A protein complex is a group of associated polypeptide chains which plays essential roles in the biological process. Given a graph representing protein-protein interactions (PPI) network, it is critical but non-trivial to detect protein complexes, the subsets of proteins that are tightly coupled, from it. Network embedding is a technique to learn low-dimensional representations of vertices in networks. It has been proved quite useful for community detection in social networks in recent years. However, unlike social networks, PPI network does not contain rich metadata, so that existing network embedding methods cannot fully capture the network structure of PPI to improve the effect of protein complexes detection significantly. We propose a semi-supervised network embedding model by adopting graph convolutional networks to detect densely connected subgraphs effectively. We compare the performance of our model with state-of-the-art approaches on three popular PPI networks with various data sizes and densities. The experimental results show that our approach significantly outperforms other approaches on all three PPI networks.

Despite the vast amount of research related to Chinese typo detection, we still lack a publicly available benchmark dataset for evaluation. Furthermore, no precise evaluation schema for Chinese typo detection has been defined. In response to these problems: (1) we release a benchmark dataset to assist research on Chinese typo correction; (2) we present an evaluation schema which was adopted in our NLPTEA 2017 Shared Task on Chinese Spelling Check; and (3) we report new improvements to our Chinese typo detection system ACT.

Protein complex is a group of associated polypeptide chains which plays essential roles in biological process. Given a graph representing protein-protein interactions (PPI) network, it is critical but non-trivial to detect protein complexes.In this paper, we propose a semi-supervised network embedding model by adopting graph convolutional networks to effectively detect densely connected subgraphs. We conduct extensive experiment on two popular PPI networks with various data sizes and densities. The experimental results show our approach achieves state-of-the-art performance.

Cancer diseases are caused by combination of genetic, environmental, and lifestyle factors. Therefore, it is difficult for health organization to treat this disease. This study focuses on identifying the landscape of Cancer research by using bibliometric methods and social network analysis methods based on a number of research articles related to Cancer retrieved from PubMed. To deeply understand the landscape of research on this disease, we adopt productivity analysis which consists of author, university/institution, country and frequent MeSH terms analysis. We specifically perform the concept graph-based network analysis by applying four centrality measures and analyzing co-occurrence of MeSH terms. In the end, we propose a method to predict the Rising Star that may be the active researcher in the field of Cancer disease in the next few years. With this method, we can possibly find more academic cooperation via academic social networks. The encouraging results show that our work is highly feasible.

One of the fundamental questions is how we can enhance our relationships with the people in our social networks. The combination of frequent engagement, deep interaction, and time spent together are what constitute to build a stronger relationship. With this knowledge in mind, it is not surprising to see many scholars claim that social networking sites may help us to re-connect some lost relationships, but has limited ability to strengthen an existing relationship. Surprisingly, from a survey we conducted, we found that most people who use Facebook or scholat.com (a scholar-oriented social networking site) claim that their relationships with some of their friends are improved, even though they do not have any in-depth or personal conversation with them and they can understand their friends better even without any communication. It contradicts with what we have known. It seems that a relationship can be improved with Facebook or scholat.com alone. In this paper, we try to analyze this finding and explain it using communication model and visualized analysis. We conclude how communication model changes as time goes and how it re-defines the meaning of communication.

Given a data point set D, a query point set Q, and an integer k, the Group Nearest Group (GNG) query finds a subset ω (|ω| ≤ k)of points from Dsuch that the total distance from all points in Q to the nearest point in ω is not greater than any other subset ω' (|ω'| ≤ k) of points in D. GNG query is a partition-based clustering problem which can be found in many real applications and is NP-hard. In this paper, Exhaustive Hierarchical Combination (EHC) algorithm and Subset Hierarchial Refinement (SHR) algorithm are developed for GNG query processing. While EHC is capable to provide the optimal solution for k = 2, SHR is an efficient approximate approach that combines database techniques with local search heuristic. The processing focus of our approaches is on minimizing the access and evaluation of subsets of cardinality k in D since the number of such subsets is exponentially greater than |D|. To do that, the hierarchical blocks of data points at high level are used to find an intermediate solution and then refined by following the guided search direction at low level so as to prune irrelevant subsets. The comprehensive experiments on both real and synthetic data sets demonstrate the superiority of SHR in terms of efficiency and quality.

