Efficient enumeration of small graphlets and orbits

As the world is flooded with data, the demand for mining data for useful purposes is increasing. An effective techniques is to model the data as networks (graphs) and then apply graph mining techniques for analysis. As on date, the algorithms available to count graphlets and orbits for various types of graphs and their generalizations are limited. The thesis aims to fill the gap by presenting a simple and efficient algorithm for 3-node graphlet and orbit counting that is generic enough to work for both undirected and directed graphs. Our algorithm is compared with the state-of-art algorithms and we show that in most cases our algorithm performs better. We demonstrate our algorithm in three case studies related to (i) enzyme and metabolite correlation network in corn, (ii) watershed governance networks, and (iii) patterns exhibited by co-expression networks of healthy and cancerous stomach cells

Mining real-world networks in systems biology and economics

Recent advances in biotechnology have yielded an explosion of data describing biological systems, creating rich opportunities for new insights into cellular inner-workings and therapeutic discoveries. To keep up with this rapid growth and increase in data complexity, we need novel static, integrative, and dynamic methodologies to continue mining these networked systems. In this thesis we introduce new static, integrative, and dynamic computational frameworks for network analysis, and combine existing ones in new ways, to elucidate the biotechnological biases and functional principles governing molecular interactions and their implications in disease. We focus on mining new knowledge from the yeast and human interactomes, since these are currently the most complete data in biology. We perform three lines of experimental work: 1) the macro-scale study, where we model the yeast and human interactomes and show that their interactome data are growing in structurally and functionally principled ways, characterised by a non-random dual topological nature; 2) the micro-scale study, where we zoom into the specifics of wiring patterns around individual genes and uncover a unique core sub-structure within the human interactome, which contains driver genes dubbed to be the main triggers for disease onset; and 3) the data integration study, where we introduce a new computational framework for fusing multiple types of molecular interaction data and use it to construct the first unified model of the cell’s functional organisation and cross-communication lines. Similarly, a new field of systems economics has gained recent attention, with more financial and economic network data emerging at an increasing pace. Hence, we introduce a new computational methodology for tracking network dynamics and use it to quantify the micro- and macro-scale topological changes in the world trade network over the past 50 years, and to demonstrate the fundamental relationship between topological perturbations and indicators of countries’ political and economic stabilities.Open Acces

Strategies For Overcoming the Grand Challenges of Implementing Environmental Flows: A Coupled Human and Natural Systems Perspective

Global declines in freshwater biodiversity and the ecosystem services freshwater ecosystems provide have prompted a call for accelerated and expanded implementation of conservation interventions to bend the curve on these losses. Environmental flows are recognized as a powerful freshwater conservation tool to boost biodiversity and ecosystem services through targeted water releases from dams, however widespread implementation is lacking. Because implementing environmental flows requires careful planning and consideration of both humans and nature, there are many challenges conservation planners face as they attempt to boost implementation. The research presented in this dissertation aims to provide strategies to overcome the challenges facing environmental flows implementation by conceptualizing and modeling environmental flows as a coupled human and natural system. The first project presented a conceptual framework to identify locations with both high biodiversity value and conservation feasibility to target for e-flows implementation across future climate uncertainty. Despite climate uncertainty, some locations were identified as high conservation priority. This research suggests that despite significant conservation planning challenges, environmental flows can still be implemented, and offers a conservation planning framework that can be used in other settings. The second project tested different simulated scenarios in an incentive-based Payment for Ecosystem Services (PES) water conservation initiative to identify tradeoffs between equity and conservation outcomes. This research found that aiming for an equitable distribution of payments to reduce water consumption and reallocate that water to environmental flows does not result in large tradeoffs to conservation outcomes. This research suggests that prioritizing equity does not sacrifice conservation outcomes and provides a framework for testing equity tradeoffs in PES schemes. The third project surveyed water decision-makers to identify their perspectives on the barriers and data needs to implementing environmental flows. This research found that despite decision makers’ different perspectives on future water conditions, they identified the same barriers and data needs. This research suggests that cooperation on complex human-environmental problems could happen despite strongly held values and beliefs that might otherwise inhibit implementation. The fourth project tested whether targeting influential individuals in conservation networks as early adopters of an environmental flows initiative would boost overall adoption. This research found robust results that targeting influential individuals boosted overall adoption across spatial scales and information diffusion models. This research suggests that to help accelerate and expand environmental flows initiative adoption, influential individuals should be targeted as early adopters. The results presented in this dissertation contribute to current high-priority research efforts in conservation science that aim to help bend the curve on freshwater biodiversity loss by accelerating and expanding the implementation of environmental flows. Overall, considering the needs of both people and nature is key to successful environmental flows implementation

Digital History and Hermeneutics

For doing history in the digital age, we need to investigate the “digital kitchen” as the place where the “raw” is transformed into the “cooked”. The novel field of digital hermeneutics provides a critical and reflexive frame for digital humanities research by acquiring digital literacy and skills. The Doctoral Training Unit "Digital History and Hermeneutics" is applying this new digital practice by reflecting on digital tools and methods

Disturbance indicators for time series reconstruction and marine ecosystem health impact assessment

