Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.最新文献

Empirical evaluation of ensemble feature subset selection methods for learning from a high-dimensional database in drug design 针对药物设计中高维数据库学习的集成特征子集选择方法的实证评价

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188959

Hiroshi Mamitsuka

{"title":"Empirical evaluation of ensemble feature subset selection methods for learning from a high-dimensional database in drug design","authors":"Hiroshi Mamitsuka","doi":"10.1109/BIBE.2003.1188959","DOIUrl":"https://doi.org/10.1109/BIBE.2003.1188959","url":null,"abstract":"Discovering a new drug is one of the most important goals in not only the pharmaceutical field but also a variety of fields including molecular biology, chemistry and medical science. The importance of computationally understanding the relationships between a given chemical compound and its drug activity has been pronounced. In the data set regarding drug activity of chemical compounds, each row corresponds to a chemical compound, and columns are the descriptors of the compound and a label indicating drug activity of the compound Recently, the size of the descriptors has become larger to obtain more detailed information from a given set of compounds. Actually, the number of columns (attributes or features) of some drug data sets reaches hundreds of thousands or a million. The purpose of this paper is to empirically evaluate the performance of ensemble feature subset selection strategies by applying them to such a high-dimensional data set actually used in the process of drug design. We examined the performance of three ensemble methods, including a query learning based method, comparing with that of one of the latest feature subset selection methods. The evaluation was performed on a data set which contains approximately 140,000 features. Our results show that the query learning based methodology outperformed the other three methods, in terms of the final prediction accuracy and time efficiency. We have also examined the effect of noise in the data and found that the advantage of the method becomes more pronounced for larger noise levels.","PeriodicalId":178814,"journal":{"name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","volume":"69 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121138595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Automatic detection of premature ventricular contraction using quantum neural networks 利用量子神经网络自动检测室性早缩

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188943

Jie Zhou

引用次数: 39

Analysis of Atlantic salmon skin mucus: COPS-a computer-based system for protein pattern analysis of 1D SDS-PAGE gels 大西洋鲑鱼皮肤粘液的分析:cops -一种基于计算机的1D SDS-PAGE凝胶蛋白质模式分析系统

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188928

Richard Eibrand, P. Kennedy, D. Cotter, U. MacEvilly, Bing Wu

引用次数: 8

A model of random sequences for de novo peptide sequencing 一种用于从头肽测序的随机序列模型

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188948

K. Jarman, W. Cannon, Kristin H. Jarman, A. Heredia-Langner

引用次数: 8

A biological mapping of a learned avoidance behavior model to the basal ganglia 学习回避行为模型到基底神经节的生物学映射

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188963

K. Biddell, Jinghong Li, Jeffrey D. Johnson

引用次数: 0

GenoMosaic: on-demand multiple genome comparison and comparative annotation 基因组:按需多基因组比较和比较注释

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188942

C. Gibas, D. Sturgill, J. Weller

{"title":"GenoMosaic: on-demand multiple genome comparison and comparative annotation","authors":"C. Gibas, D. Sturgill, J. Weller","doi":"10.1109/BIBE.2003.1188942","DOIUrl":"https://doi.org/10.1109/BIBE.2003.1188942","url":null,"abstract":"GenoMosaic is a portable database application for on demand multiple genome comparison. We discuss the methods used to generate a GenoMosaic data set from genome sequence data, and present the relational data model used in the application. We define an abstraction of genome sequence data (the feature mosaic) that allows us to bridge between annotation that describes features within single genes and that which includes possibly multiple genes and intergenic features over long stretches of genomic sequence. The goal of this project is to support new method development for on-demand multiple genome comparison. Each genome to be compared can be modeled as a string of generic features of any type that can be computationally defined, related by adjacency information within and among genomes. The generic feature abstraction makes it possible to study the arrangement of features in the genome at a level of detail which includes RNA genes, putative regulatory regions, SNPs, overlapping transcripts, intron splice junctions, alternative polyadenylation signals-in short, to incorporate significant sequence details which are not necessarily within protein-coding regions. This abstraction is amenable to functional implementation as a relational data model upon which novel query capabilities can be built, and provides objects that can be analyzed using algorithms for comparison of strings and lists. As an initial effort, we have implemented a prototype using a representative set of comparative and content-based annotation methods to reduce a collection of prokaryotic genomes to a feature mosaic representation. Entity-Relationship modeling was then used to develop a data model capable of storing detailed results, including complete parameters for each instance of analysis.","PeriodicalId":178814,"journal":{"name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","volume":"240 ","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"113996544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Augmenting SSEs with structural properties for rapid protein structure comparison 利用结构特性扩增sse，快速比较蛋白质结构

