哈斯矩阵图的G-蛋白偶联受体类型预测

利用氨基酸数字编码模型,将蛋白质序列转换为数字序列,根据偏序理论构建蛋白质哈斯矩阵。基于同一类型蛋白质哈斯矩阵图 具有相似图像纹理的假设,运用图像处理方法提取图像的几何矩作为伪氨基酸成分,对G-蛋白偶联受体类型分为2层进行预测,预测成功率分别为92.33%和85.48%。预测效果表明该方法是可行的。     

非负矩阵分解算法及其在生物信息学中的应用研究

非负矩阵分解是近年来快速发展的一类机器学习算法,能够实现对高维数据的维度规约及局部特征提取,在诸多生物信息问题的分析与处理中得到了广泛应用,并衍生出一系列实用算法。本文系统分析了非负矩阵分解的数学理论基础及其特有的局部表达属性,综述了标准非负矩阵分解与各种衍生算法的发展历程及算法初始化与参数选取方法的研究进展,并从序列特征分析、表达模式与功能模块识别、生物医学文献挖掘等几个方面总结了非负矩阵分解算法在生物信息学领域的应用成果。最后,指出了非负矩阵分解算法研究及其应用于生物信息处理所面临的问题,分析和预测了可能的发展方向。     

结合位点进化距离与支持向量机的蛋白质分类方法

生物信息学的一个关键的研究课题是理解细胞的分子机制,这依赖于对基因所决定的每一条蛋白质的含义或者功能的理解.一般通过与一条或多条功能已知的蛋白质的相似性比较来推测未知蛋白质的功能,其中,基于支持向量机的一些算法取得了很好的成果.SVM-pairwise算法是当前最好的基于支持向量机的算法中的一个,该方法利用两条序列的相似性来将蛋白质序列转化为固定长度的向量.文中提出了一种新的利用支持向量机算法对蛋白质序列进行分类的方法,这种方法使用位点进化距离代替两条序列的比对得分,该方法比SVM-pairwise有着显著的改善,在蛋白质结构分类数据库(SCOP)上进行的实验表明,该方法具有比SVM-pairwise更好的分类性能.     

基于改进Multi-Agent系统的基因表达数据的分析与研究

通过介绍改进的多代理系统在分析基因表达数据中的应用,揭示了运用普通分类器找出有效的分类基因,而且这些普通分类器在研究基因表达数据库时可被代理使用.这样就可得到一个具有大量基因特征的小子集,并且用它可以帮助辨认病人的临床状况和特征.实验表明代理通过改进和相互协作可改进其性能,并通过两个著名的基因表达问题来展示项目的研究成果,而且使得量度的准确性在维数增加时变得不很敏感.     

SORTAL ANAPHORA RESOLUTION IN MEDLINE ABSTRACTS

This paper reports our investigation of machine learning methods applied to anaphora resolution for biology texts, particularly paper abstracts. Our primary concern is the investigation of features and their combinations for effective anaphora resolution. In this paper, we focus on the resolution of demonstrative phrases and definite determiner phrases, the two most prevalent forms of anaphoric expressions that we find in biology research articles. Different resolution models are developed for demonstrative and definite determiner phrases. Our work shows that models may be optimized differently for each of the phrase types. Also, because a significant number of definite determiner phrases are not anaphoric, we induce a model to detect anaphoricity, i.e., a model that classifies phrases as either anaphoric or nonanaphoric. We propose several novel features that we call highlighting features , and consider their utility particularly for processing paper abstracts. The system using the highlighting features achieved accuracies of 78% and 71% for demonstrative phrases and definite determiner phrases, respectively. The use of the highlighting features reduced the error rate by about 10%.     

微生物亚油酸异构酶的生物信息学分析

运用生物信息学方法,对已在GenBank上公开发表的罗伊氏乳杆菌、疮疱丙酸杆菌、嗜酸乳杆菌、植物乳杆菌和短双岐杆菌等的亚油酸异构酶基因序列进行了分析,并对这些基因序列编码的蛋白质进行了预测.     

PSICO: Solving Protein Structures with Constraint Programming and Optimization

In this paper we propose PSICO (Processing Structural Information with Constraint programming and Optimisation) as a constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA (Dynamics algorithm for NMR applications) an existing commercial application based on simulated annealing. On a test case with experimental data on the dimeric protein Desulforedoxin, the method proposed here supplied similar results in less than 10 minutes compared to approximately 10 hours of computation time for DYANA. Although the quality of results can still be improved, this shows that CP technology can greatly reduce computation time, a major advantage because structural NMR technique generally demands multiple runs of structural computation.     

Colour size illusion on liquid crystal displays and design guidelines for bioinformatics tools

Although the influence of colour on size perception has been known for a century, there is only limited research on interventions that can reduce this effect. This study was therefore undertaken in order to identify appropriate interventions and propose design guidelines for information visualisation, especially in applications where size judgement is critical. The colour size illusion was replicated on an LCD monitor, revealing that yellow images appeared the smallest among a series of red, yellow, green and blue images on a white background. Three types of interventions (background brightness, border colour and background grid brightness) were tested to identify conditions that reduce the colour illusions, but none proved to be statistically significant. Based on these experimental results and an extensive literature survey, a set of design guidelines is proposed to enhance the usability of LCD monitors and a set of design recommendations given to extend these guidelines to applications in the field of bioinformatics. These design recommendations are accompanied by an evaluation of effectiveness obtained by interviewing domain experts.