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检索条件"机构=School of Computer Science and Engineering and Hunan Provincial Key Lab on Bioinformatics"

共 165 条记录，以下是21-30 订阅

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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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An integration of deep learning with feature fusion for protein-protein interaction prediction

An integration of deep learning with feature fusion for prot...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Tran, Hoai-Nhan Nguyen, Phuc-Xuan-Quynh Peng, Xiaoqing Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha410083 China

ISBN: (纸本)9781665468190

High-throughput biological and large-scale experiments for protein-protein interaction (PPI) identification provides valuable information about PPI networks but are time-consuming and limited in determining PPI between different species. We propose the integration of deep learning with feature fusion for PPI prediction, combining handcrafted features and protein sequence embedding for protein sequence representation. Our proposed method is evaluated on the Yeast full, Yeast core, Human, and eight independent datasets. The experimental results show that our method achieves 95.8% accuracy on the Yeast core, 99.2% accuracy on Human, and 100% accuracy on eight independent datasets. We also perform extensive comparisons with other existing outstanding methods and demonstrate the superior ability of the proposed method. © 2022 IEEE.

关键词： Yeast

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ASNet: An Adversarial Sparse Network for Multi-task Biomedical Named Entity Recognition

ASNet: An Adversarial Sparse Network for Multi-task Biomedic...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Duan, Junwen Guo, Huai Zeng, Min Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha410083 China

ISBN: (纸本)9781665468190

Biomedical named entity recognition (BioNER) is to extract entities, such as genes and proteins, from biomedical texts, where there is often a lack of high-quality training data. Recent work addresses this issue by multi-task learning with multiple datasets. However, these methods are usually over-parameterized, and some even suffer from negative transfer issues. To address above problems, we propose adversarial sparse sharing mechanism, which trains a sparsely shared encoder on multiple tasks with both task-agnostic and task-specific subnetworks. With adversarial training, we guide the task-agnostic subnetwork to learn shared task-invariant features and the task-specific subnetwork to learn task-dependent features. For a particular task, only the shared and its subnetwork are activated, which greatly reduces the number of parameters and avoids interference among tasks. Experimental results on 15 benchmark BioNER datasets show that our proposed method outperforms or is competitive with baseline methods with fewer parameters. Our code is released at: https://***/CSU-NLP-Group/ASNet © 2022 IEEE.

关键词： Natural language processing systems

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Predicting of microbe-drug associations via a pre-completion-based label propagation algorithm

Predicting of microbe-drug associations via a pre-completion...

引用

2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Zhao, Haochen Duan, Guihua Yang, Botu Li, Suning Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Changsha China

ISBN: (纸本)9781665468190

Identifying microbe-drug associations is important to systematically understand a drug's mechanism of action in the therapeutic application. Since identifying microbe-drug associations is expensive and time-consuming via biological experiments, in this study, we propose a Pre-completion-based label Propagation (PLP) method (called PLPMDA) to predict microbe-drug associations based on the multi-type similarities. To obtain richer information of drugs and microbes, we calculate drug chemical structure similarity, drug Anatomical Therapeutic Chemical (ATC) code similarity, microbe functional similarity, microbe sequence similarity and Gaussian Interaction Profile (GIP) kernel similarities of microbes and drugs, and then introduce a non-linear similarity fusion method. Comparing baseline methods, our advantage lies in performing an effective pre-completion step on the initial association matrix from the drug-related and microbe-related information and does not rely on the known drug-microbe associations, which can accelerate the design and discovery of the new drugs. The computational experiment results demonstrate that our proposed approach PLPMDA achieves significantly higher performance than the comparative methods in de novo and cross-validation experiments. © 2022 IEEE.

关键词： Forecasting

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ViTRMSE: a three-dimensional RMSE scoring method for protein-ligand docking models based on Vision Transformer

ViTRMSE: a three-dimensional RMSE scoring method for protein...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Guo, Linyuan Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha410083 China

ISBN: (纸本)9781665468190

Protein-ligand interactions (PLIs) play important roles in cellular activities and drug discovery. Due to the technical difficulty and high cost of experimental methods, there is considerable interest in the development of computational approaches, such as protein-ligand docking, to decipher PLI patterns. One of the most important and difficult aspects of protein-ligand docking is recognizing near-native conformations from a set of decoys, but unfortunately, traditional scoring functions still suffer from limited accuracy. Therefore, new scoring methods are pressingly needed in methodological and/or practical implications. We present a new deep learning-based scoring function for ranking protein-ligand docking models based on Vision Transformer(ViT), named ViTRMSE. To recognize near-native conformations from a set of decoys, ViTRMSE voxelizes the protein-ligand interactional pocket into a 3D grid labeled by the occupancy contribution of atoms in different physicochemical classes. Benefiting from the Vision Transformer architecture, ViTRMSE can effectively capture the subtle differences between spatially and energetically favorable near-native conformations and unfavorable non-native decoys without needing extra information. ViTRMSE is extensively evaluated on diverse test sets including PDBbind2019 and CASF2016, and obtains significant improvements over existing methods in terms of RMSE, R and docking power. © 2022 IEEE.