Given a set of lists, where items of each list are sorted by the ascending order of their values, the objective of this paper is to figure out the common items that appear in all of the lists efficiently. This problem is sometimes known as common items extraction from sorted lists. To solve this problem, one common approach is to scan all items of all lists sequentially in parallel until one of the lists is exhausted. However, we observe that if the overlap of items across all lists is not high, such sequential access approach can be significantly improved. In this paper, we propose two algorithms, MergeSkip and MergeESkip, to solve this problem by taking the idea of skipping as many items of lists as possible. As a result, a large number of comparisons among items can be saved, and hence the efficiency can be improved. We conduct extensive analysis of our proposed algorithms on one real dataset and two synthetic datasets with different data distributions. We report all our findings in this paper.

The K-Nearest Neighbor search (kNN) problem has been investigated extensively in the past due to its broad range of applications. In this paper we study this problem in the context of fuzzy objects that have indeterministic boundaries. Fuzzy objects play an important role in many areas, such as biomedical image databases and GIS. Existing research on fuzzy objects mainly focuses on modelling basic fuzzy object types and operations, leaving the processing of more advanced queries such as kNN query untouched. In this paper, we propose two new kinds of kNN queries for fuzzy objects, Ad-hoc kNN query (AKNN) and Range kNN query (RKNN), to find the k nearest objects qualifying at a probability threshold or within a probability range. For efficient AKNN query processing, we optimize the basic best-first search algorithm by deriving more accurate approximations for the distance function between fuzzy objects and the query object. To improve the performance of RKNN search, effective pruning rules are developed to significantly reduce the search space and further speed up the candidate refinement process. The efficiency of our proposed algorithms as well as the optimization techniques are verified with an extensive set of experiments using both synthetic and real datasets.

Entity resolution (ER) is a problem that arises in many areas. In most of cases, it represents a task that multiple entities from different sources require to be identified if they refer to the same or different objects because there are not unique identifiers associated with them. In this paper, we propose a model using web pages identification to identify entities and merge those entities refer to one object together. We use a classical name disambiguation problem as case study and examine our model on a subset of digital library records as the first stage of our work. The favorable results indicated that our proposed approach is highly effective. © 2010 Copyright is held by the author/owner(s).

Given a data point set D, a query point set Q and an integer k, the group nearest group (GNG) query finds a subset of points from D, omega (|omega| les k), such that the total distance from all points in Q to the nearest point in omega is no greater than any other subset of points in D, omega(|omega| les k). GNG query can be found in many real applications. In this paper, exhaustive hierarchical combination algorithm (EHC) and subset hierarchical refinement algorithm (SHR) are developed for GNG query processing. The superiority of SHR in terms of efficiency and quality compared to existing algorithms developed originally for data clustering is demonstrated.

In this paper, an algorithm called Time Driven Documents-partition (TDD) is proposed to construct an event hierarchy in a text corpus based on a given query. Specifically, assume that a query contains only one feature - Election. Election is directly related to the events such as 2006 US Midterm Elections Campaign, 2004 US Presidential Election Campaign and 2004 Taiwan Presidential Election Campaign, where these events may further be divided into several smaller events (e.g. the 2006 US Midterm Elections Campaign can be broken down into events such as campaign for vote, election results and the resignation of Donald H. Rumsfeld). As such, an event hierarchy is resulted. Our proposed algorithm, TDD, tackles the problem by three major steps: (1)Identify the features that are related to the query according to both the timestamps and the contents of the documents. The features identified are regarded as bursty features; (2) Extract the documents that are highly related to the bursty features based on time; (3) Partition the extracted documents to form events and organize them in a hierarchicalstructure. To the best of our knowledge, there is little works targeting for constructing a feature-based event hierarchy for a text corpus. Practically, event hierarchies can assist us to efficiently locate our target information in a text corpus easily. Again, assume that Election is used for a query. Without an event hierarchy, it is very difficult to identify what are the major events related to it, when do these events happened, as well as the features and the news articles that are related to each of these events. We have archived two-year news articles to evaluate the feasibility of TDD. The encouraging results indicated that TDD is practically sound and highly effective.

