Learning Dynamic Network Models for Complex Social Systems

Human societies are inherently complex and highly dynamic, resulting in rapidly changing social networks, containing multiple types of dyadic interactions. Analyzing these time-varying multiplex networks with approaches developed for static, single layer networks often produces poor results. To address this problem, our approach is to explicitly learn the dynamics of these complex networks. This dissertation focuses on five problems: 1) learning link formation rates; 2) predicting changes in community membership; 3) using time series to predict changes in network structure; 4) modeling coevolution patterns across network layers and 5) extracting information from negative layers of a multiplex network. To study these problems, we created a rich dataset extracted from observing social interactions in the massively multiplayer online game Travian. Most online social media platforms are optimized to support a limited range of social interactions, primarily focusing on communication and information sharing. In contrast, relations in massively-multiplayer online games (MMOGs) are often formed during the course of gameplay and evolve as the game progresses. To analyze the players\u27 behavior, we constructed multiplex networks with link types for raid, communication, and trading. The contributions of this dissertation include 1) extensive experiments on the dynamics of networks formed from diverse social processes; 2) new game theoretic models for community detection in dynamic networks; 3) supervised and unsupervised methods for link prediction in multiplex coevolving networks for both positive and negative links. We demonstrate that our holistic approach for modeling network dynamics in coevolving, multiplex networks outperforms factored methods that separately consider temporal and cross-layer patterns

XFlow: Benchmarking Flow Behaviors over Graphs

The occurrence of diffusion on a graph is a prevalent and significant phenomenon, as evidenced by the spread of rumors, influenza-like viruses, smart grid failures, and similar events. Comprehending the behaviors of flow is a formidable task, due to the intricate interplay between the distribution of seeds that initiate flow propagation, the propagation model, and the topology of the graph. The study of networks encompasses a diverse range of academic disciplines, including mathematics, physics, social science, and computer science. This interdisciplinary nature of network research is characterized by a high degree of specialization and compartmentalization, and the cooperation facilitated by them is inadequate. From a machine learning standpoint, there is a deficiency in a cohesive platform for assessing algorithms across various domains. One of the primary obstacles to current research in this field is the absence of a comprehensive curated benchmark suite to study the flow behaviors under network scenarios. To address this disparity, we propose the implementation of a novel benchmark suite that encompasses a variety of tasks, baseline models, graph datasets, and evaluation tools. In addition, we present a comprehensive analytical framework that offers a generalized approach to numerous flow-related tasks across diverse domains, serving as a blueprint and roadmap. Drawing upon the outcomes of our empirical investigation, we analyze the advantages and disadvantages of current foundational models, and we underscore potential avenues for further study. The datasets, code, and baseline models have been made available for the public at: https://github.com/XGraphing/XFlo

Reconstructing networks

Complex networks datasets often come with the problem of missing information: interactions data that have not been measured or discovered, may be affected by errors, or are simply hidden because of privacy issues. This Element provides an overview of the ideas, methods and techniques to deal with this problem and that together define the field of network reconstruction. Given the extent of the subject, the authors focus on the inference methods rooted in statistical physics and information theory. The discussion is organized according to the different scales of the reconstruction task, that is, whether the goal is to reconstruct the macroscopic structure of the network, to infer its mesoscale properties, or to predict the individual microscopic connections

Reconstructing networks

Complex networks datasets often come with the problem of missing information: interactions data that have not been measured or discovered, may be affected by errors, or are simply hidden because of privacy issues. This Element provides an overview of the ideas, methods and techniques to deal with this problem and that together define the field of network reconstruction. Given the extent of the subject, we shall focus on the inference methods rooted in statistical physics and information theory. The discussion will be organized according to the different scales of the reconstruction task, that is, whether the goal is to reconstruct the macroscopic structure of the network, to infer its mesoscale properties, or to predict the individual microscopic connections.Comment: 107 pages, 25 figure

