correlation between AD and MMSE score. © 2021 IEEE.

关键词： Forecasting

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Attention-based Memory Fusion Network for Clinical Outcome Prediction using Electronic Medical Records

Attention-based Memory Fusion Network for Clinical Outcome P...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Al-Dailami, Abdulrahman Kuang, Hulin Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha410083 China Sana'a University Faculty of Computers and Information Technology Sana'a Yemen

ISBN: (纸本)9781665468190

Recent methods of patient clinical outcome prediction focus on embedding the temporal time-series data by sequential data encoders without considering the dependency between the different variables and the static demographics data. To solve this problem and achieve better patient outcome prediction, we propose an attention-based memory fusion (AMF) network with Gated Recurrent Unit (GRU) (called GRU-AMFN) to model the dependency between the different time-series and static demographic data and extract effective personalized representation about the patient's clinical health status. We evaluate our proposed GRU-AMFN method on eICU, a publicly available dataset, to validate its effectiveness for the in-hospital mortality prediction task. Experimental results demonstrate that our proposed method outperforms several state-of-the-art models for the in-hospital mortality prediction task. Ablation studies show the effectiveness of the proposed attention-based memory fusion module and the adaptive fusion module. Besides, our proposed method finds several static demographic and time-series features that are important for mortality prediction. © 2022 IEEE.

关键词： Forecasting

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Integrating Multi-scale Feature Representation and Ensemble Learning for Schizophrenia Diagnosis

Integrating Multi-scale Feature Representation and Ensemble ...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Xiao, Manna Kuang, Hulin Liu, Jin Zhang, Yan Xiang, Yizhen Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha China Central South University The Second Xiangya Hospital Department of Psychiatry Hunan Changsha China

ISBN: (纸本)9781665468190

Resting-state functional magnetic resonance imaging (rs-fMRI) images have been widely used for diagnosis of schizophrenia. With rs-fMRI, most existing schizophrenia diagnostic methods have revealed schizophrenia's functional abnormalities from the following three scales, i.e., regional neural activity alterations, functional connectivity abnormalities and brain network dysfunctions. However, many schizophrenia diagnosis methods do not consider the fusion of features from the three scales. In this study, we propose a schizophrenia diagnostic method based on multi-scale feature representation and ensemble learning. Firstly, features including the three scales (region, connectivity and network) are extracted from rs-fMRI images using the brainnetome atlas. For each scale, feature selection, i.e., least absolute shrinkage and selection operator, is applied to identify effective sub-features related to schizophrenia classification by a grid search. Then the selected sub-features of each scale are input to support vector machine with linear kernel to classify schizophrenia patients and healthy controls respectively. To further improve the schizophrenia diagnostic performance, an ensemble learning framework named E-RCN is proposed to average the probabilities obtained by the classifiers of each scale in decision level. By leave-one-out cross-validation on the center for biomedical research excellence dataset (COBRE), our proposed method achieves encouraging diagnosis performance, outperforming several state-of-the-art methods. In addition, ranked by the occurence frequency of each brain region within the leave-one-out cross-validation experiments, some brain regions related to schizophrenia, i.e., thalamus and middle temporal gyrus, and important elaborate subregions, i.e., Tha_L_8_8, MTG_L_4_4 and MTG_R_4_4, are found. © 2022 IEEE.

关键词： Support vector machines

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Multi-Task Learning for Alzheimer's Disease Diagnosis and Mini-Mental State Examination Score Prediction

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Big Data Mining and Analytics 2024年第3期7卷 828-842页

作者： Jin Liu Xu Tian Hanhe Lin Hong-Dong Li Yi Pan Hunan Provincial Key Lab on Bioinformatics School of Computer Science and EngineeringCentral South UniversityChangsha 410083China Xinjiang Engineering Research Center of Big Data and Intelligent Software School of SoftwareXinjiang UniversityUrumqi 830091China School of Science and Engineering University of DundeeDundeeDD14HNUK Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China

