Evaluating diagramming as praxis

Researching into systemic failure associated with complex situations of environmental sustainability involves many different interactions amongst many different entities (human and non-human). For example, the trigger of global warming (caused primarily by use of fossil fuels in developed countries) has encouraged the rapid development of biofuel agriculture through grants from rich countries in the global North to Brazil and other tropical countries in the global South. This has generated what Sawyer (2008) calls an eco-social collapse: involving both ecological problems (deforestation, pesticide pollution, etc.) and socio-economic problems (particularly with concentration of land tenure, very poor working conditions for those forced to provide cheap labour for biofuel plantations, and increasing food prices for the population). To what extent might such a situation arise from breakdowns in the quality of communications? Apart from researching the importance of inter-human communication, there might also be important factors associated with the quality of our ‘communication’ with the natural world. In this chapter I use the metaphor of ‘conversation’ for describing praxis. The chapter weaves together three stories about diagramming as a means of developing sustainability through praxis. The first story provides some context. It is about evaluation in the field of sustainable development, and particularly the conversation between what might be called big ‘E’ evaluation – institutionalised demands for evidence-based guarantors or assurances for successful interventions as expected, for example, by funders of research – and small ‘e’ evaluation – the multitude of practices including visual based tools that may contribute towards developing value in, for example, a funded research project. The story tracks the growing importance of what has been called ‘developmental evaluation’ (Patton, 2011) – a tradition involving research evaluation – as a means of conversing between big ‘E’ and small ‘e’. The second and third stories track the history of a particular diagram developed by the author; a representation of praxis that has been shaken-up, messed-about with, and adapted for different uses during the past 15 years. The first of these two stories relates to representing the praxis of environmental responsibility (as a core constituent of developing environmental sustainability), and the second relates to making visual representations of developmental evaluation. Both stories narrate the changing form of the diagramming to suit particular needs. The purpose here is to demonstrate how a diagrammatic representation might allow space for ‘conversation’ at different levels of practice, including disciplinary (amongst specialist experts), interdisciplinary (between different experts) and transdisciplinary (between experts and civil society) practices. Weaving the stories together, a mapping tool – the heuristic of systemic triangulation – is presented as a systems-based influence diagram. The tool can be used for evaluating interventions at different levels, including the intervention of using visual techniques

Solving Graph Problems via Potential Maximal Cliques : An Experimental Evaluation of the Bouchitté-Todinca Algorithm

Peer reviewe

Finding Optimal Tree Decompositions

The task of organizing a given graph into a structure called a tree decomposition is relevant in multiple areas of computer science. In particular, many NP-hard problems can be solved in polynomial time if a suitable tree decomposition of a graph describing the problem instance is given as a part of the input. This motivates the task of finding as good tree decompositions as possible, or ideally, optimal tree decompositions. This thesis is about finding optimal tree decompositions of graphs with respect to several notions of optimality. Each of the considered notions measures the quality of a tree decomposition in the context of an application. In particular, we consider a total of seven problems that are formulated as finding optimal tree decompositions: treewidth, minimum fill-in, generalized and fractional hypertreewidth, total table size, phylogenetic character compatibility, and treelength. For each of these problems we consider the BT algorithm of Bouchitté and Todinca as the method of finding optimal tree decompositions. The BT algorithm is well-known on the theoretical side, but to our knowledge the first time it was implemented was only recently for the 2nd Parameterized Algorithms and Computational Experiments Challenge (PACE 2017). The author’s implementation of the BT algorithm took the second place in the minimum fill-in track of PACE 2017. In this thesis we review and extend the BT algorithm and our implementation. In particular, we improve the eciency of the algorithm in terms of both theory and practice. We also implement the algorithm for each of the seven problems considered, introducing a novel adaptation of the algorithm for the maximum compatibility problem of phylogenetic characters. Our implementation outperforms alternative state-of-the-art approaches in terms of numbers of test instances solved on well-known benchmarks on minimum fill-in, generalized hypertreewidth, fractional hypertreewidth, total table size, and the maximum compatibility problem of phylogenetic characters. Furthermore, to our understanding the implementation is the first exact approach for the treelength problem

A Computational Framework for Learning from Complex Data: Formulations, Algorithms, and Applications