Perspectives on adaptive dynamical systems

Adaptivity is a dynamical feature that is omnipresent in nature, socio-economics, and technology. For example, adaptive couplings appear in various real-world systems like the power grid, social, and neural networks, and they form the backbone of closed-loop control strategies and machine learning algorithms. In this article, we provide an interdisciplinary perspective on adaptive systems. We reflect on the notion and terminology of adaptivity in different disciplines and discuss which role adaptivity plays for various fields. We highlight common open challenges, and give perspectives on future research directions, looking to inspire interdisciplinary approaches.Comment: 46 pages, 9 figure

Perspectives on adaptive dynamical systems

Adaptivity is a dynamical feature that is omnipresent in nature, socio-economics, and technology. For example, adaptive couplings appear in various real-world systems, such as the power grid, social, and neural networks, and they form the backbone of closed-loop control strategies and machine learning algorithms. In this article, we provide an interdisciplinary perspective on adaptive systems. We reflect on the notion and terminology of adaptivity in different disciplines and discuss which role adaptivity plays for various fields. We highlight common open challenges and give perspectives on future research directions, looking to inspire interdisciplinary approaches

Network resilience

Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems, and social convention changes in human and animal networks. Such a regime shift demonstrates a system's resilience that characterizes the ability of a system to adjust its activity to retain its basic functionality in the face of internal disturbances or external environmental changes. In the past 50 years, attention was almost exclusively given to low dimensional systems and calibration of their resilience functions and indicators of early warning signals without considerations for the interactions between the components. Only in recent years, taking advantages of the network theory and lavish real data sets, network scientists have directed their interest to the real-world complex networked multidimensional systems and their resilience function and early warning indicators. This report is devoted to a comprehensive review of resilience function and regime shift of complex systems in different domains, such as ecology, biology, social systems and infrastructure. We cover the related research about empirical observations, experimental studies, mathematical modeling, and theoretical analysis. We also discuss some ambiguous definitions, such as robustness, resilience, and stability.Comment: Review chapter

Data-Centric Epidemic Forecasting: A Survey

The COVID-19 pandemic has brought forth the importance of epidemic forecasting for decision makers in multiple domains, ranging from public health to the economy as a whole. While forecasting epidemic progression is frequently conceptualized as being analogous to weather forecasting, however it has some key differences and remains a non-trivial task. The spread of diseases is subject to multiple confounding factors spanning human behavior, pathogen dynamics, weather and environmental conditions. Research interest has been fueled by the increased availability of rich data sources capturing previously unobservable facets and also due to initiatives from government public health and funding agencies. This has resulted, in particular, in a spate of work on 'data-centered' solutions which have shown potential in enhancing our forecasting capabilities by leveraging non-traditional data sources as well as recent innovations in AI and machine learning. This survey delves into various data-driven methodological and practical advancements and introduces a conceptual framework to navigate through them. First, we enumerate the large number of epidemiological datasets and novel data streams that are relevant to epidemic forecasting, capturing various factors like symptomatic online surveys, retail and commerce, mobility, genomics data and more. Next, we discuss methods and modeling paradigms focusing on the recent data-driven statistical and deep-learning based methods as well as on the novel class of hybrid models that combine domain knowledge of mechanistic models with the effectiveness and flexibility of statistical approaches. We also discuss experiences and challenges that arise in real-world deployment of these forecasting systems including decision-making informed by forecasts. Finally, we highlight some challenges and open problems found across the forecasting pipeline.Comment: 67 pages, 12 figure

Genetic mapping of host loci determining gut microbiota in hybrid mice

All animals and plants are colonized by microorganisms, whereby different host species contain different microbial populations. These microbial communities form long-term relationships with their hosts. Understanding the genomic basis underlying these relationships provides insight into the possible coevolution between hosts and their microbiota. This thesis aims to contribute to a deeper understanding of the forces shaping the microbiome