Latent Gaussian modeling and INLA: A review with focus on space-time applications

Bayesian hierarchical models with latent Gaussian layers have proven very flexible in capturing complex stochastic behavior and hierarchical structures in high-dimensional spatial and spatio-temporal data. Whereas simulation-based Bayesian inference through Markov Chain Monte Carlo may be hampered by slow convergence and numerical instabilities, the inferential framework of Integrated Nested Laplace Approximation (INLA) is capable to provide accurate and relatively fast analytical approximations to posterior quantities of interest. It heavily relies on the use of Gauss-Markov dependence structures to avoid the numerical bottleneck of high-dimensional nonsparse matrix computations. With a view towards space-time applications, we here review the principal theoretical concepts, model classes and inference tools within the INLA framework. Important elements to construct space-time models are certain spatial Mat\'ern-like Gauss-Markov random fields, obtained as approximate solutions to a stochastic partial differential equation. Efficient implementation of statistical inference tools for a large variety of models is available through the INLA package of the R software. To showcase the practical use of R-INLA and to illustrate its principal commands and syntax, a comprehensive simulation experiment is presented using simulated non Gaussian space-time count data with a first-order autoregressive dependence structure in time

Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter

Microbial carbon use efficiency (CUE) is a critical regulator of soil organic matter dynamics and terrestrial carbon fluxes, with strong implications for soil biogeochemistry models. While ecologists increasingly appreciate the importance of CUE, its core concepts remain ambiguous: terminology is inconsistent and confusing, methods capture variable temporal and spatial scales, and the significance of many fundamental drivers remains inconclusive. Here we outline the processes underlying microbial efficiency and propose a conceptual framework that structures the definition of CUE according to increasingly broad temporal and spatial drivers where (1) CUEP reflects population-scale carbon use efficiency of microbes governed by species-specific metabolic and thermodynamic constraints, (2) CUEC defines community-scale microbial efficiency as gross biomass production per unit substrate taken up over short time scales, largely excluding recycling of microbial necromass and exudates, and (3) CUEE reflects the ecosystem-scale efficiency of net microbial biomass production (growth) per unit substrate taken up as iterative breakdown and recycling of microbial products occurs. CUEE integrates all internal and extracellular constraints on CUE and hence embodies an ecosystem perspective that fully captures all drivers of microbial biomass synthesis and decay. These three definitions are distinct yet complementary, capturing the capacity for carbon storage in microbial biomass across different ecological scales. By unifying the existing concepts and terminology underlying microbial efficiency, our framework enhances data interpretation and theoretical advances

Vicarious learning through capturing task‐directed discussions

The vicarious learner group has been developing a multimedia database system to promote and enhance the role of dialogue in learning. A specific interest, and the origin of the projects' collective name, is in the question of whether and how dialogue can be helpfully ‘reused’. What benefits can students gain from dialogue as observers, not just as participants? We describe our initial attempts to generate and capture educationally effective discourse exchanges amongst and between students and tutors. Problems encountered with available CMC discourse formats led to our development of a set of Task Directed Discussions (TDDs). A medium‐sized corpus of discourse exchanges was collected using the TDDs. A selection of nearly two hundred of these TDD exchanges formed the multimedia discourse database to the implemented prototype system, Dissemination. Initial results from a controlled experiment and evaluation of Dissemination are outline

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform

Enhancing design learning using a digital repository

The process of design is context dependent and open-ended, and therefore does not revolve around a specific body of information or knowledge. The educational paradigm shift in the area of engineering design from teaching to coaching and the increased use of social constructivist learning ideals requires students to have access to as wide a range of information as possible. Digital resources provide an excellent opportunity for extending the range of information available to design students and to this end, as part of a joint research program with Stanford University, the University of Strathclyde has developed a groupware product called LauLima to provide students with a collaborative environment which allows them to gather, organise, store and share information. This paper describes the improvement to design learning, based on a Design Knowledge Framework, in a 3rd year product design engineering project from session 03/04 to 04/05 which has been facilitated by the implementation of this technology

Model Creation and Equivalence Proofs of Cellular Automata and Artificial Neural Networks

Computational methods and mathematical models have invaded arguably every scientific discipline forming its own field of research called computational science. Mathematical models are the theoretical foundation of computational science. Since Newton's time, differential equations in mathematical models have been widely and successfully used to describe the macroscopic or global behaviour of systems. With spatially inhomogeneous, time-varying, local element-specific, and often non-linear interactions, the dynamics of complex systems is in contrast more efficiently described by local rules and thus in an algorithmic and local or microscopic manner. The theory of mathematical modelling taking into account these characteristics of complex systems has to be established still. We recently presented a so-called allagmatic method including a system metamodel to provide a framework for describing, modelling, simulating, and interpreting complex systems. Implementations of cellular automata and artificial neural networks were described and created with that method. Guidance from philosophy were helpful in these first studies focusing on programming and feasibility. A rigorous mathematical formalism, however, is still missing. This would not only more precisely describe and define the system metamodel, it would also further generalise it and with that extend its reach to formal treatment in applied mathematics and theoretical aspects of computational science as well as extend its applicability to other mathematical and computational models such as agent-based models. Here, a mathematical definition of the system metamodel is provided. Based on the presented formalism, model creation and equivalence of cellular automata and artificial neural networks are proved. It thus provides a formal approach for studying the creation of mathematical models as well as their structural and operational comparison.Comment: 13 pages, 1 tabl

Model granularity and related concepts

Models are integral to engineering design and basis for many decisions. Therefore, it is necessary to comprehend how a model’s properties might influence its behaviour. Model granularity is an important property but has so far only received limited attention. The terminology used to describe granularity and related phenomena varies and pertinent concepts are distributed across communities. This article positions granularity in the theoretical background of models, collects formal definitions for relevant terms from a range of communities and discusses the implications for engineering design