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Metabolite-Disease Association Prediction Algorithm Combining DeepWalk and Random Forest

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Tsinghua Science and Technology 2022年第1期27卷 58-67页

作者： Jiaojiao Tie Xiujuan Lei yi pan the School of Computer Science Shaanxi Normal UniversityXi'an 710119China the the Department of Computer Science Georgia State UniversityAtlanta.GA 30302-3994USA

Identifying the association between metabolites and diseases will help us understand the pathogenesis of diseases,which has great significance in diagnosing and treating ***,traditional biometric methods are time consuming and ***,we propose a new metabolite-disease association prediction algorithm based on DeepWalk and random forest(DWRF),which consists of the following key steps:First,the semantic similarity and information entropy similarity of diseases are integrated as the final disease ***,molecular fingerprint similarity and information entropy similarity of metabolites are integrated as the final metabolite ***,DeepWalk is used to extract metabolite features based on the network of metabolite-gene ***,a random forest algorithm is employed to infer metabolite-disease *** experimental results show that DWRF has good performances in terms of the area under the curve value,leave-one-out cross-validation,and five-fold *** studies also indicate that DWRF has a reliable performance in metabolite-disease association prediction.

关键词： Deep Walk random forest metabolite-disease associations molecular fingerprint similarity of metabolites

Predicting Microbe-Disease Association Based on Heterogeneous Network and Global Graph Feature Learning

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Chinese Journal of Electronics 2022年第2期31卷 345-353页

作者： WANG Yueyue LEI Xiujuan pan yi School of Computer Science Shaanxi Normal University Department of Computer Science Georgia State University Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences

Numerous microbes inhabit human body,making a vast difference in human health. Hence, discovering associations between microbes and diseases is beneficial to disease prevention and treatment. In this study,we develop a prediction method by learning global graph feature on the heterogeneous network(called HNGFL).Firstly, a heterogeneous network is integrated by known microbe-disease associations and multiple *** on microbe Gaussian interaction profile(GIP) kernel similarity, we consider different effects of these microbes on organs in the human body to further improve microbe similarity. For disease similarity network, we combine GIP kernel similarity, disease semantic similarity and disease-symptom similarity. And then, an embedding algorithm called GraRep is used to learn global structural information for this network. According to vector feature of every node, we utilize support vector machine classifier to calculate the score for each microbe-disease pair. HNGFL achieves a reliable performance in cross validation, outperforming the compared methods. In addition, we carry out case studies of three diseases. Results show that HNGFL can be considered as a reliable method for microbe-disease association prediction.

关键词： microorganisms global graph feature learning support vector machines patient diagnosis global structural information disease semantic similarity disease-symptom similarity HNGFL pattern classification graph theory microbe Gaussian interaction profile kernel similarity bioinformatics support vector machine classifier GraRep diseases learning (artificial intelligence) microbe-disease association prediction heterogeneous network Gaussian processes GIP kernel similarity

Study on the in situ desulfurization and viscosity reduction of heavy oil over MoO_(3)–ZrO_(2)/HZSM-5 catalyst

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Petroleum Science 2023年第6期20卷 3887-3896页

作者： Rui-Qi Liu Li-Qiang Zhang Hui-Da pan yi-Ya Wang Jin-Yu Li xin-Wei Wang Zheng-Da Yang xin-Lu Han Ri-yi Lin College of New Energy Qingdao Engineering Research Center of Efficient and Clean Utilization of Fossil EnergyChina University of Petroleum(East China)Qingdao266580ShandongChina

Heavy oil is characterized by high *** viscosity makes it challenging to recover and ***-5,MoO_(3)/HZSM-5,ZrO_(2)/HZSM-5 and MoO_(3)–ZrO_(2)/HZSM-5 catalysts were developed to promote in situ desulfurization and viscosity reduction of heavy *** physical and chemical properties of catalysts were characterized by XPS,XRD,TEM,NH3-TPD,*** effects of temperature,catalyst type and addition amount on viscosity and composition of heavy oil were *** results showed that the presence of MoO_(3)–ZrO_(2)/HZSM-5 nanoparticles during aquathermolysis could improve the oil quality by reducing the heavy *** reduced viscosity by 82.56%after the reaction at 280℃ and catalyst addition of 1 wt%.The contents of resins and asphaltic in the oil samples were 5.69%lower than that in the crude *** content decreased from 1.45%to 1.03%.The concentration of H2S produced by the reaction was 2225 *** contents of sulfur-containing functional groups sulfoxide and sulfone sulfur in the oil samples decreased by 19.92%after the catalytic *** content of stable thiophene sulfur increased by 5.71%.This study provided a basis for understanding the mechanism of heavy oil desulfurization and viscosity reduction.