Accurately diagnosing Alzheimer's disease is essential for improving elderly ***,accurate prediction of the mini-mental state examination score also can measure cognition impairment and track the progression of Alzheimer's ***,most of the existing methods perform Alzheimer's disease diagnosis and mini-mental state examination score prediction separately and ignore the relation between these two *** address this challenging problem,we propose a novel multi-task learning method,which uses feature interaction to explore the relationship between Alzheimer's disease diagnosis and minimental state examination score *** our proposed method,features from each task branch are firstly decoupled into candidate and non-candidate parts for ***,we propose feature sharing module to obtain shared features from candidate features and return shared features to task branches,which can promote the learning of each *** validate the effectiveness of our proposed method on multiple *** Alzheimer's disease neuroimaging initiative 1 dataset,the accuracy in diagnosis task and the root mean squared error in prediction task of our proposed method is 87.86%and 2.5,*** results show that our proposed method outperforms most state-of-the-art *** proposed method enables accurate Alzheimer's disease diagnosis and mini-mental state examination score ***,it can be used as a reference for the clinical diagnosis of Alzheimer's disease,and can also help doctors and patients track disease progression in a timely manner.

关键词： multi-task learning Alzheimer's disease diagnosis mini-mental state examination score prediction

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TH-SLP: Web Service Link Prediction Based on Topic-aware Heterogeneous Graph Neural Network

TH-SLP: Web Service Link Prediction Based on Topic-aware Het...

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2023 IEEE International Conference on Web Services, ICWS 2023

作者： Peng, Qian Cao, Buqing Xie, Xiang Liu, Shanpeng Kang, Guosheng Liu, Jianxun Hunan University of Science and Technology Xiangtan School of Computer Science and Engineering Hunan Provincial Key Lab. for Services Computing and Novel Software Technology Hunan China

ISBN: (纸本)9798350304855

With the emergence of more and more Web services, finding suitable services becomes a difficult problem. Service link prediction is employed to disclose relationships among services, which facilitates the further development of service composition, selection, and recommendation. But the existing link prediction approaches simply utilize the structural features of the service network. In reality, the rich text content in service node description documents also carries latent but fine-grained semantics generated by multifaceted topic-aware factors, yet few efforts are committed to mining them. In this paper, we propose a Web service link prediction method based on a topic-aware heterogeneous graph neural network. Specifically, the method consists of two main layers, including the meta-path intra-decomposition and the meta-path inter-mergence. Meta-path intra-decomposition aims to mine the topic distribution of the meta-paths-based context while capturing fine-grained topic-aware semantics. Meta-path inter-mergence uniquely aggregates topic-aware factors according to the mined distribution and adopts a multifaceted attention mechanism to aggregate different meta-paths, enabling service nodes to generate multifaceted topic-aware embeddings that preserve not only the structure and but also the topic-aware semantics. In addition, a topic prior guidance regularization item is set up for quality assurance of multifaceted topic-aware embedding that depends on global knowledge of the unstructured text content in description documents. Experimental results on real datasets show that our proposed model outperforms other existing baselines methods in the link prediction task, successfully validating the effectiveness of our proposed method. © 2023 IEEE.

关键词： Semantics

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Identification of Virus-Receptor Interactions Based on Network Enhancement and Similarity 16th

Identification of Virus-Receptor Interactions Based on Netwo...

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16th International Symposium on bioinformatics Research and Applications, ISBRA 2020

作者： Zhu, Lingzhi Yan, Cheng Duan, Guihua Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Changsha410083 China School of Computer and Information Science Hunan Institute of Technology Hengyang421008 China School of Computer and Information Qiannan Normal University for Nationalities Duyun558000 China

