Sequence queries on temporal graphs

Graphs that evolve over time are called temporal graphs. They can be used to describe and represent real-world networks, including transportation networks, social networks, and communication networks, with higher fidelity and accuracy. However, research is still limited on how to manage large scale temporal graphs and execute queries over these graphs efficiently and effectively. This thesis investigates the problems of temporal graph data management related to node and edge sequence queries. In temporal graphs, nodes and edges can evolve over time. Therefore, sequence queries on nodes and edges can be key components in managing temporal graphs. In this thesis, the node sequence query decomposes into two parts: graph node similarity and subsequence matching. For node similarity, this thesis proposes a modified tree edit distance that is metric and polynomially computable and has a natural, intuitive interpretation. Note that the proposed node similarity works even for inter-graph nodes and therefore can be used for graph de-anonymization, network transfer learning, and cross-network mining, among other tasks. The subsequence matching query proposed in this thesis is a framework that can be adopted to index generic sequence and time-series data, including trajectory data and even DNA sequences for subsequence retrieval. For edge sequence queries, this thesis proposes an efficient storage and optimized indexing technique that allows for efficient retrieval of temporal subgraphs that satisfy certain temporal predicates. For this problem, this thesis develops a lightweight data management engine prototype that can support time-sensitive temporal graph analytics efficiently even on a single PC

Image Understanding by Hierarchical Symbolic Representation and Inexact Matching of Attributed Graphs

We study the symbolic representation of imagery information by a powerful global representation scheme in the form of Attributed Relational Graph (ARG), and propose new techniques for the extraction of such representation from spatial-domain images, and for performing the task of image understanding through the analysis of the extracted ARG representation. To achieve practical image understanding tasks, the system needs to comprehend the imagery information in a global form. Therefore, we propose a multi-layer hierarchical scheme for the extraction of global symbolic representation from spatial-domain images. The proposed scheme produces a symbolic mapping of the input data in terms of an output alphabet, whose elements are defined over global subimages. The proposed scheme uses a combination of model-driven and data-driven concepts. The model- driven principle is represented by a graph transducer, which is used to specify the alphabet at each layer in the scheme. A symbolic mapping is driven by the input data to map the input local alphabet into the output global alphabet. Through the iterative application of the symbolic transformational mapping at different levels of hierarchy, the system extracts a global representation from the image in the form of attributed relational graphs. Further processing and interpretation of the imagery information can, then, be performed on their ARG representation. We also propose an efficient approach for calculating a distance measure and finding the best inexact matching configuration between attributed relational graphs. For two ARGs, we define sequences of weighted error-transformations which when performed on one ARG (or a subgraph of it), will produce the other ARG. A distance measure between two ARGs is defined as the weight of the sequence which possesses minimum total-weight. Moreover, this minimum-total weight sequence defines the best inexact matching configuration between the two ARGs. The global minimization over the possible sequences is performed by a dynamic programming technique, the approach shows good results for ARGs of practical sizes. The proposed system possesses the capability to inference the alphabets of the ARG representation which it uses. In the inference phase, the hierarchical scheme is usually driven by the input data only, which normally consist of images of model objects. It extracts the global alphabet of the ARG representation of the models. The extracted model representation is then used in the operation phase of the system to: perform the mapping in the multi-layer scheme. We present our experimental results for utilizing the proposed system for locating objects in complex scenes

