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Xia X, Liu Y, Zheng C, Zhang X, Wu Q, Gao X, Zeng X, Su Y. Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space. J Chem Inf Model 2024; 64:5161-5174. [PMID: 38870455 PMCID: PMC11235097 DOI: 10.1021/acs.jcim.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Optimization techniques play a pivotal role in advancing drug development, serving as the foundation of numerous generative methods tailored to efficiently design optimized molecules derived from existing lead compounds. However, existing methods often encounter difficulties in generating diverse, novel, and high-property molecules that simultaneously optimize multiple drug properties. To overcome this bottleneck, we propose a multiobjective molecule optimization framework (MOMO). MOMO employs a specially designed Pareto-based multiproperty evaluation strategy at the molecular sequence level to guide the evolutionary search in an implicit chemical space. A comparative analysis of MOMO with five state-of-the-art methods across two benchmark multiproperty molecule optimization tasks reveals that MOMO markedly outperforms them in terms of diversity, novelty, and optimized properties. The practical applicability of MOMO in drug discovery has also been validated on four challenging tasks in the real-world discovery problem. These results suggest that MOMO can provide a useful tool to facilitate molecule optimization problems with multiple properties.
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Affiliation(s)
- Xin Xia
- The
Key Laboratory of Intelligent Computing and Signal Processing of Ministry
of Education, School of Artificial Intelligence, Anhui University, Hefei 230601, China
- Institute
of Artificial Intelligence, Hefei Comprehensive
National Science Center, 5089 Wangjiang West Road, Hefei 230088, AnhuiChina
| | - Yiping Liu
- College
of Computer Science and Electronic Engineering, Hunan University, Changsha 410012, China
| | - Chunhou Zheng
- The
Key Laboratory of Intelligent Computing and Signal Processing of Ministry
of Education, School of Artificial Intelligence, Anhui University, Hefei 230601, China
| | - Xingyi Zhang
- The
Key Laboratory of Intelligent Computing and Signal Processing of Ministry
of Education, School of Artificial Intelligence, Anhui University, Hefei 230601, China
| | - Qingwen Wu
- The
Key Laboratory of Intelligent Computing and Signal Processing of Ministry
of Education, School of Artificial Intelligence, Anhui University, Hefei 230601, China
| | - Xin Gao
- Computer
Science Program, Computer, Electrical and Mathematical Sciences and
Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology
(KAUST), Thuwal 23955-6900, Kingdom
of Saudi Arabia
| | - Xiangxiang Zeng
- College
of Computer Science and Electronic Engineering, Hunan University, Changsha 410012, China
| | - Yansen Su
- The
Key Laboratory of Intelligent Computing and Signal Processing of Ministry
of Education, School of Artificial Intelligence, Anhui University, Hefei 230601, China
- Institute
of Artificial Intelligence, Hefei Comprehensive
National Science Center, 5089 Wangjiang West Road, Hefei 230088, AnhuiChina
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2
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Xian L, Wang Y. Advances in Computational Methods for Protein–Protein Interaction Prediction. ELECTRONICS 2024; 13:1059. [DOI: 10.3390/electronics13061059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
Abstract
Protein–protein interactions (PPIs) are pivotal in various physiological processes inside biological entities. Accurate identification of PPIs holds paramount significance for comprehending biological processes, deciphering disease mechanisms, and advancing medical research. Given the costly and labor-intensive nature of experimental approaches, a multitude of computational methods have been devised to enable swift and large-scale PPI prediction. This review offers a thorough examination of recent strides in computational methodologies for PPI prediction, with a particular focus on the utilization of deep learning techniques within this domain. Alongside a systematic classification and discussion of relevant databases, feature extraction strategies, and prominent computational approaches, we conclude with a thorough analysis of current challenges and prospects for the future of this field.
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Affiliation(s)
- Lei Xian
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
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3
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Zhang M, Wu Q, Chen H, Heidari AA, Cai Z, Li J, Md Abdelrahim E, Mansour RF. Whale optimization with random contraction and Rosenbrock method for COVID-19 disease prediction. Biomed Signal Process Control 2023; 83:104638. [PMID: 36741073 PMCID: PMC9889265 DOI: 10.1016/j.bspc.2023.104638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/01/2022] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), instigated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has hugely impacted global public health. To identify and intervene in critically ill patients early, this paper proposes an efficient, intelligent prediction model based on the machine learning approach, which combines the improved whale optimization algorithm (RRWOA) with the k-nearest neighbor (KNN) classifier. In order to improve the problem that WOA is prone to fall into local optimum, an improved version named RRWOA is proposed based on the random contraction strategy (RCS) and the Rosenbrock method. To verify the capability of the proposed algorithm, RRWOA is tested against nine classical metaheuristics, nine advanced metaheuristics, and seven well-known WOA variants based on 30 IEEE CEC2014 competition functions, respectively. The experimental results in mean, standard deviation, the Friedman test, and the Wilcoxon signed-rank test are considered, proving that RRWOA won first place on 18, 24, and 25 test functions, respectively. In addition, a binary version of the algorithm, called BRRWOA, is developed for feature selection problems. An efficient prediction model based on BRRWOA and KNN classifier is proposed and compared with seven existing binary metaheuristics based on 15 datasets of UCI repositories. The experimental results show that the proposed algorithm obtains the smallest fitness value in eleven datasets and can solve combinatorial optimization problems, indicating that it still performs well in discrete cases. More importantly, the model was compared with five other algorithms on the COVID-19 dataset. The experiment outcomes demonstrate that the model offers a scientific framework to support clinical diagnostic decision-making. Therefore, RRWOA is an effectively improved optimizer with efficient value.