ISBN: (纸本)9783030578206

As a main composition of the human-associated microbiome, viruses are directly associated with our health and disease. The receptor-binding is critical for the virus infection. So identifying potential virus-receptor interactions will help systematically understand the mechanisms of virus-receptor interactions and effectively treat infectious diseases caused by viruses. Several computational models have been developed to identify virus-receptor interactions based on assumption that similar viruses show similar interaction patterns with receptors and vice versa, but the performance need to be improved. Furthermore, the virus network and the receptor network are also noisy. Therefore, we present a new prediction model (NERLS) to identify potential virus-receptor interactions based on Network Enhancement, virus sequence information and receptor sequence information by Regularized Least Squares. Firstly, the virus network is constructed based on the virus sequence similarity and Gaussian interaction profile (GIP) kernel similarity of viruses by a mean method. They are calculated based on the viral RefSeq genomes downloaded from NCBI and known virus-receptor interactions, respectively. Similarly, we also use the same mean method to construct the receptor network based on the amino acid sequence similarity and known virus-receptor interactions. Then Network Enhancement is applied to denoise the virus network and the receptor network. Finally, we employ the regularized least squares algorithm to identify potential virus-receptor interactions. The 10-fold cross validation (10CV) experimental results indicate that an average Area Under Curve (AUC) values of NERLS is 0.8930, which is superior to other computing models of 0.8675 (IILLS), 0.7959 (BRWH), 0.7577 (LapRLS), and 0.7128 (CMF). Furthermore, the Leave One Out Cross Validation (LOOCV) experimental results also show that NERLS can achieve the AUC values of 0.9210, which is better than other models (IILLS: 0.9061, BRWH: 0

关键词： Viruses

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M3CI-Net: Multi-Modal MRI-Based Characteristics Inspired Network for IDH Genotyping

M3CI-Net: Multi-Modal MRI-Based Characteristics Inspired Net...

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2023 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2023

作者： Yao, Jingxiao Liu, Jin Cheng, Jianhong Kuang, Hulin Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Changsha China Institute of Guizhou Aerospace Measuring and Testing Technology Guiyang550009 China

ISBN: (纸本)9798350337488

Isocitrate dehydrogenase (IDH) is a key molecular feature for gliomas, and the prediction of IDH is also an important task for computer-aided diagnosis using magnetic resonance imaging (MRI). To address this changllenge, we introduce a multi-modal MRI-based characteristics inspired network for IDH Genotyping (M3CI-Net), which pay more attention to the different characteristics information of different MRI modalities T1, T2, T1ce, Flair. In M3CI-Net, a pre-fusion module with multi-channel attention mechanism is used to fuse T1ce and Flair modalities and capture as much as possible luminance and contrast information, and the edge information is obtained from T2 modality by using edge detection module. Finally, the feature information between modalities are fused and input into a CNN-Transformer based encoder structure to extract shared spatial and global information from multi-modal MRI, and the information of multiple scales frome encoder are input into the linear layer for IDH genotype classification after pooling, meanwhile, the CNN based decoder with skip-connection for glioma segmentation works for assisting IDH genotyping. Then, we proposed images' pre-fusion loss, segmentation loss, IDH genotyping loss, and use uncertainty weight training method to balance the weights of these loss. we evaluate our proposed method on Brats2020, and achieve an acceracy of 0.88, an AUC of 0.94, a specificity of 0.92, a sensitivity of 0.84 in IDH genotyping, which is superior to the state-of-the-art methods. © 2023 IEEE.

关键词： Edge detection Glioma segmentation IDH genotyping Multi-modality Pre-fusion

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An approximation algorithm for lower-bounded k-median with constant factor

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science China(Information sciences) 2022年第4期65卷 93-101页

作者： Xiaoliang WU Feng SHI Yutian GUO Zhen ZHANG Junyu HUANG Jianxin WANG School of Computer Science and Engineering Central South University Hunan Provincial Key Lab on Bioinformatics Central South University School of Frontier Crossover Studies Hunan University of Technology and Business

The lower-bounded k-median problem plays a key role in many applications related to privacy protection, which requires that the amount of assigned client to each facility should not be less than the requirement. Unfortunately, the lower-bounded clustering problem remains elusive under the widely studied k-median objective. Within this paper, we convert this problem to the capacitated facility location problem and successfully give a(516+ε)-approximation for this problem.

关键词： approximation algorithm k-median lower-bounded k-median

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