This paper studies the problem of constructing an effective heterogeneous ensemble classifier for text classification. One major challenge of this problem is to formulate a good combination function, which combines the decisions of the individual classifiers in the ensemble. We show that the classification performance is affected by three weight components and they should be included in deriving an effective combination function. They are: (1) Global effectiveness, which measures the effectiveness of a member classifier in classifying a set of unseen documents; (2) Local effectiveness, which measures the effectiveness of a member classifier in classifying the particular domain of an unseen document; and (3) Decision confidence, which describes how confident a classifier is when making a decision when classifying a specific unseen document. We propose a new balanced combination function, called Dynamic Classifier Weighting (DCW), that incorporates the afore-mentioned three components. The empirical study demonstrates that the new combination function is highly effective for text classification.

Traditionally, building a classifier requires two sets of examples: positive examples and negative examples. This paper studies the problem of building a text classifier using positive examples (P) and unlabeled examples (U). The unlabeled examples are mixed with both positive and negative examples. Since no negative example is given explicitly, the task of building a reliable text classifier becomes far more challenging. Simply treating all of the unlabeled examples as negative examples and building a classifier thereafter is undoubtedly a poor approach to tackling this problem. Generally speaking, most of the studies solved this problem by a two-step heuristic: first, extract negative examples (N) from U. Second, build a classifier based on P and N. Surprisingly, most studies did not try to extract positive examples from U. Intuitively, enlarging P by P' (positive examples extracted from U) and building a classifier thereafter should enhance the effectiveness of the classifier. Throughout our study, we find that extracting P' is very difficult. A document in U that possesses the features exhibited in P does not necessarily mean that it is a positive example, and vice versa. The very large size of and very high diversity in U also contribute to the difficulties of extracting P'. In this paper, we propose a labeling heuristic called PNLH to tackle this problem. PNLH aims at extracting high quality positive examples and negative examples from U and can be used on top of any existing classifiers. Extensive experiments based on several benchmarks are conducted. The results indicated that PNLH is highly feasible, especially in the situation where |P| is extremely small.

This paper presents a new solution for the problem of building a text classifier with a small yet of labeled positive documents (P) and a large set of unlabeled documents (U). Here, the unlabeled documents are mixed with both of the positive and negative documents. In other words, no document is labeled as negative. This makes the task of building a reliable text classifier challenging. In general, the existing approaches for solving this kind of problem use a two-step approach: i) extract the negative documents (N) from U; and ii) build a classifier based on P and N. However, none of the reported studies tries to further extract any positive documents (P') from U. Intuitively, extracting P' from U will increase the reliability of the classifier. However, extracting P' from U is difficult. A document in U that possesses some of the features exhibited in P does not necessarily mean that it is a positive document, and vice versa. It is very sensitive to extract positive documents, because those extracted positive samples may become noises. The very large size of U and the very high diversity exhibited there also contribute to the difficulty of extracting any positive documents. In this paper, we propose a partition-based heuristic which aims at extracting both of the positive and negative documents in U. Extensive experiments based on three benchmarks are conducted. The favorable results indicated that our proposed heuristic outperforms all of the existing approaches significantly, especially in the case where the size of P is extremely small.

Mining textual documents and time series concurrently, such as predicting the movements of stock prices based on news articles, is an emerging topic in data mining society nowadays. Previous research has already suggested that the relationship between news articles and stock prices do exist. However, all of the existing approaches are concerning in mining single time series only. The interrelationships among different stocks are not well-addressed. Mining multiple time series concurrently is not only more informative but also far more challenging. Research in such a direction is lacking. In this paper, we try to explore such an opportunity and propose a systematic framework for mining multiple time series based on Efficient Market Hypothesis.

With the rapid growth of textual information available on the Internet, having a good model for classifying and managing documents automatically is undoubtedly important. When more documents are archived, new terms, new concepts and concept-drift will frequently appear Without a doubt, updating the classification model frequently, rather than using the old model for a very long period is absolutely essential. Here, the challenges are: a) obtain a high accuracy classification model; b) consume low computational time for both model training and operation; and c) occupy low storage space. However, none of the existing classification approaches could achieve all of these requirements. In this paper, we propose a novel text classification approach, called discriminative category matching, which could achieve all of the stated characteristics. Extensive experiments using two benchmarks and a large real-life collection are conducted. The encouraging results indicated that our approach is highly feasible.