Many real-world processes are dynamically changing over time. As a consequence, the observed complex data generated by these processes also evolve smoothly. For example, in computational biology, the expression data matrices are evolving, since gene expression controls are deployed sequentially during development in many biological processes. Investigations into the spatial and temporal gene expression dynamics are essential for understanding the regulatory biology governing development. In this dissertation, I mainly focus on two types of complex data: genome-wide spatial gene expression patterns in the model organism fruit fly and Allen Brain Atlas mouse brain data. I provide a framework to explore spatiotemporal regulation of gene expression during development. I develop evolutionary co-clustering formulation to identify co-expressed domains and the associated genes simultaneously over different temporal stages using a mesh-generation pipeline. I also propose to employ the deep convolutional neural networks as a multi-layer feature extractor to generate generic representations for gene expression pattern in situ hybridization (ISH) images. Furthermore, I employ the multi-task learning method to fine-tune the pre-trained models with labeled ISH images. My proposed computational methods are evaluated using synthetic data sets and real biological data sets including the gene expression data from the fruit fly BDGP data sets and Allen Developing Mouse Brain Atlas in comparison with baseline existing methods. Experimental results indicate that the proposed representations, formulations, and methods are efficient and effective in annotating and analyzing the large-scale biological data sets

Microgastrinae (Hymenoptera: Braconidae) parasitizing Epirrita autumnata (Lepidoptera: Geometridae) larvae in Fennoscandia with description of Cotesia autumnatae Shaw, sp. n.

The microgastrine subset of hymenopteran parasitoids of the geometrid Epirrita autumnata is investigated in Fennoscandia. Ecology, including population dynamics, of the moth has been intensively studied in northern and mountainous Finland, Norway and Sweden. Recently supported hypotheses about the causes of its cyclic population dynamics stress the role of parasitoids, while the parasitoid complex with some 15 species is insufficiently known. The complex includes four solitarymicrogastrine species, Protapanteles anchisiades (Nixon), P. immunis (Wesmael), Cotesia salebrosa (Marshall) and C. autumnatae Shaw, sp. n. Here, we provide detailed figures for the latter, which is morphologically close to C. jucunda (Marshall), and describe the species as new to science. We also providemore general habitus figures of the other three species, as well as an identification key for the four species, aiming to aid recognition of these species by ecologists dealingwithmicrogastrine parasitoids of E. autumnata and their alternative geometrid hosts

Singular Continuation: Generating Piece-wise Linear Approximations to Pareto Sets via Global Analysis

We propose a strategy for approximating Pareto optimal sets based on the global analysis framework proposed by Smale (Dynamical systems, New York, 1973, pp. 531-544). The method highlights and exploits the underlying manifold structure of the Pareto sets, approximating Pareto optima by means of simplicial complexes. The method distinguishes the hierarchy between singular set, Pareto critical set and stable Pareto critical set, and can handle the problem of superposition of local Pareto fronts, occurring in the general nonconvex case. Furthermore, a quadratic convergence result in a suitable set-wise sense is proven and tested in a number of numerical examples.Comment: 29 pages, 12 figure

Bi-objective optimization of organ properties for the simulation of intracavitary brachytherapy applicator placement in cervical cancer

Validation of deformable image registration techniques is extremely important, but hard, especially when complex deformations or content mismatch are involved. These complex deformations and content mismatch, for example, occur after the placement of an applicator for brachytherapy for cervical cancer. Virtual phantoms could enable the creation of validation data sets with ground truth deformations that simulate the large deformations that occur between image acquisitions. However, the quality of the multi-organ Finite Element Method (FEM)-based simulations is dependent on the patient-specific external forces and mechanical properties assigned to the organs. A common approach to calibrate these simulation parameters is through optimization, finding the parameter settings that optimize the match between the outcome of the simulation and reality. When considering inherently simplified organ models, we hypothesize that the optimal deformations of one organ cannot be achieved with a single parameter setting without compromising the optimality of the deformation of the surrounding organs. This means that there will be a trade-off between the optimal deformations of adjacent organs, such as the vagina-uterus and bladder. This work therefore proposes and evaluates a multi-objective optimization approach where the trade-off between organ deformations can be assessed after optimization. We showcase what the extent of the trade-off looks like when bi-objectively optimizing the patient-specific mechanical properties and external forces of the vagina-uterus and bladder for FEM-based simulations

Parallel software tool for decomposing and meshing of 3d structures

An algorithm for automatic parallel generation of three-dimensional unstructured computational meshes based on geometrical domain decomposition is proposed in this paper. Software package build upon proposed algorithm is described. Several practical examples of mesh generation on multiprocessor computational systems are given. It is shown that developed parallel algorithm enables us to reduce mesh generation time significantly (dozens of times). Moreover, it easily produces meshes with number of elements of order 5 · 107, construction of those on a single CPU is problematic. Questions of time consumption, efficiency of computations and quality of generated meshes are also considered

Analysis of the Effects of Curvature on the Solutions of Shallow Water Equations

The most used form of the Shallow Water Equations doesn't take into account the variation of the curvature of the base flow surface. In this paper, we compare the theoretical and numerical solutions of the standard model and with the solutions of an extended model and for a large class of base flow surfaces. We find that the solution of the standard model is still a good approximation for the extended model for many real life applications