Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Network-based ranking in social systems: three challenges

Ranking algorithms are pervasive in our increasingly digitized societies, with important real-world applications including recommender systems, search engines, and influencer marketing practices. From a network science perspective, network-based ranking algorithms solve fundamental problems related to the identification of vital nodes for the stability and dynamics of a complex system. Despite the ubiquitous and successful applications of these algorithms, we argue that our understanding of their performance and their applications to real-world problems face three fundamental challenges: (i) Rankings might be biased by various factors; (2) their effectiveness might be limited to specific problems; and (3) agents' decisions driven by rankings might result in potentially vicious feedback mechanisms and unhealthy systemic consequences. Methods rooted in network science and agent-based modeling can help us to understand and overcome these challenges.Comment: Perspective article. 9 pages, 3 figure

Bibliometric cartography of information retrieval research by using co-word analysis

The aim of this study is to map the intellectual structure of the field of Information Retrieval (IR) during the period of 1987-1997. Co-word analysis was employed to reveal patterns and trends in the IR field by measuring the association strengths of terms representative of relevant publications or other texts produced in IR field. Data were collected from Science Citation Index (SCI) and Social Science Citation Index (SSCI) for the period of 1987-1997. In addition to the keywords added by the SCI and SSCI databases, other important keywords were extracted from titles and abstracts manually. These keywords were further standardized using vocabulary control tools. In order to trace the dynamic changes of the IR field, the whole 11-year period was further separated into two consecutive periods: 1987-1991 and 1992-1997. The results show that the IR field has some established research themes and it also changes rapidly to embrace new themes

Cross‐campus Collaboration: A Scientometric and Network Case Study of Publication Activity Across Two Campuses of a Single Institution

Team science and collaboration have become crucial to addressing key research questions confronting society. Institutions that are spread across multiple geographic locations face additional challenges. To better understand the nature of cross‐campus collaboration within a single institution and the effects of institutional efforts to spark collaboration, we conducted a case study of collaboration at Cornell University using scientometric and network analyses. Results suggest that cross‐campus collaboration is increasingly common, but is accounted for primarily by a relatively small number of departments and individual researchers. Specific researchers involved in many collaborative projects are identified, and their unique characteristics are described. Institutional efforts, such as seed grants and topical retreats, have some effect for researchers who are central in the collaboration network, but were less clearly effective for others

A framework for the forensic investigation of unstructured email relationship data

Our continued reliance on email communications ensures that it remains a major source of evidence during a digital investigation. Emails comprise both structured and unstructured data. Structured data provides qualitative information to the forensics examiner and is typically viewed through existing tools. Unstructured data is more complex as it comprises information associated with social networks, such as relationships within the network, identification of key actors and power relations, and there are currently no standardised tools for its forensic analysis. Moreover, email investigations may involve many hundreds of actors and thousands of messages. This paper posits a framework for the forensic investigation of email data. In particular, it focuses on the triage and analysis of unstructured data to identify key actors and relationships within an email network. This paper demonstrates the applicability of the approach by applying relevant stages of the framework to the Enron email corpus. The paper illustrates the advantage of triaging this data to identify (and discount) actors and potential sources of further evidence. It then applies social network analysis techniques to key actors within the data set. This paper posits that visualisation of unstructured data can greatly aid the examiner in their analysis of evidence discovered during an investigation