Tree comparison: enumeration and application to cheminformatics

Graphs are a well-known data structure used in many application domains that rely on relationships between individual entities. Examples are social networks, where the users may be in friendship with each other, road networks, where one-way or bidirectional roads connect crossings, and work package assignments, where workers are assigned to tasks. In chem- and bioinformatics, molecules are often represented as molecular graphs, where vertices represent atoms, and bonds between them are represented by edges connecting the vertices. Since there is an ever-increasing amount of data that can be treated as graphs, fast algorithms are needed to compare such graphs. A well-researched concept to compare two graphs is the maximum common subgraph. On the one hand, this allows finding substructures that are common to both input graphs. On the other hand, we can derive a similarity score from the maximum common subgraph. A practical application is rational drug design which involves molecular similarity searches. In this thesis, we study the maximum common subgraph problem, which entails finding a largest graph, which is isomorphic to subgraphs of two input graphs. We focus on restrictions that allow polynomial-time algorithms with a low exponent. An example is the maximum common subtree of two input trees. We succeed in improving the previously best-known time bound. Additionally, we provide a lower time bound under certain assumptions. We study a generalization of the maximum common subtree problem, the block-and-bridge preserving maximum common induced subgraph problem between outerplanar graphs. This problem is motivated by the application to cheminformatics. First, the vast majority of drugs modeled as molecular graphs is outerplanar, and second, the blocks correspond to the ring structures and the bridges to atom chains or linkers. If we allow disconnected common subgraphs, the problem becomes NP-hard even for trees as input. We propose a second generalization of the maximum common subtree problem, which allows skipping vertices in the input trees while maintaining polynomial running time. Since a maximum common subgraph is not unique in general, we investigate the problem to enumerate all maximum solutions. We do this for both the maximum common subtree problem and the block-and-bridge preserving maximum common induced subgraph problem between outerplanar graphs. An arising subproblem which we analyze is the enumeration of maximum weight matchings in bipartite graphs. We support a weight function between the vertices and edges for all proposed common subgraph methods in this thesis. Thus the objective is to compute a common subgraph of maximum weight. The weights may be integral or real-valued, including negative values. A special case of using such a weight function is computing common subgraph isomorphisms between labeled graphs, where labels between mapped vertices and edges must be equal. An experimental study evaluates the practical running times and the usefulness of our block-and-bridge preserving maximum common induced subgraph algorithm against state of the art algorithms

The power of implicit social relation in rating prediction of social recommender systems of social recommender

The explosive growth of social networks in recent times has presented a powerful source of information to be utilized as an extra source for assisting in the social recommendation problems. The social recommendation methods that are based on probabilistic matrix factorization improved the recommendation accuracy and partly solved the cold-start and data sparsity problems. However, these methods only exploited the explicit social relations and almost completely ignored the implicit social relations. In this article, we firstly propose an algorithm to extract the implicit relation in the undirected graphs of social networks by exploiting the link prediction techniques. Furthermore, we propose a new probabilistic matrix factorization method to alleviate the data sparsity problem through incorporating explicit friendship and implicit friendship. We evaluate our proposed approach on two real datasets, Last.Fm and Douban. The experimental results show that our method performs much better than the state-of-the-art approaches, which indicates the importance of incorporating implicit social relations in the recommendation process to address the poor prediction accuracy

Extremal results on degree powers in some classes of graphs

Let $G$ be a simple graph of order $n$ with degree sequence $(d_1,d_2,\cdots,d_n)$. For an integer $p>1$, let $e_p(G)=\sum_{i=1}^n d^{p}_i$ and let $ex_p(n,H)$ be the maximum value of $e_p(G)$ among all graphs with $n$ vertices that do not contain $H$ as a subgraph (known as $H$-free graphs). Caro and Yuster proposed the problem of determining the exact value of $ex_2(n,C_4)$, where $C_4$ is the cycle of length $4$. In this paper, we show that if $G$ is a $C_4$-free graph having $n\geq 4$ vertices and $m\leq \lfloor 3(n-1)/2\rfloor$ edges and no isolated vertices, then $e_p(G)\leq e_p(F_n)$, with equality if and only if $G$ is the friendship graph $F_n$. This yields that for $n\geq 4$, $ex_p(n,\mathcal{C}^*)=e_p(F_n)$ and $F_n$ is the unique extremal graph, which is an improved complement of Caro and Yuster's result on $ex_p(n,\mathcal{C}^*)$, where $\mathcal{C}^*$ denotes the family of cycles of even lengths. We also determine the maximum value of $e_p(\cdot)$ among all minimally $t$-(edge)-connected graphs with small $t$ or among all $k$-degenerate graphs, and characterize the corresponding extremal graphs. A key tool in our approach is majorization

Extraction and Analysis of Facebook Friendship Relations

Online Social Networks (OSNs) are a unique Web and social phenomenon, affecting tastes and behaviors of their users and helping them to maintain/create friendships. It is interesting to analyze the growth and evolution of Online Social Networks both from the point of view of marketing and other of new services and from a scientific viewpoint, since their structure and evolution may share similarities with real-life social networks. In social sciences, several techniques for analyzing (online) social networks have been developed, to evaluate quantitative properties (e.g., defining metrics and measures of structural characteristics of the networks) or qualitative aspects (e.g., studying the attachment model for the network evolution, the binary trust relationships, and the link prediction problem).\ud However, OSN analysis poses novel challenges both to Computer and Social scientists. We present our long-term research effort in analyzing Facebook, the largest and arguably most successful OSN today: it gathers more than 500 million users. Access to data about Facebook users and their friendship relations, is restricted; thus, we acquired the necessary information directly from the front-end of the Web site, in order to reconstruct a sub-graph representing anonymous interconnections among a significant subset of users. We describe our ad-hoc, privacy-compliant crawler for Facebook data extraction. To minimize bias, we adopt two different graph mining techniques: breadth-first search (BFS) and rejection sampling. To analyze the structural properties of samples consisting of millions of nodes, we developed a specific tool for analyzing quantitative and qualitative properties of social networks, adopting and improving existing Social Network Analysis (SNA) techniques and algorithms

Further Studies on the Sparing Number of Graphs

Let $\mathbb{N}_0$ denote the set of all non-negative integers and $\mathcal{P}(\mathbb{N}_0)$ be its power set. An integer additive set-indexer is an injective function $f:V(G)\to \mathcal{P}(\mathbb{N}_0)$ such that the induced function $f^+:E(G) \to \mathcal{P}(\mathbb{N}_0)$ defined by $f^+ (uv) = f(u)+ f(v)$ is also injective, where $f(u)+f(v)$ is the sum set of $f(u)$ and $f(v)$. If $f^+(uv)=k~\forall~uv\in E(G)$, then $f$ is said to be a $k$-uniform integer additive set-indexer. An integer additive set-indexer $f$ is said to be a weak integer additive set-indexer if $|f^+(uv)|=\max(|f(u)|,|f(v)|)~\forall ~ uv\in E(G)$. In this paper, we study the admissibility of weak integer additive set-indexer by certain graphs and graph operations.Comment: 10 Pages, Submitted. arXiv admin note: substantial text overlap with arXiv:1310.609