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Affiliation(s)
- Meilin Zhang
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China
| | - Qianxi Wu
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China
| | - Huiling Chen
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China
| | - Ali Asghar Heidari
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China
| | - Zhennao Cai
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China
| | - Jiaren Li
- Wenzhou People's Hospital, Wenzhou, Zhejiang 325099, China
| | - Elsaid Md Abdelrahim
- Faculty of Science, Northern Border University, Arar, Saudi Arabia.,Faculty of Science, Tanta University, Tanta, Egypt
| | - Romany F Mansour
- Department of Mathematics, Faculty of Science, New Valley University, El-Kharga 72511, Egypt
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4
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Wei PJ, Ma W, Li Y, Su Y. Disease biomarker identification based on sample network optimization. Methods 2023; 213:42-49. [PMID: 37001685 DOI: 10.1016/j.ymeth.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
A large amount of evidence shows that biomarkers are discriminant features related to disease development. Thus, the identification of disease biomarkers has become a basic problem in the analysis of complex diseases in the medical fields, such as disease stage judgment, disease diagnosis and treatment. Research based on networks have become one of the most popular methods. Several algorithms based on networks have been proposed to identify biomarkers, however the networks of genes or molecules ignored the similarities and associations among the samples. It is essential to further understand how to construct and optimize the networks to make the identified biomarkers more accurate. On this basis, more effective strategies can be developed to improve the performance of biomarkers identification. In this study, a multi-objective evolution algorithm based on sample similarity networks has been proposed for disease biomarker identification. Specifically, we design the sample similarity networks to extract the structural characteristic information among samples, which used to calculate the influence of the sample to each class. Besides, based on the networks and the group of biomarkers we choose in every iteration, we can divide samples into different classes by the importance for each class. Then, in the process of evolution algorithm population iteration, we develop the elite guidance strategy and fusion selection strategy to select the biomarkers which make the sample classification more accurate. The experiment results on the five gene expression datasets suggests that the algorithm we proposed is superior over some state-of-the-art disease biomarker identification methods.
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Affiliation(s)
- Pi-Jing Wei
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, 230601 Hefei, Anhui, China
| | - Wenwen Ma
- Key Laboratory of Intelligent Computing and Signal Processing, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, 230601 Hefei, China
| | - Yanxin Li
- Department of Cardiology, The Third Hospital of Xingtai, Xingtai 054000, Hebei, China
| | - Yansen Su
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, 5089 Wangjiang West Road, 230088 Hefei, China; School of Artificial Intelligence, Anhui University, 111 Jiulong Road, 230601 Hefei, China.
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5
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Chen H, Liu X. Reweighted multi-view clustering with tissue-like P system. PLoS One 2023; 18:e0269878. [PMID: 36763648 PMCID: PMC9917278 DOI: 10.1371/journal.pone.0269878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/29/2022] [Indexed: 02/12/2023] Open
Abstract
Multi-view clustering has received substantial research because of its ability to discover heterogeneous information in the data. The weight distribution of each view of data has always been difficult problem in multi-view clustering. In order to solve this problem and improve computational efficiency at the same time, in this paper, Reweighted multi-view clustering with tissue-like P system (RMVCP) algorithm is proposed. RMVCP performs a two-step operation on data. Firstly, each similarity matrix is constructed by self-representation method, and each view is fused to obtain a unified similarity matrix and the updated similarity matrix of each view. Subsequently, the updated similarity matrix of each view obtained in the first step is taken as the input, and then the view fusion operation is carried out to obtain the final similarity matrix. At the same time, Constrained Laplacian Rank (CLR) is applied to the final matrix, so that the clustering result is directly obtained without additional clustering steps. In addition, in order to improve the computational efficiency of the RMVCP algorithm, the algorithm is embedded in the framework of the tissue-like P system, and the computational efficiency can be improved through the computational parallelism of the tissue-like P system. Finally, experiments verify that the effectiveness of the RMVCP algorithm is better than existing state-of-the-art algorithms.
