Greg Madey

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Papers by Greg Madey

A stochastic model for the synthesis and degradation of natural organic matter. Part III: Modeling Cu(II) complexation

Applied Geochemistry, 2007

A stochastic biogeochemical model has been developed to simulate the transformation and degradati... more A stochastic biogeochemical model has been developed to simulate the transformation and degradation of natural organic matter (NOM) using an agent-based algorithm which treats each molecule as a separate and potentially unique entity. Molecules react when a pseudo-random number is lower than the calculated reaction probability in a given time step; repeated time steps simulate the transformation of precursor molecules into a complex NOM assemblage. The data for each molecule-elemental and functional group composition-can be used to calculate many properties directly and exactly for each molecule in the assemblage, e.g., molecular weight (MW), fraction of aromatic C (Ar), and charge at pH 7 (Z). Empirical quantitative structure activity relationships (QSARs) are developed which permit the estimation of thermodynamic quantities K ow (the octanol-water partition coefficient) and pK a (acidity) for each molecule. Root mean square errors for these QSARs are 0.39 log units for log K ow and 0.45 log units for pK a . Distributions of both exactly calculated (MW, Ar, Z) and estimated thermodynamic (K ow , pK a ) properties are examined and compared with published experimental data. Molecular weight distributions from size exclusion HPLC experiments on aquatic NOM are quantitatively similar to simulation results. pH titrations and polarity distributions from reversed-phase HPLC are qualitatively similar to simulation results. This agreement suggests that the agent-based model can be used to explore hypotheses regarding both compositional and thermodynamic properties of NOM.

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Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

by Henk Braig, Greg Madey, Evgenia Kriventseva, Barry Pittendrigh, Barry Pittendrigh, D. Reed, and M. Alejandra Perotti

Proceedings of the National Academy of Sciences, 2010

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PGMS: A Case Study of Collecting PDA-Based Geo-Tagged Malaria-Related Survey Data

by Sulistyawati Suyanto, Ying Zhou, and Greg Madey

Using mobile devices, such as personal digital assistants (PDAs), smartphones, tablet computers, ... more Using mobile devices, such as personal digital assistants (PDAs), smartphones, tablet computers, etc., to electronically collect malaria-related field data is the way for the field questionnaires in the future. This case study seeks to design a generic survey framework PDA-based geo-tagged malaria-related data collection tool (PGMS) that can be used not only for large-scale community-level geo-tagged electronic malaria-related surveys, but also for a wide variety of electronic data collections of other infectious diseases. The framework includes two parts: the database designed for subsequent cross-sectional data analysis and the customized programs for the six study sites (two in Kenya, three in Indonesia, and one in Tanzania). In addition to the framework development, we also present our methods used when configuring and deploying the PDAs to 1) reduce data entry errors, 2) conserve battery power, 3) field install the programs onto dozens of handheld devices, 4) translate electronic questionnaires into local languages, 5) prevent data loss, and 6) transfer data from PDAs to computers for future analysis and storage. Since 2008, PGMS has successfully accomplished quite a few surveys that recorded 10,871 compounds and households, 52,126 persons, and 17,100 bed nets from the six sites. These numbers are still growing.

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The Importance of Social Network Structure in the Open Source Software Developer Community

2010 43rd Hawaii International Conference on System Sciences, 2010

suggested social network structure was instrumental towards the success of an OSS project, as mea... more suggested social network structure was instrumental towards the success of an OSS project, as measured by activity and output. The follow-up paper by Hinds discovered that his hypotheses, based on social network theory and previous research on the importance of subgroup connectedness, were vastly different than the results of his study of over 100 successful OSS projects. He concluded that the social network structure had no significant effect on project success. We outline how his approach disregarded potentially important factors and through a new study evaluate the role of the OSS developer network as it pertains to long-term project popularity. We also present an initial investigation into the adequacy of using the SourceForge activity percentile as a long-term success metric. In contrast with Hinds, we show that previously existing developer-developer ties are an indicator of past and future project popularity.

