arXiv subjects

Martin Jones

Publications and source records attributed to Martin Jones.

5 recordsLinked to original sources

arXiv2023

MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis

Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standards for sharing datasets. We brought together community experts in a workshop to develop guidelines to improve the reuse of bioimages and annotations for AI applications. These include standards on data formats, metadata, data presentation and sharing, and incentives to generate new datasets. We are positive that the MIFA (Metadata, Incentives, Formats, and Accessibility) recommendations will accelerate the development of AI tools for bioimage analysis by facilitating access to high quality training data.

q-bio.OT↗

arXiv2017

Reinforcement Learning Produces Dominant Strategies for the Iterated Prisoner's Dilemma

We present tournament results and several powerful strategies for the Iterated Prisoner's Dilemma created using reinforcement learning techniques (evolutionary and particle swarm algorithms). These strategies are trained to perform well against a corpus of over 170 distinct opponents, including many well-known and classic strategies. All the trained strategies win standard tournaments against the total collection of other opponents. The trained strategies and one particular human made designed strategy are the top performers in noisy tournaments also.

cs.GT↗

arXiv2016

An open reproducible framework for the study of the iterated prisoner's dilemma

The Axelrod library is an open source Python package that allows for reproducible game theoretic research into the Iterated Prisoner's Dilemma. This area of research began in the 1980s but suffers from a lack of documentation and test code. The goal of the library is to provide such a resource, with facilities for the design of new strategies and interactions between them, as well as conducting tournaments and ecological simulations for populations of strategies. With a growing collection of 139 strategies, the library is a also a platform for an original tournament that, in itself, is of interest to the game theoretic community. This paper describes the Iterated Prisoner's Dilemma, the Axelrod library and its development, and insights gained from some novel research.

cs.GT↗

arXiv2014

Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis

There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In the current paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurring in areas where wall shear stress gradients exist. We propose two possible mechanisms to account for the observed increase in velocity and wall shear stress between P5 and P6: i) the measured reduction in typical vessel diameter between both time points, ii) the reduction in network density triggered by the pruning process. The methodology developed herein is applicable to other biomedical domains where microvasculature can be imaged but experimental flow measurements are unavailable or difficult to obtain.

cs.CE↗

arXiv2007

Relation between exchange-only optimized potential and Kohn-Sham methods with finite basis sets; solution of a paradox

Arguments showing that exchange-only optimized effective potential (xOEP) methods, with finite basis sets, cannot in general yield the Hartree-Fock (HF) ground state energy, but a higher one, are given. While the orbital products of a complete basis are linearly dependent, the HF ground state energy can only be obtained via a basis set xOEP scheme in the special case that all products of occupied and unoccupied orbitals emerging from the employed orbital basis set are linearly independent from each other. In this case, however, exchange potentials leading to the HF ground state energy exhibit unphysical oscillations and do not represent a Kohn-Sham (KS) exchange potential. These findings solve the seemingly paradoxical results of Staroverov, Scuseria and Davidson that certain finite basis set xOEP calculations lead to the HF ground state energy despite the fact that within a real space (or complete basis) representation the xOEP ground state energy is always higher than the HF energy. Moreover, whether or not the occupied and unoccupied orbital products are linearly independent, it is shown that basis set xOEP methods only represent exact exchange-only (EXX) KS methods, i.e., proper density-functional methods, if the orbital basis set and the auxiliary basis set representing the exchange potential are balanced to each other, i.e., if the orbital basis is comprehensive enough for a given auxiliary basis. Otherwise xOEP methods do not represent EXX KS methods and yield unphysical exchange potentials.

physics.chem-ph↗