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Affiliation(s)
- Huijian Chen
- Business School, Shandong Normal University, Jinan, China
| | - Xiyu Liu
- Business School, Shandong Normal University, Jinan, China
- * E-mail:
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6
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Li X, Han P, Chen W, Gao C, Wang S, Song T, Niu M, Rodriguez-Patón A. MARPPI: boosting prediction of protein-protein interactions with multi-scale architecture residual network. Brief Bioinform 2023; 24:6887309. [PMID: 36502435 DOI: 10.1093/bib/bbac524] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) are a major component of the cellular biochemical reaction network. Rich sequence information and machine learning techniques reduce the dependence of exploring PPIs on wet experiments, which are costly and time-consuming. This paper proposes a PPI prediction model, multi-scale architecture residual network for PPIs (MARPPI), based on dual-channel and multi-feature. Multi-feature leverages Res2vec to obtain the association information between residues, and utilizes pseudo amino acid composition, autocorrelation descriptors and multivariate mutual information to achieve the amino acid composition and order information, physicochemical properties and information entropy, respectively. Dual channel utilizes multi-scale architecture improved ResNet network which extracts protein sequence features to reduce protein feature loss. Compared with other advanced methods, MARPPI achieves 96.03%, 99.01% and 91.80% accuracy in the intraspecific datasets of Saccharomyces cerevisiae, Human and Helicobacter pylori, respectively. The accuracy on the two interspecific datasets of Human-Bacillus anthracis and Human-Yersinia pestis is 97.29%, and 95.30%, respectively. In addition, results on specific datasets of disease (neurodegenerative and metabolic disorders) demonstrate the ability to detect hidden interactions. To better illustrate the performance of MARPPI, evaluations on independent datasets and PPIs network suggest that MARPPI can be used to predict cross-species interactions. The above shows that MARPPI can be regarded as a concise, efficient and accurate tool for PPI datasets.
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Affiliation(s)
- Xue Li
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Peifu Han
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Wenqi Chen
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Changnan Gao
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Shuang Wang
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Tao Song
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Muyuan Niu
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
| | - Alfonso Rodriguez-Patón
- School of Computer Science and Technology, China University of Petroleum, Qingdao 266580, China
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7
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Shang J, Zhu X, Sun Y, Li F, Kong X, Liu JX. DM-MOGA: a multi-objective optimization genetic algorithm for identifying disease modules of non-small cell lung cancer. BMC Bioinformatics 2023; 24:13. [PMID: 36624376 PMCID: PMC9830734 DOI: 10.1186/s12859-023-05136-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Constructing molecular interaction networks from microarray data and then identifying disease module biomarkers can provide insight into the underlying pathogenic mechanisms of non-small cell lung cancer. A promising approach for identifying disease modules in the network is community detection. RESULTS In order to identify disease modules from gene co-expression networks, a community detection method is proposed based on multi-objective optimization genetic algorithm with decomposition. The method is named DM-MOGA and possesses two highlights. First, the boundary correction strategy is designed for the modules obtained in the process of local module detection and pre-simplification. Second, during the evolution, we introduce Davies-Bouldin index and clustering coefficient as fitness functions which are improved and migrated to weighted networks. In order to identify modules that are more relevant to diseases, the above strategies are designed to consider the network topology of genes and the strength of connections with other genes at the same time. Experimental results of different gene expression datasets of non-small cell lung cancer demonstrate that the core modules obtained by DM-MOGA are more effective than those obtained by several other advanced module identification methods. CONCLUSIONS The proposed method identifies disease-relevant modules by optimizing two novel fitness functions to simultaneously consider the local topology of each gene and its connection strength with other genes. The association of the identified core modules with lung cancer has been confirmed by pathway and gene ontology enrichment analysis.
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Affiliation(s)
- Junliang Shang
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Xuhui Zhu
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Yan Sun
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Feng Li
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Xiangzhen Kong
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
| | - Jin-Xing Liu
- grid.412638.a0000 0001 0227 8151School of Computer Science, Qufu Normal University, Rizhao, 276826 China
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8
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Han Y, Chen W, Heidari AA, Chen H. Multi-verse Optimizer with Rosenbrock and Diffusion Mechanisms for Multilevel Threshold Image Segmentation from COVID-19 Chest X-Ray Images. JOURNAL OF BIONIC ENGINEERING 2023; 20:1198-1262. [PMID: 36619872 PMCID: PMC9811903 DOI: 10.1007/s42235-022-00295-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) is the most severe epidemic that is prevalent all over the world. How quickly and accurately identifying COVID-19 is of great significance to controlling the spread speed of the epidemic. Moreover, it is essential to accurately and rapidly identify COVID-19 lesions by analyzing Chest X-ray images. As we all know, image segmentation is a critical stage in image processing and analysis. To achieve better image segmentation results, this paper proposes to improve the multi-verse optimizer algorithm using the Rosenbrock method and diffusion mechanism named RDMVO. Then utilizes RDMVO to calculate the maximum Kapur's entropy for multilevel threshold image segmentation. This image segmentation scheme is called RDMVO-MIS. We ran two sets of experiments to test the performance of RDMVO and RDMVO-MIS. First, RDMVO was compared with other excellent peers on IEEE CEC2017 to test the performance of RDMVO on benchmark functions. Second, the image segmentation experiment was carried out using RDMVO-MIS, and some meta-heuristic algorithms were selected as comparisons. The test image dataset includes Berkeley images and COVID-19 Chest X-ray images. The experimental results verify that RDMVO is highly competitive in benchmark functions and image segmentation experiments compared with other meta-heuristic algorithms.