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Open Source Software Developer and Project Networks

IFIP Advances in Information and Communication Technology, 2010

This paper outlines complex network concepts and how social networks are built from Open Source S... more This paper outlines complex network concepts and how social networks are built from Open Source Software (OSS) data. We present an initial study of the social networks of three different OSS forges, BerliOS Developer, GNU Savannah, and SourceForge. Much research has been done on snapshot or conflated views of these networks, especially SourceForge, due to the size of the SourceForge community. The degree distribution, connectedness, centrality, and scale-free nature of SourceForge has been presented for the network at particular points in time. However, very little research has been done on how the network grows, how connections were made, especially during its infancy, and how these metrics evolve over time.

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Warehousing and Studying Open Source Versioning Metadata

IFIP Advances in Information and Communication Technology, 2010

In this paper, we describe the downloading and warehousing of Open Source Software (OSS) versioni... more In this paper, we describe the downloading and warehousing of Open Source Software (OSS) versioning metadata from SourceForge, BerliOS Developer, and GNU Savannah. This data enables and supports research in areas such as software engineering, open source phenomena, social network analysis, data mining, and project management. This newly-formed database containing Concurrent Versions System (CVS) and Subversion (SVN) metadata offers new

PUBLIC GOODS THEORY OF THE OPEN SOURCE DEVELOPMENT COMMUNITY USING AGENT-BASED SIMULATION

Creation of open source software (OSS) can be considered a collective action by individuals with ... more Creation of open source software (OSS) can be considered a collective action by individuals with the mutual self-interest of creating and maintaining a public good. We explain the OSS development process in terms of public goods theory including the notions of connectivity and communality for interactive communication systems; we add an additional feature which is the characteristics of the environment as it interacts with the OSS development community. OSS is more than a simple, classical, physical good; it is a complex, socially-constructed, informational good that has heterogeneous resource requirements and provides heterogeneous benefits to its users. Critical mass occurs not at a singular point in time but is ongoing adaptive process, and the notion of success for a project is dependent upon both the group's cognitive purpose of the software and each member's cognitive belief in the project's success. In this paper, we describe in detail the connection between the OSS development community and public goods theory, and we explore the hypothesis of open source software as a public good by using agent-based modeling and simulation.

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A SYSTEM FOR DETECTING ANOMALIES IN DATA STREAMS FOR EMERGENCY RESPONSE APPLICATIONS

Using Agent-Based Modeling in the Exploration of Self-Organizing Neural Networks

In this paper we leverage the power of agent-based modeling to explore a novel self-organizing ne... more In this paper we leverage the power of agent-based modeling to explore a novel self-organizing neural network topology. We have drawn inspiration from recent research into complex networks and advances in neurobiology, and applied it towards the construction of a neural network. Techniques from agent-based modeling are used to simplify the construction process and provide flexibility in modifying the simulation. The experiment also implements ideas from swarm programming, using local information to develop global structure. We demonstrate our simulation, modeled using the RePast framework.

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Activity Mining in Open Source Software

Open Source software repository is a collection of various projects with varying levels of activi... more Open Source software repository is a collection of various projects with varying levels of activities, participations, and downloads. In this paper, we attempt to categorize and mine activity, thus discovering success, by focusing on the Games group. However, we observe that there are a significant number of projects within the Games category that are inactive or have no ranking assigned by Sourceforge. So, we first segmented our dataset based on just the ranking or activity assigned. We then constructed a set of characteristics, such as number of developers; number of posters; number of downloads, to identify associations, activity, and relationships in the smaller active set. We used regression rules and association rules to discover the associations and relationships.

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Modeling and simulation of Open Source Software community

Affective Dialogue Systems, 2000

The Open Source Software (OSS) development movement is a classic example of a social network; it ... more The Open Source Software (OSS) development movement is a classic example of a social network; it is also a prototype of a complex evolving network. In this research, we used simulation to help us with understanding the OSS development movement. First we generate a model to depict the evolution of the SourceForge community, one of the biggest OSS communities, as a network. And then we simulate the evolution of the network using Java/Swarm and calibrate the simulation with the empirical data we collected from SourceForge. In simulation, we used several different models to find the best fit model for the empirical data in an iterative fashion. These models include a random network, a scale-free network and a scale-free network with constant fitness. Also we proposed and verified the scale-free network with dynamic fitness model at the end of the simulation iterations. 2 http://sourceforge.net ADS'05 113 ISBN-1-56555-291

