Local search: A guide for the information retrieval practitioner

There are a number of combinatorial optimisation problems in information retrieval in which the use of local search methods are worthwhile. The purpose of this paper is to show how local search can be used to solve some well known tasks in information retrieval (IR), how previous research in the field is piecemeal, bereft of a structure and methodologically flawed, and to suggest more rigorous ways of applying local search methods to solve IR problems. We provide a query based taxonomy for analysing the use of local search in IR tasks and an overview of issues such as fitness functions, statistical significance and test collections when conducting experiments on combinatorial optimisation problems. The paper gives a guide on the pitfalls and problems for IR practitioners who wish to use local search to solve their research issues, and gives practical advice on the use of such methods. The query based taxonomy is a novel structure which can be used by the IR practitioner in order to examine the use of local search in IR

Building a cell and anatomy ontology of Caenorhabditis elegans

We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress

Optimizing Photonic Nanostructures via Multi-fidelity Gaussian Processes

We apply numerical methods in combination with finite-difference-time-domain (FDTD) simulations to optimize transmission properties of plasmonic mirror color filters using a multi-objective figure of merit over a five-dimensional parameter space by utilizing novel multi-fidelity Gaussian processes approach. We compare these results with conventional derivative-free global search algorithms, such as (single-fidelity) Gaussian Processes optimization scheme, and Particle Swarm Optimization---a commonly used method in nanophotonics community, which is implemented in Lumerical commercial photonics software. We demonstrate the performance of various numerical optimization approaches on several pre-collected real-world datasets and show that by properly trading off expensive information sources with cheap simulations, one can more effectively optimize the transmission properties with a fixed budget.Comment: NIPS 2018 Workshop on Machine Learning for Molecules and Materials. arXiv admin note: substantial text overlap with arXiv:1811.0075