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Affiliation(s)
- Yan Han
- Department of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, 325035 China
| | - Weibin Chen
- Department of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, 325035 China
| | - Ali Asghar Heidari
- School of Surveying and Geospatial Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Huiling Chen
- Department of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, 325035 China
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Li J, Liu K, Hu Y, Zhang H, Heidari AA, Chen H, Zhang W, Algarni AD, Elmannai H. Eres-UNet++: Liver CT image segmentation based on high-efficiency channel attention and Res-UNet+. Comput Biol Med 2022; 158:106501. [PMID: 36635120 DOI: 10.1016/j.compbiomed.2022.106501] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 01/11/2023]
Abstract
Computerized tomography (CT) is of great significance for the localization and diagnosis of liver cancer. Many scholars have recently applied deep learning methods to segment CT images of liver and liver tumors. Unlike natural images, medical image segmentation is usually more challenging due to its nature. Aiming at the problem of blurry boundaries and complex gradients of liver tumor images, a deep supervision network based on the combination of high-efficiency channel attention and Res-UNet++ (ECA residual UNet++) is proposed for liver CT image segmentation, enabling fully automated end-to-end segmentation of the network. In this paper, the UNet++ structure is selected as the baseline. The residual block feature encoder based on context awareness enhances the feature extraction ability and solves the problem of deep network degradation. The introduction of an efficient attention module combines the depth of the feature map with spatial information to alleviate the uneven sample distribution impact; Use DiceLoss to replace the cross-entropy loss function to optimize network parameters. The liver and liver tumor segmentation accuracy on the LITS dataset was 95.8% and 89.3%, respectively. The results show that compared with other algorithms, the method proposed in this paper achieves a good segmentation performance, which has specific reference significance for computer-assisted diagnosis and treatment to attain fine segmentation of liver and liver tumors.
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Affiliation(s)
- Jian Li
- College of Information Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Kongyu Liu
- College of Information Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Yating Hu
- College of Information Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Hongchen Zhang
- College of Information Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Ali Asghar Heidari
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China.
| | - Huiling Chen
- Institute of Big Data and Information Technology, Wenzhou University, Wenzhou 325000, China.
| | - Weijiang Zhang
- College of Information Technology, Jilin Agricultural University, Changchun, 130118, China.
| | - Abeer D Algarni
- Department of Information Technology, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Hela Elmannai
- Department of Information Technology, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
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10
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Han P, Li X, Wang X, Wang S, Gao C, Chen W. Exploring the effects of drug, disease, and protein dependencies on biomedical named entity recognition: A comparative analysis. Front Pharmacol 2022; 13:1020759. [PMID: 36618912 PMCID: PMC9812568 DOI: 10.3389/fphar.2022.1020759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Biomedical named entity recognition is one of the important tasks of biomedical literature mining. With the development of natural language processing technology, many deep learning models are used to extract valuable information from the biomedical literature, which promotes the development of effective BioNER models. However, for specialized domains with diverse and complex contexts and a richer set of semantically related entity types (e.g., drug molecules, targets, pathways, etc., in the biomedical domain), whether the dependencies of these drugs, diseases, and targets can be helpful still needs to be explored. Method: Providing additional dependency information beyond context, a method based on the graph attention network and BERT pre-training model named MKGAT is proposed to improve BioNER performance in the biomedical domain. To enhance BioNER by using external dependency knowledge, we integrate BERT-processed text embeddings and entity dependencies to construct better entity embedding representations for biomedical named entity recognition. Results: The proposed method obtains competitive accuracy and higher efficiency than the state-of-the-art method on three datasets, namely, NCBI-disease corpus, BC2GM, and BC5CDR-chem, with a precision of 90.71%, 88.19%, and 95.71%, recall of 92.52%, 88.05%, and 95.62%, and F1-scores of 91.61%, 88.12%, and 95.66%, respectively, which performs better than existing methods. Conclusion: Drug, disease, and protein dependencies can allow entities to be better represented in neural networks, thereby improving the performance of BioNER.
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11
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Li C, Hou L, Pan J, Chen H, Cai X, Liang G. Tuberculous pleural effusion prediction using ant colony optimizer with grade-based search assisted support vector machine. Front Neuroinform 2022; 16:1078685. [PMID: 36601381 PMCID: PMC9806141 DOI: 10.3389/fninf.2022.1078685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Although tuberculous pleural effusion (TBPE) is simply an inflammatory response of the pleura caused by tuberculosis infection, it can lead to pleural adhesions and cause sequelae of pleural thickening, which may severely affect the mobility of the chest cavity. Methods In this study, we propose bGACO-SVM, a model with good diagnostic power, for the adjunctive diagnosis of TBPE. The model is based on an enhanced continuous ant colony optimization (ACOR) with grade-based search technique (GACO) and support vector machine (SVM) for wrapped feature selection. In GACO, grade-based search greatly improves the convergence performance of the algorithm and the ability to avoid getting trapped in local optimization, which improves the classification capability of bGACO-SVM. Results To test the performance of GACO, this work conducts comparative experiments between GACO and nine basic algorithms and nine state-of-the-art variants as well. Although the proposed GACO does not offer much advantage in terms of time complexity, the experimental results strongly demonstrate the core advantages of GACO. The accuracy of bGACO-predictive SVM was evaluated using existing datasets from the UCI and TBPE datasets. Discussion In the TBPE dataset trial, 147 TBPE patients were evaluated using the created bGACO-SVM model, showing that the bGACO-SVM method is an effective technique for accurately predicting TBPE.