Graphs in machine learning: an introduction

Graphs are commonly used to characterise interactions between objects of interest. Because they are based on a straightforward formalism, they are used in many scientific fields from computer science to historical sciences. In this paper, we give an introduction to some methods relying on graphs for learning. This includes both unsupervised and supervised methods. Unsupervised learning algorithms usually aim at visualising graphs in latent spaces and/or clustering the nodes. Both focus on extracting knowledge from graph topologies. While most existing techniques are only applicable to static graphs, where edges do not evolve through time, recent developments have shown that they could be extended to deal with evolving networks. In a supervised context, one generally aims at inferring labels or numerical values attached to nodes using both the graph and, when they are available, node characteristics. Balancing the two sources of information can be challenging, especially as they can disagree locally or globally. In both contexts, supervised and un-supervised, data can be relational (augmented with one or several global graphs) as described above, or graph valued. In this latter case, each object of interest is given as a full graph (possibly completed by other characteristics). In this context, natural tasks include graph clustering (as in producing clusters of graphs rather than clusters of nodes in a single graph), graph classification, etc. 1 Real networks One of the first practical studies on graphs can be dated back to the original work of Moreno [51] in the 30s. Since then, there has been a growing interest in graph analysis associated with strong developments in the modelling and the processing of these data. Graphs are now used in many scientific fields. In Biology [54, 2, 7], for instance, metabolic networks can describe pathways of biochemical reactions [41], while in social sciences networks are used to represent relation ties between actors [66, 56, 36, 34]. Other examples include powergrids [71] and the web [75]. Recently, networks have also been considered in other areas such as geography [22] and history [59, 39]. In machine learning, networks are seen as powerful tools to model problems in order to extract information from data and for prediction purposes. This is the object of this paper. For more complete surveys, we refer to [28, 62, 49, 45]. In this section, we introduce notations and highlight properties shared by most real networks. In Section 2, we then consider methods aiming at extracting information from a unique network. We will particularly focus on clustering methods where the goal is to find clusters of vertices. Finally, in Section 3, techniques that take a series of networks into account, where each network i

Rank-aware, Approximate Query Processing on the Semantic Web

Search over the Semantic Web corpus frequently leads to queries having large result sets. So, in order to discover relevant data elements, users must rely on ranking techniques to sort results according to their relevance. At the same time, applications oftentimes deal with information needs, which do not require complete and exact results. In this thesis, we face the problem of how to process queries over Web data in an approximate and rank-aware fashion

Building Blocks for Mapping Services

Mapping services are ubiquitous on the Internet. These services enjoy a considerable user base. But it is often overlooked that providing a service on a global scale with virtually millions of users has been the playground of an oligopoly of a select few service providers are able to do so. Unfortunately, the literature on these solutions is more than scarce. This thesis adds a number of building blocks to the literature that explain how to design and implement a number of features

Geometric, Feature-based and Graph-based Approaches for the Structural Analysis of Protein Binding Sites : Novel Methods and Computational Analysis

In this thesis, protein binding sites are considered. To enable the extraction of information from the space of protein binding sites, these binding sites must be mapped onto a mathematical space. This can be done by mapping binding sites onto vectors, graphs or point clouds. To finally enable a structure on the mathematical space, a distance measure is required, which is introduced in this thesis. This distance measure eventually can be used to extract information by means of data mining techniques

Aspects of Record Linkage

This thesis is an exploration of the subject of historical record linkage. The general goal of historical record linkage is to discover relations between historical entities in a database, for any specific definition of relation, entity and database. Although this task originates from historical research, multiple disciplines are involved. Increasing volumes of data necessitate the use of automated or semi-automated linkage procedures, which is in the domain of computer science. Linkage methodologies depend heavily on the nature of the data itself, often requiring analysis based on onomastics (i.e., the study of person names) or general linguistics. To understand the dynamics of natural language one could be tempted to look at the source of language, i.e., humans, either on the individual cognitive level or as group behaviour. This further increases the multidisciplinarity of the subject by including cognitive psychology. Every discipline addresses a subset of problem aspects, all of which can contribute either to practical solutions for linkage problems or to further insights into the subject matter.Algorithms and the Foundations of Software technolog

