presentations talks
  1. Why do metabolic networks look like they do?, September 13, 2011 It is a decade since the discovery that metabolic networks are scale-free. I will make a brief review of this decade of research relating network topology and function in metabolic reaction systems with a focus on our contributions. I discuss the hypothesis that network clusters correspond to functional modules. Metabolic network, however represented, are not as distinctly modular as the cartoon picture of intricately wired subsystems with few I/O-terminals. Does this reflect a trade-off between functionality and robustness, or is it an inevitable consequence of non-enzymatic reaction kinetics, or something else? I also discuss optimal levels of representations—if one uses a multiplex, directed, and perhaps bipartite, representation one can encode more information, but standard methods are harder to apply. If one goes for a simple-graph representation with vertices connected by undirected edges, then how can one encode as much functional information as possible? I will also mention how one can use other types of reaction systems, like reactions in planetary atmospheres, as null-models of metabolic networks. Finally I look forward and discuss open questions within reach with current and future data sets. Made for ECCS 2011.
  2. Temporal network structure and its implications for disease spreading and control, June 9, 2011 Contacts between individuals form the infrastructure over which diseases spread. Such contact patterns are far from random -- there are correlations both in the network of who has been in contact with whom, and when these contacts happen. These structures affect the dynamics of disease spreading but can also be exploited in preventive action such as vaccination campaigns. In this talk, I will use datasets from the proximity of patients in hospitals, online dating services and Internet-mediated prostitution to discuss some methods to analyze such temporal network structures and evaluate their effects on disease spreading. I will also discuss targeted immunization protocols utilizing such structures. Made for NetSci 2011.
  3. Biologiska nätverks struktur och funktion, September 8, 2008 Många storskaliga biologiska system - nervsystemet, metabolismen, genregleringen med mera - är uppbyggda av en stor mängkomponenter.Funktionen av systemet som helhet beror både på komponenternas individuella funktion och sättet på vilket de interagerar. Komplexa-nätverksstudier fokuserar på det sistnämnda orepresenterar systemet så enkelt som möjligt-- som en graf av nod kopplade parvis. Med hjälp av statistiska mått av hur en sådan grskiljer sig från en helt slumpmässig graf kan man få information systemets dynamik och även om hur nätverket växt fram. Jag kommer agå igenom de teoretiska grunderna för komplexa nätverk och berätta denna metod kan användas för att studera biologiska system i allmänhmed specifika exempel. Docentföreläsning at KTH.
  4. Simple models of teens, diplomats, religious cults and more January 12, 2008 Simple models of social phenomena can be used as tools for building hypotheses about the transition from micro- to macro-phenomena. I will discuss a few such models of phenomena such as: youth subcultures, new religions, diplomatic networking, and friendship dynamics; and the general ideas behind this class of models. Presented at: Is There a Physics of Society?, SFI.
  5. Network modularity, currency metabolites and graph representations of metabolism December 17, 2007 The large-scale shape and function of metabolic network is an intriguing topic of systems biology. Such networks are on one hand commonly regarded as modular (i.e. built by a number of relatively independent subsystems) on the other hand they are robust in a way maybe not expected for a purely modular system. To address this question we discuss the partition of metabolic networks into subnetworks. The practice of preprocessing such networks by removing the most abundant substrates, "currency metabolites," is formalized into a network-based algorithm. We study such partitions for metabolic networks of many organisms and find cores of currency metabolites and modular peripheries of what we call commodity metabolites. The networks are found to be more modular than random networks but far from perfectly divisible into modules. Presented at: Mathematics for Biological Networks, Institut Henri Poincare, Paris, France.
  6. Structure & function of metabolic networks October 10, 2007. Modern technology provides us with large amounts of biological data. This opens possibilities to study the large-scale organization and function of biological systems. The information is, however, typically not comprehensive enough to use the same tools for studying large-scale systems (e.g. the metabolism) as small subsystems (e.g. the citric acid cycle). I will discuss network theory in general, and how statistical graph theory can be used to study the organization of metabolism. Specifically I will talk about the role, definition and detection of "currency metabolites" -- ubiquitous substances (like water, carbon dioxide, ATP, etc.) that occur in a multitude of reactions. Presented at: SBC seminar series.
  7. Efficiency of navigation in indexed networks October 4, 2007. We investigate efficient methods for packets to navigate in complex networks. The packets are assumed to have memory, but no previous knowledge of the graph. We assume the graph to be indexed, i.e. every vertex is associated with a number (accessible to the packets) between one and the size of the graph. We test different schemes to assign indices and utilize them in packet navigation. Four different network models with very different topological characteristics are used for testing the schemes. We find that one scheme outperform the others, and has an efficiency close to the theoretical optimum. We discuss the use of indexed-graph navigation in peer-to-peer networking and other distributed information systems. Presented at: Dynamics on and of complex networks, satellite workshop of European Conference on Complex Systems, Dresden, Germany, October 1-5, 2007.