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Affiliation(s)
- Chengye Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lingxian Hou
- Department of Rehabilitation, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, China
| | - Jingye Pan
- Key Laboratory of Intelligent Treatment and Life Support for Critical Diseases of Zhejiang Province, Wenzhou, Zhejiang, China,Collaborative Innovation Center for Intelligence Medical Education, Wenzhou, Zhejiang, China,Zhejiang Engineering Research Center for Hospital Emergency and Process Digitization, Wenzhou, Zhejiang, China,Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huiling Chen
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, Zhejiang, China,*Correspondence: Huiling Chen,
| | - Xueding Cai
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China,Xueding Cai,
| | - Guoxi Liang
- Department of Information Technology, Wenzhou Polytechnic, Wenzhou, China
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12
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Su H, Han Z, Fu Y, Zhao D, Yu F, Heidari AA, Zhang Y, Shou Y, Wu P, Chen H, Chen Y. Detection of pulmonary embolism severity using clinical characteristics, hematological indices, and machine learning techniques. Front Neuroinform 2022; 16:1029690. [PMID: 36590906 PMCID: PMC9800512 DOI: 10.3389/fninf.2022.1029690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Pulmonary embolism (PE) is a cardiopulmonary condition that can be fatal. PE can lead to sudden cardiovascular collapse and is potentially life-threatening, necessitating risk classification to modify therapy following the diagnosis of PE. We collected clinical characteristics, routine blood data, and arterial blood gas analysis data from all 139 patients. Methods Combining these data, this paper proposes a PE risk stratified prediction framework based on machine learning technology. An improved algorithm is proposed by adding sobol sequence and black hole mechanism to the cuckoo search algorithm (CS), called SBCS. Based on the coupling of the enhanced algorithm and the kernel extreme learning machine (KELM), a prediction framework is also proposed. Results To confirm the overall performance of SBCS, we run benchmark function experiments in this work. The results demonstrate that SBCS has great convergence accuracy and speed. Then, tests based on seven open data sets are carried out in this study to verify the performance of SBCS on the feature selection problem. To further demonstrate the usefulness and applicability of the SBCS-KELM framework, this paper conducts aided diagnosis experiments on PE data collected from the hospital. Discussion The experiment findings show that the indicators chosen, such as syncope, systolic blood pressure (SBP), oxygen saturation (SaO2%), white blood cell (WBC), neutrophil percentage (NEUT%), and others, are crucial for the feature selection approach presented in this study to assess the severity of PE. The classification results reveal that the prediction model's accuracy is 99.26% and its sensitivity is 98.57%. It is expected to become a new and accurate method to distinguish the severity of PE.
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Affiliation(s)
- Hang Su
- College of Computer Science and Technology, Changchun Normal University, Changchun, Jilin, China
| | - Zhengyuan Han
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yujie Fu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dong Zhao
- College of Computer Science and Technology, Changchun Normal University, Changchun, Jilin, China,*Correspondence: Dong Zhao,
| | - Fanhua Yu
- College of Computer Science and Technology, Changchun Normal University, Changchun, Jilin, China
| | - Ali Asghar Heidari
- School of Surveying and Geospatial Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Yu Zhang
- College of Computer Science and Technology, Changchun Normal University, Changchun, Jilin, China
| | - Yeqi Shou
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Peiliang Wu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huiling Chen
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, Zhejiang, China,Huiling Chen,
| | - Yanfan Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China,Yanfan Chen,
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13
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Li Y, Zhao D, Liu G, Liu Y, Bano Y, Ibrohimov A, Chen H, Wu C, Chen X. Intradialytic hypotension prediction using covariance matrix-driven whale optimizer with orthogonal structure-assisted extreme learning machine. Front Neuroinform 2022; 16:956423. [PMID: 36387587 PMCID: PMC9659657 DOI: 10.3389/fninf.2022.956423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/28/2022] [Indexed: 09/19/2023] Open
Abstract
Intradialytic hypotension (IDH) is an adverse event occurred during hemodialysis (HD) sessions with high morbidity and mortality. The key to preventing IDH is predicting its pre-dialysis and administering a proper ultrafiltration prescription. For this purpose, this paper builds a prediction model (bCOWOA-KELM) to predict IDH using indices of blood routine tests. In the study, the orthogonal learning mechanism is applied to the first half of the WOA to improve the search speed and accuracy. The covariance matrix is applied to the second half of the WOA to enhance the ability to get out of local optimum and convergence accuracy. Combining the above two improvement methods, this paper proposes a novel improvement variant (COWOA) for the first time. More, the core of bCOWOA-KELM is that the binary COWOA is utilized to improve the performance of the KELM. In order to verify the comprehensive performance of the study, the paper sets four types of comparison experiments for COWOA based on 30 benchmark functions and a series of prediction experiments for bCOWOA-KELM based on six public datasets and the HD dataset. Finally, the results of the experiments are analyzed separately in this paper. The results of the comparison experiments prove fully that the COWOA is superior to other famous methods. More importantly, the bCOWOA performs better than its peers in feature selection and its accuracy is 92.41%. In addition, bCOWOA improves the accuracy by 0.32% over the second-ranked bSCA and by 3.63% over the worst-ranked bGWO. Therefore, the proposed model can be used for IDH prediction with future applications.