关键词： Heavy oil Hydrothermal cracking MoO_(3)-ZrO_(2)/HZSM-5 catalyst Desulfurization Viscosity reduction

A new mutation (1062 del 16) of iduronate-2-sulfatase gene from a Chinese patient with Hunter syndrome

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2007年第8期8卷 566-569页

作者： GUO yi-bin pan Jing-xin MENG Ya-xian Department of Medical Genetics Sun Yat-sen Medical College Sun Yat-sen University Guangzhou 510080 China Department of Internal Medicine the Second Affiliated Hospital Fujian University of Medical Science Quanzhou 362000 China

Objective: To identify the mutations of iduronate-2-sulfatase (IDS) gene, to reveal its mutation features, and to establish a basis for genetic counseling and prenatal gene diagnosis of Hunter syndrome. Methods: Urine glycosaminoglycans (GAGs) assay, PCR and DNA sequencing were performed to detect mutation of IDS gene of the patient and his parents. Results: The result showed that the patient was: DS(++), HS(++), KS(-), CS(-), and that both of his parents were negative. A frame-shift deletion mutation (1062 del 16) was identified in exon 7 of the patient's IDS gene. His parents' genotypes were normal. Conclusion:The patient's mutation was not inherited by his parents but a novel one. The mutation probably altered the primary structure and tertiary structure of IDS enzyme protein remarkably and lowered the activity of IDS enzyme greatly. Therefore it is supposed to be the direct cause of the disorder.

关键词： Hunter syndrome Mucopolysaccharidosis typeⅡ (MPSⅡ) Glycosaminoglycan (GAG) Iduronate-2-sulfatase (IDS) Mutation Gene diagnosis DNA sequencing

A survey on intelligence approaches that may be useful for information and communication technology research

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The Journal of China Universities of Posts and Telecommunications 2008年第1期15卷 1-5,17页

作者： ZHONG yi-xin School of Information Engineering Beijing University of Posts and Telecommunications Beijing 100876 China

The concepts on information and communication technology （ICT） and ＂intelligence＂ are defined firstly and the analyses on the environment and requirements for ICT are then followed. Based on the definitions and the analyses, a survey on intelligence approaches that may be useful for ICT is thus made. The conclusion drawn from the survey is a recommendation by saying that intelligence approaches have been one of the keys for further development of the entirety of ICT and therefore should receive much more attentions from ICT researchers in the years to come.

关键词： uncertainty complexity intelligence approaches,ICT

A new study on formation mechanism of ordered porous anodized metal oxides

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Rare Metals 2024年第10期43卷 5410-5418页

作者： Xi-Di Sun xin Guo Jia-Han Zhang Jing Wu yi Shi Hui-Yuan Sun Cao-Feng pan Li-Jia pan Collaborative Innovation Center of Advanced Microstructures School of Electronic Science and EngineeringNanjing UniversityNanjing 210093China College of Physics and Hebei Advanced Thin Film Laboratory Hebei Normal UniversityShijiazhuang 050024China Institute of Atomic Manufacturing Beihang UniversityBeijing 100191China

The preparation of ordered porous metal oxide films by anodic oxidation is an efficient and simple preparation ***,there has been no unified explanation about the formation mechanism of the porous structure for many *** this paper,the relationship between the crystal structure of metals and the morphology of ordered porous metal oxide films is *** influence of the crystal structures of different metals on the optimal morphology of porous films is discussed.

关键词： ordered mechanism metals

Guest Editorial: Special Issue on Bioinformatics and Computational Biology

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Tsinghua Science and Technology 2013年第5期18卷 429-430页

作者： yi pan Department of Computer Science Georgia State University

Bioinformatics and computational biology research is fundamental to our understanding of complex biological systems,impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical *** is one of the fastest developing research fields in the last two *** throughput biological data that are used to provide information at molecular and genetic level are rapidly *** all research problems in biological and medical sciences nowadays are computationally *** techniques

关键词： Cytoscape Guest Editorial Special Issue on Bioinformatics and Computational Biology

Application of Fusobacterium nucleatum as a biomarker in gastrointestinal malignancies

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2271-2283页

作者： Long-Chen Yu Ya-Ping Li Yue-Ming xin Mai Mao Ya-xin pan yi-Xuan Qu Zheng-Dong Luo yi Zhang xin Zhang Department of Clinical Laboratory Qilu Hospital of Shandong UniversityShandong Engineering Research Center of Biomarker and Artificial Intelligence ApplicationJinan 250012Shandong ProvinceChina

The morbidity and mortality of gastrointestinal(GI)malignancies are among the highest in the world,posing a serious threat to human *** of the insidious onset of the cancer,it is difficult for patients to be diagnosed at an early stage,and it rapidly progresses to an advanced stage,resulting in poor treatment and *** nucleatum(***)is a gram-negative,sporefree anaerobic bacterium that primarily colonizes the oral cavity and is implicated in the development of colorectal,esophageal,gastric,and pancreatic cancers via various intricate *** development in novel research suggests that *** may function as a biomarker in GI *** the abundance of *** in stool,saliva,and serum samples of patients may aid in the diagnosis,risk assessment,and prognosis monitoring of GI *** editorial systematically describes the biological roles and mechanisms of *** in GI malignancies focusing on the application of *** as a biomarker in the diagnosis and prognosis of GI malignancies to promote the clinical translation of *** and GI tumors-related research.

关键词： Gastrointestinal malignancies Fusobacterium nucleatum Biomarker Diagnosis Prognosis

Supnorm Estimates for ā on Product Domains in C^(n)

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Acta Mathematica Sinica,English Series 2024年第10期40卷 2307-2323页

作者： Martino FASSINA yi Fei pan Department of Mathematics University of Illinois at Urbana-Champaign1409 West Green StreetUrbanaIL 61801USA Department of Mathematical Sciences Purdue University Fort Wayne2101 East Coliseum BoulevardFort WayneIN 46805USA

Using methods from complex analysis in one variable,we define an integral operator that solves ā with supnorm estimates on product domains in C^(n).

关键词： Supnorm estimates product domains Cauchy Riemann equation