  8. Two models of networking social agents September 18, 2006. We discuss two models of networks coevolving with a system of social agents. In the first model we combine opinion spreading on the network with the “homophily assumption” (that people with the same opinions, interests and other traits are more likely than expected to become acquainted). We construct a model with a single parameter controlling the balance of the two processes. We find that the model undergoes a continuous phase transition as this parameter is varied, from a regime in which opinions are arbitrarily diverse to one in which most individuals hold the same opinion. The second model consider a system of networking agents that seek to optimize their centrality in the network while keeping their cost, the number of connections they are participating in, low. Unlike other game-theory based models for network evolution, the success of the agents is related only to their position in the network. The agents use strategies based on local information to improve their chance of success. Presented at: International School of Complexity on Physics and Socio-Economics Phenomena, Erice, Italy, September, 2006. SIAM Conference on Dynamical Systems, Snowbird UT, April, 2007. Santa Fe Institute workshop on Scaling in Social and Biological Systems, Santa Fe NM, July, 2007.
  9. Local symmetries in complex networks July 12, 2006. Symmetry -- invariance to certain transformations -- is a fundamental concept in many branches of physics. We propose ways to measure symmetric properties of vertices in networks. To be stable to the randomness inherent in many complex networks we consider measures that are continuous rather than dichotomous. The main operator we suggest is permutations of the paths of length l leading out from a vertex. If these paths are more similar (in some sense) than expected the vertex is a local center of symmetry in networks. We discuss different precise definitions based on this idea and evaluate them on real and model networks. Presented at DDAP4, Pohang, Korea.
  10. Large-scale biological networks I, Complex network theory: An introduction July7, 2006. A network in its simplest representation is a set of point that are connected pairwise. The connections can be either random or have some regularities, or structure. If one assumes there is a relation between the network structure and the function of the networked system, then the question is: How can we extract this information? We will discuss methods to measure network structure, and how one can analyze networks with these measures. Lecture at Summer School on Computational Biology, Pohang, Korea. The 2nd lecture presentation contains copyrighted material and is not posed here.
  11. Modeling the coevolution of networks and opinions July 4, 2006. Models of the convergence of opinion in social systems have been the subject of a considerable amount of recent attention in the physics literature. These models divide into two classes, those in which individuals form their beliefs based on the opinions of their neighbors in a social network of personal acquaintances, and those in which, conversely, network connections form between individuals of similar beliefs. While both of these processes can give rise to realistic levels of agreement between acquaintances, practical experience suggests that opinion formation in the real world is not a result of one process or the other, but a combination of the two. We present a simple model of this combination, with a single parameter controlling the balance of the two processes. Our model undergoes a continuous phase transition as this parameter is varied, from a regime in which opinions are arbitrarily diverse to one in which most individuals hold the same opinion. We characterize the static and dynamical properties of this transition. Presented at NSPCS06, Seoul, Korea.
  12. Vertex similarity and its application to functional prediction November 18, 2005. In networks of heterogenous vertices, two vertices are likely to be functionally similar if the network look similar from their respective perspectives. By a formalization of this argument I will discuss how one can base vertex similarity measures on path counts. Similarity measures can form the basis for functional prediction algorithms. This will be illustrated by prediction of S. cerevisiae protein functions. (Talk at European Conference for Complex Systems, Paris, France.)
  13. Romance, vertex similarity and functional prediction in networks September 21, 2005. This talk covers two topics of statistical networks studies: 1.Internet dating is a fairly new social phenomenon. The size and time resolution of the datasets are quite unique to systems of social interaction. I will talk about the network structure of online dating and how it compares with what is known about offline dating. 2. In many networks the function of a vertex relates to its position in the network. I will discuss how this information can be extracted to create functional classification and prediction schemes. Applications to protein interaction and ecological networks (e.g. food webs) will be discussed. Talk at University of New Mexico.
  14. The proximity network of patients in a healthcare systems December 2004 -- February 2005. Infectious diseases pose a general threat to human health. Some pathogens (e.g. MRSA or Mycoplasma Pneumoniae) spread primarily within hospitals. To understand the epidemiology of such diseases one has to understand the flow of patients within a health care system. In this talk I will discuss how to define a contact network of patients in a health care system. I will also present the topological properties of such networks constructed from 570,382 hospitalizations over a two year period from the Stockholm region of Sweden. Talks at University of Michigan, Niels Bohr Institute, Ajou University, KAIST and Seoul National University.