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Affiliation(s)
- Yupeng Li
- College of Computer Science and Technology, Changchun Normal University, Changchun, China
| | - Dong Zhao
- College of Computer Science and Technology, Changchun Normal University, Changchun, China
| | - Guangjie Liu
- College of Computer Science and Technology, Changchun Normal University, Changchun, China
| | - Yi Liu
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yasmeen Bano
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Alisherjon Ibrohimov
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huiling Chen
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, China
| | - Chengwen Wu
- College of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou, China
| | - Xumin Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou University, Wenzhou, China
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14
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Song T, Dai H, Wang S, Wang G, Zhang X, Zhang Y, Jiao L. TransCluster: A Cell-Type Identification Method for single-cell RNA-Seq data using deep learning based on transformer. Front Genet 2022; 13:1038919. [PMID: 36303549 PMCID: PMC9592860 DOI: 10.3389/fgene.2022.1038919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022] Open
Abstract
Recent advances in single-cell RNA sequencing (scRNA-seq) have accelerated the development of techniques to classify thousands of cells through transcriptome profiling. As more and more scRNA-seq data become available, supervised cell type classification methods using externally well-annotated source data become more popular than unsupervised clustering algorithms. However, accurate cellular annotation of single cell transcription data remains a significant challenge. Here, we propose a hybrid network structure called TransCluster, which uses linear discriminant analysis and a modified Transformer to enhance feature learning. It is a cell-type identification tool for single-cell transcriptomic maps. It shows high accuracy and robustness in many cell data sets of different human tissues. It is superior to other known methods in external test data set. To our knowledge, TransCluster is the first attempt to use Transformer for annotating cell types of scRNA-seq, which greatly improves the accuracy of cell-type identification.
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Affiliation(s)
- Tao Song
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
- Department of Artificial Intelligence, Faculty of Computer Science, Campus de Montegancedo, Polytechnical University of Madrid, Boadilla Del Monte, Madrid, Spain
- *Correspondence: Tao Song, ; Shuang Wang,
| | - Huanhuan Dai
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Shuang Wang
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
- *Correspondence: Tao Song, ; Shuang Wang,
| | - Gan Wang
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Xudong Zhang
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Ying Zhang
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Linfang Jiao
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
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15
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Qiu F, Zheng P, Heidari AA, Liang G, Chen H, Karim FK, Elmannai H, Lin H. Mutational Slime Mould Algorithm for Gene Selection. Biomedicines 2022; 10:2052. [PMID: 36009599 PMCID: PMC9406076 DOI: 10.3390/biomedicines10082052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 02/02/2023] Open
Abstract
A large volume of high-dimensional genetic data has been produced in modern medicine and biology fields. Data-driven decision-making is particularly crucial to clinical practice and relevant procedures. However, high-dimensional data in these fields increase the processing complexity and scale. Identifying representative genes and reducing the data's dimensions is often challenging. The purpose of gene selection is to eliminate irrelevant or redundant features to reduce the computational cost and improve classification accuracy. The wrapper gene selection model is based on a feature set, which can reduce the number of features and improve classification accuracy. This paper proposes a wrapper gene selection method based on the slime mould algorithm (SMA) to solve this problem. SMA is a new algorithm with a lot of application space in the feature selection field. This paper improves the original SMA by combining the Cauchy mutation mechanism with the crossover mutation strategy based on differential evolution (DE). Then, the transfer function converts the continuous optimizer into a binary version to solve the gene selection problem. Firstly, the continuous version of the method, ISMA, is tested on 33 classical continuous optimization problems. Then, the effect of the discrete version, or BISMA, was thoroughly studied by comparing it with other gene selection methods on 14 gene expression datasets. Experimental results show that the continuous version of the algorithm achieves an optimal balance between local exploitation and global search capabilities, and the discrete version of the algorithm has the highest accuracy when selecting the least number of genes.
