Tian Bai

An improved k-prototypes clustering algorithm for mixed numeric and categorical data

Abstract Data objects with mixed numeric and categorical attributes are commonly encountered in real world. The k-prototypes algorithm is one of the principal algorithms for clustering this type of data objects. In this paper, we propose an improved k-prototypes algorithm to cluster mixed data. In our method, we first introduce the concept of the distribution centroid for representing the prototype of categorical attributes in a cluster. Then we combine both mean with distribution centroid to represent the prototype of the cluster with mixed attributes, and thus propose a new measure to calculate the dissimilarity between data objects and prototypes of clusters. This measure takes into account the significance of different attributes towards the clustering process. Finally, we present our algorithm for clustering mixed data, and the performance of our method is demonstrated by a series of experiments on four real-world datasets in comparison with that of traditional clustering algorithms.

CDBIA: A dynamic community detection method based on incremental analysis

Most existing community detection methods ignored the dynamic nature, a key property of social networks and these methods often lead to unreasonable divisions when faced with dynamic environments. Although there have been several dynamic community detection algorithms, low accuracy and low performing are still two challenging problems to be solved. In order to solve above problems, we proposed a new algorithm based on incremental analysis to mine communities in dynamic social networks. Extensive experimental results demonstrate the performance of our propose algorithm.

A new Community Detection algorithm based on Distance Centrality

Community detection is important for many complex network applications. A major challenge lies in that the number of communities in a given social network is usually unknown. This paper presents a new community detection algorithm-Distance Centrality based Community Detection (DCCD). The proposed method is capable of detecting the community of network without a preset community number. The method has two components. First we choose the initial center nodes by calculating the centrality of each node using their distance information. Then we measure the similarity between the center nodes and each other nodes in the network, and assign each node to the most similar community. We demonstrate that the proposed distance centrality based community detection algorithm terminated on a good community number, and also has comparable detection accuracy with other existing approaches.

An improved fruit fly optimization algorithm for solving traveling salesman problem

The traveling salesman problem (TSP), a typical non-deterministic polynomial (NP) hard problem, has been used in many engineering applications. As a new swarm-intelligence optimization algorithm, the fruit fly optimization algorithm (FOA) is used to solve TSP, since it has the advantages of being easy to understand and having a simple implementation. However, it has problems, including a slow convergence rate for the algorithm, easily falling into the local optimum, and an insufficient optimi-zation precision. To address TSP effectively, three improvements are proposed in this paper to improve FOA. First, the vision search process is reinforced in the foraging behavior of fruit flies to improve the convergence rate of FOA. Second, an elimination mechanism is added to FOA to increase the diversity. Third, a reverse operator and a multiplication operator are proposed. They are performed on the solution sequence in the fruit fly’s smell search and vision search processes, respectively. In the experiment, 10 benchmarks selected from TSPLIB are tested. The results show that the improved FOA outperforms other alternatives in terms of the convergence rate and precision.

MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization

BackgroundPrioritizing genes according to their associations with a cancer allows researchers to explore genes in more informed ways. By far, Gene-centric or network-centric gene prioritization methods are predominated. Genes and their protein products carry out cellular processes in the context of functional modules. Dysfunctional gene modules have been previously reported to have associations with cancer. However, gene module information has seldom been considered in cancer-related gene prioritization.ResultsIn this study, we propose a novel method, MGOGP (Module and Gene Ontology-based Gene Prioritization), for cancer-related gene prioritization. Different from other methods, MGOGP ranks genes considering information of both individual genes and their affiliated modules, and utilize Gene Ontology (GO) based fuzzy measure value as well as known cancer-related genes as heuristics. The performance of the proposed method is comprehensively validated by using both breast cancer and prostate cancer datasets, and by comparison with other methods. Results show that MGOGP outperforms other methods, and successfully prioritizes more genes with literature confirmed evidence.ConclusionsThis work will aid researchers in the understanding of the genetic architecture of complex diseases, and improve the accuracy of diagnosis and the effectiveness of therapy.

Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method

The number of gene-related databases has been growing largely along with the research on genes of bioinformatics. Those databases are filled with various gene functions, pathways, interactions, and so forth, while much biomedical knowledge about human diseases is stored as text in all kinds of literatures. Researchers have developed many methods to extract structured biomedical knowledge. Some study and improve text mining algorithms to achieve efficiency in order to cover as many data sources as possible, while some build open source database to accept individual submissions in order to achieve accuracy. This paper combines both efforts and biomedical ontologies to build an interaction network of multiple biomedical ontologies, which guarantees its robustness as well as its wide coverage of biomedical publications. Upon the network, we accomplish an algorithm which discovers paths between concept pairs and shows potential relations.

Implicit knowledge discovery in biomedical ontologies: Computing interesting relatednesses

Ontologies, seen as effective representations for sharing and reusing knowledge, have become increasingly important in biomedicine, usually focusing on taxonomic knowledge specific to a subject. Efforts have been made to uncover implicit knowledge within large biomedical ontologies by exploring semantic similarity and relatedness between concepts. However, much less attention has been paid to another potentially helpful approach: discovering implicit knowledge across multiple ontologies of different types, such as disease ontologies, symptom ontologies, and gene ontologies. In this paper, we propose a unified approach to the problem of ontology based implicit knowledge discovery - a Multi-Ontology Relatedness Model (MORM), which includes the formation of multiple related ontologies, a relatedness network and a formal inference mechanism based on set-theoretic operations. Experiments for biomedical applications have been carried out, and preliminary results show the potential value of the proposed approach for biomedical knowledge discovery.