关键词： Proteins

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LDAGSO: Predicting 1ncRNA-Disease Associations from Graph Sequences and Disease Ontology via Deep Learning techniques

LDAGSO: Predicting 1ncRNA-Disease Associations from Graph Se...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Awn, Norah Saeed Li, Yiming Zhao, Baoying Zeng, Min Li, Min Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha410083 China

ISBN: (纸本)9781665468190

Recent studies have confirmed the significant effects of long non-coding RNAs (1ncRNAs) in understanding the mechanism of diseases. Because of the relatively small number of validated associations between 1ncRNAs and diseases, and previous computational methods have limited performance without capturing important features of sequences and ontology information, we developed LDAGSO, a novel deep learning framework to predict 1ncRNA and disease associations from 1ncRNA sequences and disease ontology. For 1ncRNA sequences, we converted them into graph structure based on k-mer technique and de Bruijn graph, and captured high-level features of the graph using graph convolutional networks. For diseases, we extracted ontology term paths from the disease ontology tree, and treated them as sentences to obtain their feature representation using Bidirectional Encoder Representations from Transformers (BERT) technique. Finally, these two kinds of features were fed into a fully connected layer to perform the task of association prediction between 1ncRNAs and diseases. According to the results, our approach provides state-of-the-art results when evaluated by leave-one-out cross-validation. © 2022 IEEE.

关键词： Forecasting

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Multi-view Hypergraph-based Self-supervised Learning Model for Web API Recommendation 22

Multi-view Hypergraph-based Self-supervised Learning Model f...

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22nd IEEE International Symposium on Parallel and Distributed Processing with Applications, ISPA 2024

作者： Shen, Jiexun Li, Dongfan Chen, Wanjun Xiao, Yong Kang, Guosheng Liu, Jianxun Peng, Zhenlian School of Computer Science and Engineering Hunan University of Science and Technology Xiangtan China Hunan Provincial Key Lab. for Services Computing and Novel Software Technology HNUST Xiangtan China

ISBN: (纸本)9798331509712

With the rapid development of service computing technology, how to recommend the desirable Web APIs to developers from the large number of APIs is a challenge. The traditional methods based on collaborative filtering are limited by data sparsity. With the support of multi-dimensional relational feature modeling, graph neural network-based methods are proposed to mitigate data sparsity, but their convolution nature may amplify the noise effect. Therefore, how to simultaneously reduce the impact of sparsity and noisy data has been an open question in the field of API recommendation. To address the problem, this paper proposes a self-supervised learning method based on multi-view hypergraph for Web API recommendation. First, the Mashup-API interaction graph is transformed into a hypergraph, and the hyperedges are used as intermediate hubs to transfer messages between nodes, maintaining the global collaboration effect between Mashup and API nodes. Then, a multi-view strategy is adopted to generate embeddings of Mashups and APIs through information fusion, by which recommendation probability is derived by dot product between the embeddings of Mashups and Web APIs. To train the model parameters effectively, a self-supervised learning method is used to reduce the effect of noisy data to improve the embeddings. Extensive experiments are conducted on a real-world dataset, and the experimental results show that the proposed model outperforms the baselines. © 2024 IEEE.

关键词： Self-supervised learning

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Crawling and Exploring RESTful Web APIs from RapidAPI 17th

Crawling and Exploring RESTful Web APIs from RapidAPI

引用

CCF 17th International Conference on Service science, CCF ICSS 2024

作者： Li, Wen Ren, Hongshuai Nie, Yamei Liu, Zihao Kang, Guosheng Liu, Jianxun Peng, Zhenlian School of Computer Science and Engineering Hunan University of Science and Technology Xiangtan China Hunan Provincial Key Lab. for Services Computing and Novel Software Technology HNUST Xiangtan China

ISBN: (纸本)9789819757596

RapidAPI serves as a marketplace and management platform that integrates a wide range of Web APIs, offering developers access to a rich pool of API resources. More and more researchers are delving into ways to maximize the value created by leveraging these resources. Thus, acquiring the Web API data and knowing the details is of significance for researchers and ordinary users. In this paper, we propose the methodology of crawling Web APIs from RapidAPI (https://***/hub) and provide rich visualizations and statistical analysis for the crawled dataset. The crawling code and the crawled dataset are open for public access (https://***/IntelligentServicelab/RESTful-API-Crawler) so that researchers and users can acquire them with no effort. Moreover, the use cases of RESTful Web APIs are provided as a usage reference for users and developers. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： Web crawler

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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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Prediction of virus-receptor interactions based on multi-view learning and link prediction

Prediction of virus-receptor interactions based on multi-vie...

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Zhu, Lingzhi Zheng, Kai Duan, Guihua Wang, Jianxin Central South University Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Hunan Changsha410083 China Hunan Institute of Technology Hengyang School of Computer Science and Engineering Hunan421008 China

ISBN: (纸本)9781665468190

Receptor-binding is the first step of viral infection. Discovering potential virus-receptor interactions may give insight into potential strategies for treating viral infectious diseases. Most of computational methods for the virus-receptor interaction prediction are mainly based on sequence information. They neither makes effective use of structure information nor effectively handles with missing values of multiple similarities. In addition, the Link Prediction via linear optimization (LP) only uses contribution of neighbors of a node and ignores contribution of neighbors of another node on the network link. In this article, we present a virus-receptor interaction prediction method (MVLP) based on Multi-View learning and LP via contributions of all neighbors of two nodes on the network link. First, missing values of the receptor secondary structure similarity, the receptor conserved domain secondary structure similarity, the viral protein secondary structure similarity, the viral protein sequence similarity and the viral genome sequence similarity are updated by the gaussian radial basis function (GRB). To improve these similarities, we fuse updated and initial values of each similarity with multi-view learning, respectively. Next, three virus values and receptor similarities are integrated into the comprehensive virus and receptor similarity by the averaging method, respectively. Finally, LP based on contribution of neighbors of two nodes is presented for the virus-receptor interaction prediction. To evaluate the ability of MVLP, we compare MVLP with four related methods in 10 fold Cross-Validation (10CV). Computational results indicate that an average Area Under Curve (AUC) values of MVLP on viralReceptor sup and viralReceptor are 0.9427 and 0.9444, respectively, which are superior to other related methods. Furthermore, a case study also demonstrates the ability of MVLP in practice. © 2022 IEEE.

关键词： Viruses

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