Pragmatic Ontology Evolution: Reconciling User Requirements and Application Performance

Increasingly, organizations are adopting ontologies to describe their large catalogues of items. These ontologies need to evolve regularly in response to changes in the domain and the emergence of new requirements. An important step of this process is the selection of candidate concepts to include in the new version of the ontology. This operation needs to take into account a variety of factors and in particular reconcile user requirements and application performance. Current ontology evolution methods focus either on ranking concepts according to their relevance or on preserving compatibility with existing applications. However, they do not take in consideration the impact of the ontology evolution process on the performance of computational tasks – e.g., in this work we focus on instance tagging, similarity computation, generation of recommendations, and data clustering. In this paper, we propose the Pragmatic Ontology Evolution (POE) framework, a novel approach for selecting from a group of candidates a set of concepts able to produce a new version of a given ontology that i) is consistent with the a set of user requirements (e.g., max number of concepts in the ontology), ii) is parametrised with respect to a number of dimensions (e.g., topological considerations), and iii) effectively supports relevant computational tasks. Our approach also supports users in navigating the space of possible solutions by showing how certain choices, such as limiting the number of concepts or privileging trendy concepts rather than historical ones, would reflect on the application performance. An evaluation of POE on the real-world scenario of the evolving Springer Nature taxonomy for editorial classification yielded excellent results, demonstrating a significant improvement over alternative approaches

The interplay between tissue growth and scaffold degradation in engineered tissue constructs

In vitro tissue engineering is emerging as a potential tool to meet the high demand for replacement tissue, caused by the increased incidence of tissue degeneration and damage. A key challenge in this field is ensuring that the mechanical properties of the engineered tissue are appropriate for the in vivo environment. Achieving this goal will require detailed understanding of the interplay between cell proliferation, extracellular matrix (ECM) deposition and scaffold degradation.\ud \ud In this paper, we use a mathematical model (based upon a multiphase continuum framework) to investigate the interplay between tissue growth and scaffold degradation during tissue construct evolution in vitro. Our model accommodates a cell population and culture medium, modelled as viscous fluids, together with a porous scaffold and ECM deposited by the cells, represented as rigid porous materials. We focus on tissue growth within a perfusion bioreactor system, and investigate how the predicted tissue composition is altered under the influence of (i) differential interactions between cells and the supporting scaffold and their associated ECM, (ii) scaffold degradation, and (iii) mechanotransduction-regulated cell proliferation and ECM deposition.\ud \ud Numerical simulation of the model equations reveals that scaffold heterogeneity typical of that obtained from μCT scans of tissue engineering scaffolds can lead to significant variation in the flow-induced mechanical stimuli experienced by cells seeded in the scaffold. This leads to strong heterogeneity in the deposition of ECM. Furthermore, preferential adherence of cells to the ECM in favour of the artificial scaffold appears to have no significant influence on the eventual construct composition; adherence of cells to these supporting structures does, however, lead to cell and ECM distributions which mimic and exaggerate the heterogeneity of the underlying scaffold. Such phenomena have important ramifications for the mechanical integrity of engineered tissue constructs and their suitability for implantation in vivo

Computing eigenvalues of ordinary differential equations

Discretisations of differential eigenvalue problems have a sensitivity to perturbations which is asymptotically least as h ? 0 when the differential equation is in first order system form. Both second and fourth order accurate discretisations of the first order system are straightforward to derive and lead to generalised eigenvalue problems of the form ?? where both A and B are narrow-banded, block bidiagonal (hence unsymmetric) matrices, and typically B is singular. Solutions of the differential equation associated with eigenvalues of small magnitude are best determined by the discretisations. Thus Krylov subspace methods (for example) require A to be invertible and seek large solutions of ?? This already requires rational methods in principle. It follows that rapidly convergent methods based on inverse iteration applied to the original formulation as a nonstandard generalised eigenvalue problem prove attractive for the narrow-banded systems considered here. Also they have the advantage that they are applicable under the weaker condition A ? ?B ? =? . We have had extensive experience with a method combining aspects of Newton's method and inverse iteration and having a convergence rate of 3.56 . Our implementation combines this basic algorithm with a limiting form of Weilandt deflation to find a sequence of eigenvalues. It has proved extremely satisfactory in a range of applications. This formulation has the further advantage that it is easy to insert the eigenvalue calculation inside an outer loop to satisfy a constraint on an auxiliary parameter. Examples to illustrate both the robustness of the deflation and the flexibility of the approach are provided

Quantum states far from the energy eigenstates of any local Hamiltonian

What quantum states are possible energy eigenstates of a many-body Hamiltonian? Suppose the Hamiltonian is non-trivial, i.e., not a multiple of the identity, and L-local, in the sense of containing interaction terms involving at most L bodies, for some fixed L. We construct quantum states \psi which are ``far away'' from all the eigenstates E of any non-trivial L-local Hamiltonian, in the sense that |\psi-E| is greater than some constant lower bound, independent of the form of the Hamiltonian.Comment: 4 page

A universal GRB photon energy-peak luminosity relation

The energetics and emission mechanism of GRBs are not well understood. Here we demonstrate that the instantaneous peak flux or equivalent isotropic peak luminosity, L_iso ergs s^-1, rather than the integrated fluence or equivalent isotropic energy, E_iso ergs, underpins the known high-energy correlations. Using new spectral/temporal parameters calculated for 101 bursts with redshifts from BATSE, BeppoSAX, HETE-II and Swift we describe a parameter space which characterises the apparently diverse properties of the prompt emission. We show that a source frame characteristic-photon-energy/peak luminosity ratio, K_z, can be constructed which is constant within a factor of 2 for all bursts whatever their duration, spectrum, luminosity and the instrumentation used to detect them. The new parameterization embodies the Amati relation but indicates that some correlation between E_peak and E_iso follows as a direct mathematical inference from the Band function and that a simple transformation of E_iso to L_iso yields a universal high energy correlation for GRBs. The existence of K_z indicates that the mechanism responsible for the prompt emission from all GRBs is probably predominantly thermal.Comment: Submitted to Ap