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188972

C. Chionh, Zhiyong Huang, K. Tan, Zhen Yao

{"title":"Augmenting SSEs with structural properties for rapid protein structure comparison","authors":"C. Chionh, Zhiyong Huang, K. Tan, Zhen Yao","doi":"10.1109/BIBE.2003.1188972","DOIUrl":"https://doi.org/10.1109/BIBE.2003.1188972","url":null,"abstract":"Comparing protein structures in three dimensions is a computationally expensive process that makes a full scan of a protein against a library of known protein structures impractical. To reduce the cost, we can use an approximation of the three dimensional structure that allows protein comparison to be performed quickly to filter away dissimilar proteins. In this paper we present a new algorithm, called SCALE, for protein structure comparison. In SCALE, a protein is represented as a sequence of secondary structure elements (SSEs) augmented with 3D structural properties such as the distances and angles between the SSEs. As such, the comparison between two proteins is reduced to a sequence alignment problem between their corresponding sequences of SSEs. The 3-D structural properties of the proteins contribute to the similarity score between the two sequences. We have implemented SCALE, and compared its performance against existing schemes. Our performance study shows that SCALE outperforms existing methods in terms of both efficiency and effectiveness (measured in terms of precision and recall).","PeriodicalId":178814,"journal":{"name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134298418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22

Streamlining biological data analysis using BioFlow 使用BioFlow简化生物数据分析

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188960

Zhijie Guan, H. Jamil

{"title":"Streamlining biological data analysis using BioFlow","authors":"Zhijie Guan, H. Jamil","doi":"10.1109/BIBE.2003.1188960","DOIUrl":"https://doi.org/10.1109/BIBE.2003.1188960","url":null,"abstract":"For several obvious and practical reasons, resources needed for biological data analysis are often geographically distributed and are accessible through the Internet. Such resources usually include data repositories, analysis tools, digital documents, and so on. Such an arrangement warrants sophisticated data and process integration tools in order to design ad hoc higher level applications using these online resources. In this paper we present such a system, called the BioFlow, that exploits recent advances in workflow technology and Internet computing in order to provide support for ad hoc application development by hiding aspects related to the heterogeneity and distributive nature of the resources required by user applications. We introduce the salient features of the BioFlow system, discuss briefly its architecture and implementation issues using simple but real life applications. We demonstrate that the declarative language on which BioFlow is based makes our system quite intuitive, easy to use, effective and efficient for ad hoc application design. The approach taken in BioFlow is somewhat similar to the idea of web services in semantic web computing for biological applications.","PeriodicalId":178814,"journal":{"name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124449232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Combining few neural networks for effective secondary structure prediction 结合几种神经网络进行有效的二次结构预测

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188981

K. Guimaraes, J. Melo, George D. C. Cavalcanti

引用次数: 7

A framework for cancer-related genes mining over the Internet 互联网上癌症相关基因挖掘的框架

Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings. Pub Date : 2003-03-10 DOI: 10.1109/BIBE.2003.1188983

J. Tsai, Jan-Gowth Chang, S. H. Shih, Rong-Ming Chen, H. Hsiao, Rouh-Mei Hu, S. N. Chen, M. M. Lee, Falcon F. M. Liu, Wen-Ling Chan

{"title":"A framework for cancer-related genes mining over the Internet","authors":"J. Tsai, Jan-Gowth Chang, S. H. Shih, Rong-Ming Chen, H. Hsiao, Rouh-Mei Hu, S. N. Chen, M. M. Lee, Falcon F. M. Liu, Wen-Ling Chan","doi":"10.1109/BIBE.2003.1188983","DOIUrl":"https://doi.org/10.1109/BIBE.2003.1188983","url":null,"abstract":"Clinically, cancer is a complex family of diseases. From the view of molecular biology, cancer is a genetic disease resulting from abnormal gene expression. This alternation of gene expression could be resulting from DNA instability, such as translocation, amplification, deletion or point mutations. A large amplification or deletion of a chromosome region can be easily detected by two methods: loss of heterozygosity (LOH) and comparative genomic hybridization (CGH). The different gene expression pattern can be monitored by high throughput microarray analysis. Enormous data accumulated by practicing these technologies and the data pool is continuing enlarging with an amazing rate. To aid investigators mining useful information in these data deposits, new data storing and analysis tools must be developed. Two value-added databases are constructed to achieve this purpose. They contain information of genes in the unstable regions of cancer cells basing on the data accumulated from LOH and CGH experiments and information of cancer cell gene expression profiles according to microarray analysis, respectively. An automatic system to retrieve interesting gene information, to compare with the known databases, to analyze and predict the protein functions, and to group the genes of the same function will be integrated into the database circuit. An automatic update system will be installed and performed after the setup of the two databases. The system keeps also the probability to modify and to accept new data obtained from any new techniques. Our goal is to help biologists to find the needles in a haystack that is, to find the real cancer-related genes (oncogenes or tumor suppressor genes) for further research purpose.","PeriodicalId":178814,"journal":{"name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128318015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2