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Affiliation(s)
- Feng Qiu
- Department of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
| | - Pan Zheng
- Information Systems, University of Canterbury, Christchurch 8014, New Zealand
| | - Ali Asghar Heidari
- Department of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
| | - Guoxi Liang
- Department of Information Technology, Wenzhou Polytechnic, Wenzhou 325035, China
| | - Huiling Chen
- Department of Computer Science and Artificial Intelligence, Wenzhou University, Wenzhou 325035, China
| | - Faten Khalid Karim
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hela Elmannai
- Department of Information Technology, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Haiping Lin
- Department of Information Engineering, Hangzhou Vocational & Technical College, Hangzhou 310018, China
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16
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Wong WK, Zhou J. Using CVX to construct optimal designs for biomedical studies with multiple objectives. J Comput Graph Stat 2022. [DOI: 10.1080/10618600.2022.2104858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Weng Kee Wong
- Department of Biostatistics, University of California, Los Angeles, CA 90095-1772, U.S.A.
| | - Julie Zhou
- Department of Mathematics and Statistics, University of Victoria, Victoria, BC, Canada V8W 2Y2
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17
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Liang J, Li ZW, Yue CT, Hu Z, Cheng H, Liu ZX, Guo WF. Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer. Brief Bioinform 2022; 23:6647504. [PMID: 35858208 DOI: 10.1093/bib/bbac254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 11/14/2022] Open
Abstract
Finding personalized biomarkers for disease prediction of patients with cancer remains a massive challenge in precision medicine. Most methods focus on one subnetwork or module as a network biomarker; however, this ignores the early warning capabilities of other modules with different configurations of biomarkers (i.e. multi-modal personalized biomarkers). Identifying such modules would not only predict disease but also provide effective therapeutic drug target information for individual patients. To solve this problem, we developed a novel model (denoted multi-modal personalized dynamic network biomarkers (MMPDNB)) based on a multi-modal optimization mechanism and personalized dynamic network biomarker (PDNB) theory, which can provide multiple modules of personalized biomarkers and unveil their multi-modal properties. Using the genomics data of patients with breast or lung cancer from The Cancer Genome Atlas database, we validated the effectiveness of the MMPDNB model. The experimental results showed that compared with other advanced methods, MMPDNB can more effectively predict the critical state with the highest early warning signal score during cancer development. Furthermore, MMPDNB more significantly identified PDNBs containing driver and biomarker genes specific to cancer tissues. More importantly, we validated the biological significance of multi-modal PDNBs, which could provide effective drug targets of individual patients as well as markers for predicting early warning signals of the critical disease state. In conclusion, multi-modal optimization is an effective method to identify PDNBs and offers a new perspective for understanding tumor heterogeneity in cancer precision medicine.
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Affiliation(s)
- Jing Liang
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zong-Wei Li
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Tong Yue
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhuo Hu
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Wei-Feng Guo
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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18
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Multilevel threshold image segmentation for COVID-19 chest radiography: A framework using horizontal and vertical multiverse optimization. Comput Biol Med 2022; 146:105618. [PMID: 35690477 PMCID: PMC9113963 DOI: 10.1016/j.compbiomed.2022.105618] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
Abstract
COVID-19 is currently raging worldwide, with more patients being diagnosed every day. It usually is diagnosed by examining pathological photographs of the patient's lungs. There is a lot of detailed and essential information on chest radiographs, but manual processing is not as efficient or accurate. As a result, how efficiently analyzing and processing chest radiography of COVID-19 patients is an important research direction to promote COVID-19 diagnosis. To improve the processing efficiency of COVID-19 chest films, a multilevel thresholding image segmentation (MTIS) method based on an enhanced multiverse optimizer (CCMVO) is proposed. CCMVO is improved from the original Multi-Verse Optimizer by introducing horizontal and vertical search mechanisms. It has a more assertive global search ability and can jump out of the local optimum in optimization. The CCMVO-based MTIS method can obtain higher quality segmentation results than HHO, SCA, and other forms and is less prone to stagnation during the segmentation process. To verify the performance of the proposed CCMVO algorithm, CCMVO is first compared with DE, MVO, and other algorithms by 30 benchmark functions; then, the proposed CCMVO is applied to image segmentation of COVID-19 chest radiography; finally, this paper verifies that the combination of MTIS and CCMVO is very successful with good segmentation results by using the Feature Similarity Index (FSIM), the Peak Signal to Noise Ratio (PSNR), and the Structural Similarity Index (SSIM). Therefore, this research can provide an effective segmentation method for a medical organization to process COVID-19 chest radiography and then help doctors diagnose coronavirus pneumonia (COVID-19).
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19
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Li X, Han P, Wang G, Chen W, Wang S, Song T. SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction. BMC Genomics 2022; 23:474. [PMID: 35761175 PMCID: PMC9235110 DOI: 10.1186/s12864-022-08687-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/10/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Protein-protein interactions (PPIs) dominate intracellular molecules to perform a series of tasks such as transcriptional regulation, information transduction, and drug signalling. The traditional wet experiment method to obtain PPIs information is costly and time-consuming. RESULT In this paper, SDNN-PPI, a PPI prediction method based on self-attention and deep learning is proposed. The method adopts amino acid composition (AAC), conjoint triad (CT), and auto covariance (AC) to extract global and local features of protein sequences, and leverages self-attention to enhance DNN feature extraction to more effectively accomplish the prediction of PPIs. In order to verify the generalization ability of SDNN-PPI, a 5-fold cross-validation on the intraspecific interactions dataset of Saccharomyces cerevisiae (core subset) and human is used to measure our model in which the accuracy reaches 95.48% and 98.94% respectively. The accuracy of 93.15% and 88.33% are obtained in the interspecific interactions dataset of human-Bacillus Anthracis and Human-Yersinia pestis, respectively. In the independent data set Caenorhabditis elegans, Escherichia coli, Homo sapiens, and Mus musculus, all prediction accuracy is 100%, which is higher than the previous PPIs prediction methods. To further evaluate the advantages and disadvantages of the model, the one-core and crossover network are conducted to predict PPIs, and the data show that the model correctly predicts the interaction pairs in the network. CONCLUSION In this paper, AAC, CT and AC methods are used to encode the sequence, and SDNN-PPI method is proposed to predict PPIs based on self-attention deep learning neural network. Satisfactory results are obtained on interspecific and intraspecific data sets, and good performance is also achieved in cross-species prediction. It can also correctly predict the protein interaction of cell and tumor information contained in one-core network and crossover network.The SDNN-PPI proposed in this paper not only explores the mechanism of protein-protein interaction, but also provides new ideas for drug design and disease prevention.