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WIPER: An Emergency Response System

This paper describes the WIPER system, a proof of concept prototype, and progress made on its dev... more This paper describes the WIPER system, a proof of concept prototype, and progress made on its development to date. WIPER is intended to provide emergency response managers with an integrated system that detects possible emergencies from cellular communication data, attempts to predict the development of emergency situations, and provides tools for evaluating possible courses of action in dealing with emergency situations. We describe algorithms for detecting anomalies in streaming cellular communication network data, the implementation of a simulation system that validates running simulations with new real world data, and a web-based front end to the WIPER system. We also discuss issues relating to the real-time aggregation of data from the cellular service provider and its distribution to components of the WIPER system.

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Evaluation of Measurement Techniques for the Validation of Agent-Based Simulations Against Streaming Data

Lecture Notes in Computer Science, 2008

Expert-Citizen Engineering: "Crowdsourcing" Skilled Citizens

2011 IEEE Ninth International Conference on Dependable, Autonomic and Secure Computing, 2011

... Daniel Wei, Ahsan Kareem Department of Civil Engineering and Geological Sciences University o... more

Feature Clustering for Data Steering in Dynamic Data Driven Application Systems

Lecture Notes in Computer Science, 2009

... system. In: Fiedrich, F., de Walle, BV (eds.) Proceedings of the 5th International ISCRAM Con... more

Anomaly Detection in Streaming Sensor Data

Concepts, Methodologies, Tools and Applications, 2012

In this chapter we consider a cell phone network as a set of automatically deployed sensors that ... more In this chapter we consider a cell phone network as a set of automatically deployed sensors that records movement and interaction patterns of the population. We discuss methods for detecting anomalies in the streaming data produced by the cell phone network. We motivate this discussion by describing the Wireless Phone Based Emergency Response (WIPER) system, a proof-of-concept decision support system for emergency response managers. We also discuss some of the scientific work enabled by this type of sensor data and the related privacy issues. We describe scientific studies that use the cell phone data set and steps we have taken to ensure the security of the data. We describe the overall decision support system and discuss three methods of anomaly detection that we have applied to the data.

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Anomaly Detection in Streaming Sensor Data

Mobile communication networks produce massive amounts of data which may be useful in identifying ... more Mobile communication networks produce massive amounts of data which may be useful in identifying the location of an emergency situation and the area it affects. We propose a one pass clustering algorithm's for quickly identifying anomalous data points. We evaluate this algorithms ability to detect outliers in a data set and describe how such an algorithm may be used as a component of an emergency response management system.

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Citizen Engineering: Methods for "Crowdsourcing" Highly Trustworthy Results

Hawaii International Conference on System Sciences, 2012

Citizen Engineering seeks to leverage a large number of ordinary citizens to solve real-world pro... more Citizen Engineering seeks to leverage a large number of ordinary citizens to solve real-world problems. Emerging information technologies provide us with opportunities to answer a long-standing challenge in citizen engineering -- can we effectively extract reliable results from a myriad of crowd inputs of varying quality? To investigate efficient approaches to achieving this &amp;amp;amp;quot;wisdom of crowds&amp;amp;amp;quot;, we established a prototype

Uncovering individual and collective human dynamics from mobile phone records

Journal of Physics A-mathematical and Theoretical, 2008

Novel aspects of human dynamics and social interactions are investigated by means of mobile phone... more Novel aspects of human dynamics and social interactions are investigated by means of mobile phone data. Using extensive phone records resolved in both time and space, we study the mean collective behavior at large scales and focus on the occurrence of anomalous events. We discuss how these spatiotemporal anomalies can be described using standard percolation theory tools. We also investigate patterns of calling activity at the individual level and show that the interevent time of consecutive calls is heavy-tailed. This finding, which has implications for dynamics of spreading phenomena in social networks, agrees with results previously reported on other human activities.

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Student Engineers Reaching Out: Case studies in service learning and a survey of technical need

2007 37th annual frontiers in education conference - global engineering: knowledge without borders, opportunities without passports, 2007

... Paul R. Brenner, Megan Schroeder, and Greg Madey University of Notre Dame, College of Enginee... more

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