Advanced Methods for Entity Linking in the Life Sciences

The amount of knowledge increases rapidly due to the increasing number of available data sources. However, the autonomy of data sources and the resulting heterogeneity prevent comprehensive data analysis and applications. Data integration aims to overcome heterogeneity by unifying different data sources and enriching unstructured data. The enrichment of data consists of different subtasks, amongst other the annotation process. The annotation process links document phrases to terms of a standardized vocabulary. Annotated documents enable effective retrieval methods, comparability of different documents, and comprehensive data analysis, such as finding adversarial drug effects based on patient data. A vocabulary allows the comparability using standardized terms. An ontology can also represent a vocabulary, whereas concepts, relationships, and logical constraints additionally define an ontology. The annotation process is applicable in different domains. Nevertheless, there is a difference between generic and specialized domains according to the annotation process. This thesis emphasizes the differences between the domains and addresses the identified challenges. The majority of annotation approaches focuses on the evaluation of general domains, such as Wikipedia. This thesis evaluates the developed annotation approaches with case report forms that are medical documents for examining clinical trials. The natural language provides different challenges, such as similar meanings using different phrases. The proposed annotation method, AnnoMap, considers the fuzziness of natural language. A further challenge is the reuse of verified annotations. Existing annotations represent knowledge that can be reused for further annotation processes. AnnoMap consists of a reuse strategy that utilizes verified annotations to link new documents to appropriate concepts. Due to the broad spectrum of areas in the biomedical domain, different tools exist. The tools perform differently regarding a particular domain. This thesis proposes a combination approach to unify results from different tools. The method utilizes existing tool results to build a classification model that can classify new annotations as correct or incorrect. The results show that the reuse and the machine learning-based combination improve the annotation quality compared to existing approaches focussing on the biomedical domain. A further part of data integration is entity resolution to build unified knowledge bases from different data sources. A data source consists of a set of records characterized by attributes. The goal of entity resolution is to identify records representing the same real-world entity. Many methods focus on linking data sources consisting of records being characterized by attributes. Nevertheless, only a few methods can handle graph-structured knowledge bases or consider temporal aspects. The temporal aspects are essential to identify the same entities over different time intervals since these aspects underlie certain conditions. Moreover, records can be related to other records so that a small graph structure exists for each record. These small graphs can be linked to each other if they represent the same. This thesis proposes an entity resolution approach for census data consisting of person records for different time intervals. The approach also considers the graph structure of persons given by family relationships. For achieving qualitative results, current methods apply machine-learning techniques to classify record pairs as the same entity. The classification task used a model that is generated by training data. In this case, the training data is a set of record pairs that are labeled as a duplicate or not. Nevertheless, the generation of training data is a time-consuming task so that active learning techniques are relevant for reducing the number of training examples. The entity resolution method for temporal graph-structured data shows an improvement compared to previous collective entity resolution approaches. The developed active learning approach achieves comparable results to supervised learning methods and outperforms other limited budget active learning methods. Besides the entity resolution approach, the thesis introduces the concept of evolution operators for communities. These operators can express the dynamics of communities and individuals. For instance, we can formulate that two communities merged or split over time. Moreover, the operators allow observing the history of individuals. Overall, the presented annotation approaches generate qualitative annotations for medical forms. The annotations enable comprehensive analysis across different data sources as well as accurate queries. The proposed entity resolution approaches improve existing ones so that they contribute to the generation of qualitative knowledge graphs and data analysis tasks

Graph Perturbation as Noise Graph Addition: A New Perspective for Graph Anonymization

Different types of data privacy techniques have been applied to graphs and social networks. They have been used under different assumptions on intruders’ knowledge. i.e., different assumptions on what can lead to disclosure. The analysis of different methods is also led by how data protection techniques influence the analysis of the data. i.e., information loss or data utility. One of the techniques proposed for graph is graph perturbation. Several algorithms have been proposed for this purpose. They proceed adding or removing edges, although some also consider adding and removing nodes. In this paper we propose the study of these graph perturbation techniques from a different perspective. Following the model of standard database perturbation as noise addition, we propose to study graph perturbation as noise graph addition. We think that changing the perspective of graph sanitization in this direction will permit to study the properties of perturbed graphs in a more systematic way