A systematic reconstruction of Multiple Marine Ecological Disturbances (MMEDs) involving disease occurrence, morbidity and mortality events has been undertaken so that a taxonomy of globally distributed marine disturbance types can be better quantified and common forcing factors identified. Combined disturbance data include indices of morbidity, mortality and disease events affecting humans, marine invertebrates, flora and wildlife populations. In the search for the best disturbance indicators of ecosystem change, the unifying solution for joining data from disparate fields is to organize data into space/time/topic hierarchies that permit convergence of data due to shared and appropriate scaling. The scale of the data selects for compatible methodologies, leading to better data integration, dine series reconstruction and the discovery of new relationships. Information technology approaches designed to assist this process include bibliographic keyword searches, data-mining, data-modeling and geographic information system design. Expert consensus, spatial, temporal, categorical and statistical data reduction methods are used to reclassify thousands of independent anomaly observations into eight functional impact groups representing anoxic-hypoxic, biotoxin-exposure, disease, keystone-chronic, mass-lethal, new-novel-invasive, physically forced and trophic-magnification disturbances. Data extracted from the relational database and Internet (http://www.heedmd.org) geographic information system demonstrate non-random patterns relative to expected dependencies. When data are combined they better reflect response to exogenous forcing factors at larger scales (e.g. North Atlantic and Southern Ocean Oscillation index scales) than is apparent without grouping. New hypotheses have been generated linking MMEDs to climate system forcing , variability and changes within the Northwestern Atlantic Ocean, Gulf of Mexico and Caribbean Sea. A more general global survey known collectively as the Health Ecological and Economic Dimensions (HEED) project demonstrates the potential application of the methodology to the Baltic Sea and other large marine ecosystems. The rescue of multi-decadal climatic, oceanographic, fisheries economic, and public health anomaly data combined with MMED data provides a tool to help researchers create regional disturbance regimes to illustrate disturbance impact. A recommendation for a central data repository is proposed to better coordinate the many data observers, resource managers, and agencies collecting pieces of marine disturbance information needed for monitoring ecosystem condition

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested

Políticas de Copyright de Publicações Científicas em Repositórios Institucionais: O Caso do INESC TEC

A progressiva transformação das práticas científicas, impulsionada pelo desenvolvimento das novas Tecnologias de Informação e Comunicação (TIC), têm possibilitado aumentar o acesso à informação, caminhando gradualmente para uma abertura do ciclo de pesquisa. Isto permitirá resolver a longo prazo uma adversidade que se tem colocado aos investigadores, que passa pela existência de barreiras que limitam as condições de acesso, sejam estas geográficas ou financeiras. Apesar da produção científica ser dominada, maioritariamente, por grandes editoras comerciais, estando sujeita às regras por estas impostas, o Movimento do Acesso Aberto cuja primeira declaração pública, a Declaração de Budapeste (BOAI), é de 2002, vem propor alterações significativas que beneficiam os autores e os leitores. Este Movimento vem a ganhar importância em Portugal desde 2003, com a constituição do primeiro repositório institucional a nível nacional. Os repositórios institucionais surgiram como uma ferramenta de divulgação da produção científica de uma instituição, com o intuito de permitir abrir aos resultados da investigação, quer antes da publicação e do próprio processo de arbitragem (preprint), quer depois (postprint), e, consequentemente, aumentar a visibilidade do trabalho desenvolvido por um investigador e a respetiva instituição. O estudo apresentado, que passou por uma análise das políticas de copyright das publicações científicas mais relevantes do INESC TEC, permitiu não só perceber que as editoras adotam cada vez mais políticas que possibilitam o auto-arquivo das publicações em repositórios institucionais, como também que existe todo um trabalho de sensibilização a percorrer, não só para os investigadores, como para a instituição e toda a sociedade. A produção de um conjunto de recomendações, que passam pela implementação de uma política institucional que incentive o auto-arquivo das publicações desenvolvidas no âmbito institucional no repositório, serve como mote para uma maior valorização da produção científica do INESC TEC.The progressive transformation of scientific practices, driven by the development of new Information and Communication Technologies (ICT), which made it possible to increase access to information, gradually moving towards an opening of the research cycle. This opening makes it possible to resolve, in the long term, the adversity that has been placed on researchers, which involves the existence of barriers that limit access conditions, whether geographical or financial. Although large commercial publishers predominantly dominate scientific production and subject it to the rules imposed by them, the Open Access movement whose first public declaration, the Budapest Declaration (BOAI), was in 2002, proposes significant changes that benefit the authors and the readers. This Movement has gained importance in Portugal since 2003, with the constitution of the first institutional repository at the national level. Institutional repositories have emerged as a tool for disseminating the scientific production of an institution to open the results of the research, both before publication and the preprint process and postprint, increase the visibility of work done by an investigator and his or her institution. The present study, which underwent an analysis of the copyright policies of INESC TEC most relevant scientific publications, allowed not only to realize that publishers are increasingly adopting policies that make it possible to self-archive publications in institutional repositories, all the work of raising awareness, not only for researchers but also for the institution and the whole society. The production of a set of recommendations, which go through the implementation of an institutional policy that encourages the self-archiving of the publications developed in the institutional scope in the repository, serves as a motto for a greater appreciation of the scientific production of INESC TEC

A Function-based Relevance Model for Making Sense of Technological Change in the Context of a Firm

Industrial Engineerin