Artificial Life (PI: Larry Yaeger)

Polyworld: We evolve minimal models of intelligent, adaptive behavior by artificial agents in a computational ecology. Information-theoretic measures of complexity are used to assess the dynamics of the agents' artificial neural network "brains". More

Larry Yaeger, Virgil Griffith, Joseph Biberstine

Systems Biology (PI: Santiago Schnell)

Determination of kinetic parameter and reaction mechanisms in biochemistry: Biochemical reactions take place continuously in all living organisms, and most of them involve proteins called enzymes, which act as remarkably efficient catalysts. Therefore, almost everything that happens in life is affected by enzymatic catalysis and biochemical kinetics. Our research has focused on developing new techniques for measuring the kinetic parameters of biochemical reactions and rethinking old theories of enzyme action. We also focus on the development of algorithms and approaches to determining reaction network mechanisms from time course data. More	S. Schnell, E. Flach, J. Srividhya
Macromolecular crowding as a factor in cellular evolution: Nowadays there is no doubt that living cells have high macromolecular content. We are studying the effect of macromolecular crowding in the reaction kinetics. We also are focussing our attention to the evolutionary role of crowding in cells. Is macromolecular crowding essential to life? As far as we know, all modern cells have a high macromolecular content. In fact, it is now recognise that cells must have a mechanism for the synthesis and regulation of crowding agents. This system seems to be energetically expensive. If evolution has selected cells which maintain with a high macromolecular content, crowding must be important for the cell. What are the roles that crowding is playing as a factor in the cellular evolution? More	S. Schnell, R. Grima
Multiscale Modelling in Biology: Understanding biology at larger scales of integration remains fascinating and vitally important for applications ranging from biosciences to psychology and population biology. Indeed, biological phenomena no longer seem arbitrary. They share many organizing principles from signal transduction to developmental regulation, which allow parsimonious descriptions despite historical contingency. Unravelling these principles requires novel interdisciplinary approaches unifying physical, computational and biological techniques. Spurred by this realization, as well as by increases in computing power, scientists have increasingly sought to understand the shared principles of how the collective interactions of biological agents can produce emergent phenomena: how do developing cells interact locally to produce a spherical cluster of cells such as a somite or a tumour? More	S. Schnell, R. Grima E. Flach

Adaptive Behavior and Cognition--West (PI: Peter M. Todd)

The Adaptive Behavior and Cognition Lab--West (ABC-West) is dedicated to exploring the cognitive mechanisms that people (and other animals) use to behave adaptively in their environments. We study the interactions between behavior and environment at multiple scales--including how cognitive mechanisms have evolved in response to particular environmental structures, how behaviors are learned through interactions with the environment, and how behaving and acting in the world can change the environmental structures that agents face in the future. We look at particular adaptively important domains such as mate choice and food choice, and we use tools including agent-based modeling and simulation and laboratory experiments. ABC-West was formed in 2005 through budding from the original ABC Research Group in Berlin, Germany.

Search strategies, food choice	Peter M. Todd
Mate assessment in speed-dating	Skyler Place, Peter M. Todd

Complex Adaptive Systems and Computational Intelligence (PI: Luis M. Rocha)

Perhaps the key research focus in complex systems is the search for fundamental principles of the living organization and the application of these principles to enhance human technology at large, and computers in particular. We are interested in the informational properties of natural and artificial systems which enable them to adapt and evolve. We are interested both in understanding how information is fundamental for the evolutionary capabilities of natural systems, as well as in abstracting principles from natural systems to produce adaptive information technology. Below are short descriptions of some of the projects we are pursuing. Information about our group meetings, projects, and ongoing work is availavle on the CASCI Website. All are welcome to our meetings.

Adaptive web: Bio-inspired designs for Recommendation Systems; adaptive knowledge networks for collaboration and personalization; knowledge self-organization; digital libraries; fuzzy and weighted networks. More	Alaa Abihaidar, Ana Maguitman, Tiago Simas
Semi-metric networks: Study of the topological chracteristics of associative networks; using strong semi-metric associations (items whose distance relation breaks the triangle inequality) to identify trends, items with a higher probability of co-occurring in the future, as well the dynamics of networks in general; transitivite constraints of fuzzy and weighted networks;. More	Bharat Dravid, Tiago Simas
Bibliome informatics: Literature mining for biomedical research; Large-scale validation of bibliome algorithms with applications to genomics and proteomics; automatic functional annotation of biological entities. More	Alaa Abihaidar, Wei Chen, Jasleen Kaur, Ana Maguitman, Andreas Rechtsteiner, Zhiping Wang
Microarray analysis: Singular value decomposition; clustering methods via literature mining; clustering of patient data. More	Alaa Abihaidar, Jasleen Kaur, Andreas Rechtsteiner, Zhiping Wang
Evolutionary models of RNA Editing: Computational models to study the evolutionary implications of genotype editing in the living organization; study of how genotype editing leads to a different evolutionary search algorithm; investigate the conditions under which genotype editing improves the optimization performance of traditional evolutionary algorithms; evolutionary and agent-based computation; genotype-phenotype mappings; indirect encoding via RNOmics. More	Jasleen Kaur, Chien-feng Huang, Ana Maguitman
Bio-semiotics and representations: Simulations of evolving agents with different kinds of reproduction strategies; genotype-phenotype mappings; indirect encoding via development; Fuzzy development programs; More. Study of how information, symbols, representations and the like can arise from a purely dynamical system of many components; Emergent Computation in Cellular Automata; re-formulation of the concept of representation for embodied cognition; origin of representations; More.	Luis M. Rocha, Wim Hordijk

