Finding finer functions for partially characterized proteins by protein-protein interaction networks

Based on high-throughput data, numerous algorithms have been designed to find functions of novel proteins. However, the effectiveness of such algorithms is currently limited by some fundamental factors, including (1) the low a-priori probability of novel proteins participating in a detailed function; (2) the huge false data present in high-throughput datasets; (3) the incomplete data coverage of functional classes; (4) the abundant but heterogeneous negative samples for training the algorithms; and (5) the lack of detailed functional knowledge for training algorithms. Here, for partially characterized proteins, we suggest an approach to finding their finer functions based on protein interaction sub-networks or gene expression patterns, defined in function-specific subspaces. The proposed approach can lessen the above-mentioned problems by properly defining the prediction range and functionally filtering the noisy data, and thus can efficiently find proteins’ novel functions. For thousands of yeast and human proteins partially characterized, it is able to reliably find their finer functions (e.g., the translational functions) with more than 90% precision. The predicted finer functions are highly valuable both for guiding the follow-up wet-lab validation and for providing the necessary data for training algorithms to learn other proteins.     

基于Gene Ontology的表达谱与基因功能相似性的相关性研究

聚类是芯片数据分析中被广泛使用的方法。未知基因的功能通常通过其与已知基因在不同生物状态下具有表达相似性来进行预测。然而，还未有人就这种通过表达相似性来进行功能注释的方法的可靠性进行评估。本文利用Gene Ontology对表达相似性和基因功能相似性的相关关系进行了全面的研究。研究表明，尽管表达谱的相似性和基因功能相似性之间有一定的依赖关系，但相关性较弱。在Gene Ontology的三大类中，相对生物过程和分子功能，基因表达谱的相似性更有助于细胞组分的注释。本文的研究结果对于基因功能的预测有一定的指导意义。     

非乌托邦社会里生态乌托邦的实现——评加里·斯奈德《返乡栖居》

在一个以科技活动为主的"非乌托邦"社会里,人类自身以及与自然之间的关系均已陷入了困境,面对这样的世界黑夜,人类通过努力寻求摆脱危机的方式,以求实现一个美好的"生态乌托邦"社会。在种种方式中,"诗意的栖居"不乏是一种简便易行、行之有效的方式。当今美国深度生态学桂冠诗人加里·斯奈德不仅躬行"诗意的栖居",而且不断地参与创作,从理论高度上阐发了"诗意的栖居"。其散文《返乡栖居》扼述了作者随"返乡运动"回归到家乡后的所见所感,凸显了"地方感",感触了"返本归源"时的真正"归家",凸显了包括生态联系观、生态整体观和生态多样性在内的生态中心主义,饱含着生态本体论和生态存在论的思想理念,昭告人们在"非乌托邦"的社会里也有"诗意的栖居"。     

Subsumption Checking between Concept Queries in Different Ontologies Based on Mutual Instances

This paper proposes a checking method based on mutual instances and discusses three key problems in the method： how to deal with mistakes in the mutual instances and how to deal with too many or too few mutual instances. It provides the checking based on the weighted mutual instances considering fault tolerance, gives a way to partition the large-scale mutual instances, and proposes a process greatly reducing the manual annotation work to get more mutual instances. Intension annotation that improves the checking method is also discussed. The method is practical and effective to check subsumption relations between concept queries in different ontologies based on mutual instances.     

Incorporating Domain Knowledge into Data Mining Process： An Ontology Based Framework

0 IntroductionTeosda,yth meyan hya voerg daantiazbaatisoenss t hhaatv ec hmaonrgee t ahnadn glarrogwe cdoatnatibnaus--ously. One of the i mportant research issues is incrementalmining. Otherwise, various researchers have made sugges-tions that domain knowledge should be incorporated intoknowledge discovery ( KDD) process[1]. We focus on somesteps of the KDDprocess-those steps tying up with data min-ing,called a data mining (DM) process .Agrawalet al[2]showed an active data mining process ,…     

Query through heterogeneous ontologies using association matrix

This paper introduces the definition and calculation of the association matrix between ontologies, h uses the association matrix to describe the relations between concepls ill different ontologics and uses concept vectors to represent queries; then computes the vectors with the association matrix in order to rewrite queries, This paper proposes a simple method of querying through heterogeneous Ontology using association matrix. This method is based on the correctness of approximate information filtering theory; and it is simple to be implemented and expected to run quite fast.     

Integrated semantic similarity model based on ontology

To solve the problem of the inadequacy of semantic processing in the intelligent question answering system. an integrated semantic similarity model which calculates the semantic similarity using the geometric distance and informarion content is presented in this paper. With the help of interrelationship between concepts, the information content ofconcepts and the strength of the edges in the ontology network. we can calculate the semantic similarity between two concepts and provide information for the further calculation of the semantic similarity between user‘s question and answers in knowlegdge base. The results of the experiments on the prototype have shown that the semantic problem in natural language processing can also be solved with the help of the knowledge and the abundant semantic information in ontology. More than 90% accuracy with less than 50 ms average searching time in the intelligent question answering prototype system based on ontology has been reached. The result is vety satisfied.     

教育本质：知识论的困惑与存在论的彰显－兼论教育本质探讨思路的转向

教育本质的论争之所以陷入“疑无路”的境地,根本在于论争只是囿于探究知识论的“教育是什么”而遗忘了追寻存在论的“怎样教育”这一教育之“根”与“本”,以致教育之本质与语言遭际异化。缘此,本文拟在反思以往教育本质论争的基础上,试图走向“怎样教育”,以期扬弃异化,返朴归真。     

“实事求是”命题的存在论意义——依据马克思“实践主义”哲学的思考

过去对“实事求是”的解说 ,都仅仅是从认识论层面理解的 ,缺乏存在论的高度。如果说“实践”是马克思存在论的初始范畴 ,那么“实事求是” ,作为对实践范畴的中国式表述 ,也是人自身的存在论事实。“实事”并不是外在于人的存在的 ,而是人的存在本身 ;因而“是”也并不是那种与人无关的所谓“客观规律” ,而是关于人自己的存在的真理 ;“求”作为对这种存在论真理的追求 ,本身也属于人自己的一种存在论事实