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Affiliation(s)
- Xue Li
- College of Computer Science and technology, China University of Petroleum (East China), Qingdao, China
| | - Peifu Han
- College of Computer Science and technology, China University of Petroleum (East China), Qingdao, China
| | - Gan Wang
- College of Computer Science and technology, China University of Petroleum (East China), Qingdao, China
| | - Wenqi Chen
- College of Computer Science and technology, China University of Petroleum (East China), Qingdao, China
| | - Shuang Wang
- College of Computer Science and technology, China University of Petroleum (East China), Qingdao, China
| | - Tao Song
- College of Computer Science and technology, China University of Petroleum (East China), Qingdao, China.
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20
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Boosted machine learning model for predicting intradialytic hypotension using serum biomarkers of nutrition. Comput Biol Med 2022; 147:105752. [DOI: 10.1016/j.compbiomed.2022.105752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/22/2022]
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21
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Tool for Predicting College Student Career Decisions: An Enhanced Support Vector Machine Framework. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The goal of this research is to offer an effective intelligent model for forecasting college students’ career decisions in order to give a useful reference for career decisions and policy formation by relevant departments. The suggested prediction model is mainly based on a support vector machine (SVM) that has been modified using an enhanced butterfly optimization approach with a communication mechanism and Gaussian bare-bones mechanism (CBBOA). To get a better set of parameters and feature subsets, first, we added a communication mechanism to BOA to improve its global search capability and balance exploration and exploitation trends. Then, Gaussian bare-bones was added to increase the population diversity of BOA and its ability to jump out of the local optimum. The optimal SVM model (CBBOA-SVM) was then developed to predict the career decisions of college students based on the obtained parameters and feature subsets that are already optimized by CBBOA. In order to verify the effectiveness of CBBOA, we compared it with some advanced algorithms on all benchmark functions of CEC2014. Simulation results demonstrated that the performance of CBBOA is indeed more comprehensive. Meanwhile, comparisons between CBBOA-SVM and other machine learning approaches for career decision prediction were carried out, and the findings demonstrate that the provided CBBOA-SVM has better classification and more stable performance. As a result, it is plausible to conclude that the CBBOA-SVM is capable of being an effective tool for predicting college student career decisions.
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22
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An efficient rotational direction heap-based optimization with orthogonal structure for medical diagnosis. Comput Biol Med 2022; 146:105563. [PMID: 35551010 DOI: 10.1016/j.compbiomed.2022.105563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/24/2022] [Accepted: 04/24/2022] [Indexed: 12/17/2022]
Abstract
The heap-based optimizer (HBO) is an optimization method proposed in recent years that may face local stagnation problems and show slow convergence speed due to the lack of detailed analysis of optimal solutions and a comprehensive search. Therefore, to mitigate these drawbacks and strengthen the performance of the algorithm in the field of medical diagnosis, a new MGOHBO method is proposed by introducing the modified Rosenbrock's rotational direction method (MRM), an operator from the grey wolf optimizer (GWM), and an orthogonal learning strategy (OL). The MGOHBO is compared with eleven famous and improved optimizers on IEEE CEC 2017. The results on benchmark functions indicate that the boosted MGOHBO has several significant advantages in terms of convergence accuracy and speed of the process. Additionally, this article analyzed the diversity and balance of MGOHBO in detail. Finally, the proposed MGOHBO algorithm is utilized to optimize the kernel extreme learning machines (KELM), and a new MGOHBO-KELM is proposed. To validate the performance of MGOHBO-KELM, seven disease diagnostic questions were introduced for testing in this work. In contrast to advanced models such as HBO-KELM and BP, it can be concluded that the MGOHBO-KELM model can achieve optimal results, which also proves that it has practical significance in solving medical diagnosis problems.
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23
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Yang X, Zhao D, Yu F, Heidari AA, Bano Y, Ibrohimov A, Liu Y, Cai Z, Chen H, Chen X. An optimized machine learning framework for predicting intradialytic hypotension using indexes of chronic kidney disease-mineral and bone disorders. Comput Biol Med 2022; 145:105510. [DOI: 10.1016/j.compbiomed.2022.105510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/03/2022]
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