Complex Networks (PIs: Alex Vespignani, Sandro Flammini)

Epidemic Modeling: We are interested in the study of epidemic models in complex networks and systems. We approach this area from two directions. The first one is the theoretical perspective aimed at studying the basic theory that govern epidemic behavior in large-scale complex multi-scale network and agent-based epidemic models. The second one is the study of realistic models that progressively incorporate different social databases and infrastructures networks. This implies the construction of an open source computational platform that integrates epidemic models with a large variety of social and transportation data.	Vittoria Colizza, Alain Barrat, Marc Barthelemy, Alex Vespignani
Internet Structure: The Internet was originally conceived as an infrastructure aimed at helping the research effort, and surprisingly enough its success has led to a large-scale system that has become a scientific challenge by itself. This network is the outcome of a self organization process that gives rise to a large-scale infrastructure whose study is the object of an intense research activity. We are interested in both the characterization and modeling of these networks in connection with the social systems driving their growth and function.More	Romualdo Pastor-Satorras, Alain Barrat, Fil Menczer, Alex Vespignani
Network theory, structure and models: Network theory has recently become a key ingredient in the description, analysis and understanding of a large variety of complex systems which can be characterized in terms of networks. Real-world examples range from networks of social contacts to networks of biological interactions, ecological systems, information architectures, infrastructures and many others. The main activity of our research in this area is the analysis and characterization of the network's structure and the development of models aimed at the understanding of the global behavior of these systems.	Vittoria Colizza, Sandro Flammini, Santo Fortunato, Mariangeles Serrano, Alex Vespignani
NetworkWorkbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research. More	Katy Borner, Albert-Laszlo Barabasi, Santiago Schnell, Alex Vespignani, Stan Wasserman, Eric Wernert, Santo Fortunato
Lanet-vi: A tool for the visualization of the k-core structure of large scale graphs. More	Ignacio Alvarez-Hamelin, Luca Dall'Asta, Alain Barrat, Alessandro Vespignani

Networks and agents Network (PI: Filippo Menczer)

The Networks and agents Network deals with applications and modeling of technological, communication, social, and information networks such as the Web. Our meetings are open to anyone interested.

Search Engines and Web Dynamics: We study how search affects the traffic patterns and the evolution of the Web. More	Santo Fortunato, Sandro Flammini, Alex Vespignani, Jacob Ratkiewicz, Fil Menczer
Internet Traffic Analysis: Analysis of the statistical behavioral patterns that emerge from Internet traffic data may lead to robust design/planning/management tools as well as methods for mitigating attacks by early detection of anomalous patterns correlated with malicious behavior. More	Mark Meiss, Alex Vespignani, Fil Menczer
GiveALink: A social bookmarking network exploring collaborative, hierarchical Web search and recommendation algorithms. More	Ben Markines, Heather Roinestad, Mike Conover, Mira Stoilova, Fil Menczer
6S: Distributed, collaborative Web crawling and searching algorithms inspired by ecological and artificial life systems. Peer-based search driven by adaptive query routing can spontaneously organize into small-world networks with efficient communication capturing semantic locality. More	Le-Shin Wu, Ruj Akavipat, Fil Menczer
Web Similarity Maps: The relationships between different types of Web topology based on hyperlinks, words, and page meaning, and their impact on ranking and crawling algorithms. More	Ana Maguitman, Fulya Erdinc, Heather Roinestad, Alex Vespignani, Fil Menczer
BioNets: Machine learning algorithms for clustering, inference, and vulnerability in biological (eg, protein interaction and metabolic) networks. More	Gayathri Athreya, Divya Rao, Sandro Flammini, Fil Menczer
Social Phishing: Exploitation of social networking sites for identity theft. More	Tom Jagatic, Nate Johnson, Markus Jakobsson, Fil Menczer