  15. Komplexa nätverk [Complex Networks] November 17, 2004 Det senaste fem åren har inneburit en explosion av tvärvetenskaplig nätverksforskning. Den främsta orsaken till denna aktivitet är tillgången på stora, automatiskt insamlade, dataset (från genetik, elektronisk kommunikation, databaser över infrastruktur, o s v). Så stora dataset ställer nya krav på analysmetoder och modeller. Jag presenterar en översikt över denna utveckling, med exempel på och modeller för: Tillväxten av olika slags nätverk. Överbelastningskaskader, illvilliga attacker och vaccinationsstrategier. Spridningsprocesser på nätverk. Talk at Karolinska Institutet in Stockholm, Sweden.
  16. Networks in Molecular Biology June 2, 2004 With modern database technology a new wave of statistical network science has emerged. I will give a brief introduction to this vibrant field. In molecular biology there are a number of systems that can, quite naturally, be represented as networks: genetic regulation, protein interaction, the metabolism, etc. I will discuss what network science can contribute with in these areas. Talk at the Royal Institute of Technology, Stockholm, Sweden.
  17. Modeling group formation in society: The networked seceder model January 14, 2004. Talk at KAIST, Daejon, Korea
  18. Centrala noders roll i katastrofer och andra besvärligheter [The role of central vertices in diasters and other annoyances] November 28, 2003 Talk at FOI Stockholm, Sweden.
  19. Discovery and analysis of biochemical subnetwork hierarchies October 6, 2003 Invited talk at The 3rd workshop on computation of biochemical pathways and genetic networks, Heidelberg, Germany.
  20. Structure and dynamics of online romance August 28, 2003 Invited talk at the Niels Bohr summer institute, Copenhagen, Denmark
  21. The structure of an Internet community (introducing bipartivity) January, 2003 Held at KIAS, Seoul, Korea and KAIST, Daejon, Korea.
  22. Social networks for physicists and the structure of an Internet dating community January, 2003 Talk at Ajou University, Suwon, Korea.
  23. Structure of the Internet community pussokram.com September 4, 2002 Part of the PhD seminar series at Umeå University.
  24. Dynamical systems on complex networks Mars 19, 2002 Part of the seminar series Mathematical Modelling of Biological Systems at Umeå University.
  25. Dynamical systems on complex networks Mars 14, 2002 Part of the seminar series Mathematical Modelling of Biological Systems at Umeå University.
  26. A Zero-Temperature Study of Vortex Mobility in Two-Dimensional Vortex Glass Models January 18, 2002 Held at the Sphinx Workshop "Disordered systems at low temperatures and their topological properties" in Helsinki, Finland.
  27. Licentiate Seminar November 6, 2001 A presentation of my Licentiate Thesis Physics of Two-Dimensional Vortex Glass Models.
  28. Two Studies of Two-Dimensional Vortex Glass Models August 7, 2001 Over a decade after its introduction, the possible existance of a two-dimensional vortex glass phase of high temperature superconductors still remains fully clearified. In this seminar I presented a zero temperature study of three vortex glass models: the random gauge XY model, the XY spin glass model, and the random pinning model. I also presented a Monte Carlo simulation of the random gauge XY model. Seminar at Seoul National University.
  29. A Scale-Free Network Model with tunable clustering August 3, 2001 A power-law degree distribution and a high clustering coefficient is a common combination in real-world network. In this seminar I present an algorithm that generates network with a perfect scale-free degree distribution and a clustering that can be continously tuned by an input parameter. Presented at Chungbuk University.
  30. Networks of Scientific Citations and Collaborations May 11, 2001 From the reading group that led me in to network studies.
  32. Characteristics of Small World Networks April 20, 2001 From the reading group that led me in to network studies.
posters
  1. Statistical physics approach to landscape modeling: Neighborhood interaction and aridity explain the forest distribution of the Southwest US March 30, 2006. Presented at the US-IALE 2006 Annual Symposium in San Diego, US
  2. Congestion and centrality in complex networks December 12-13, 2003 Presented at the workshop Robust Communication Dynamics in Complex Networks (NIPS satellite), Whistler, Canada.
  3. Prisoners' dilemma in real-world acquaintance networks May-September, 2003 Presented at Networks: Structure, Dynamics and Function, CNLS 23rd annual conference, Santa Fe, NM; and growing Networks and Graphs in Statistical Physics, Finance, Biology and Social Systems, COSIN midterm conference, Rome, Italy.
  4. Subnetwork hierarchies of biochemical pathways 10-17 August 2002 Presented at Dynamics of Biological Systems: From Molecules to Networks, Humlebæk, Denmark.
  5. Overload breakdown in evolving networks June 10-14, 2002 Presented at Statistical mechanics of complex networks, XII Sitges conference, Sitges, Spain.
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