Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

Bayesian optimization using sequential Monte Carlo

We consider the problem of optimizing a real-valued continuous function $f$ using a Bayesian approach, where the evaluations of $f$ are chosen sequentially by combining prior information about $f$, which is described by a random process model, and past evaluation results. The main difficulty with this approach is to be able to compute the posterior distributions of quantities of interest which are used to choose evaluation points. In this article, we decide to use a Sequential Monte Carlo (SMC) approach

The four-loop DRED gauge beta-function and fermion mass anomalous dimension for general gauge groups

We present four-loop results for the gauge beta-function and the fermion mass anomalous dimension for a gauge theory with a general gauge group and a multiplet of fermions transforming according to an arbitrary representation, calculated using the dimensional reduction scheme. In the special case of a supersymmetric theory we confirm previous calculations of both the gauge beta-function and the gaugino mass beta-function.Comment: 44 pages, added references (v2) minor changes (v3

Grid simulation services for the medical community

The first part of this paper presents a selection of medical simulation applications, including image reconstruction, near real-time registration for neuro-surgery, enhanced dose distribution calculation for radio-therapy, inhaled drug delivery prediction, plastic surgery planning and cardio-vascular system simulation. The latter two topics are discussed in some detail. In the second part, we show how such services can be made available to the clinical practitioner using Grid technology. We discuss the developments and experience made during the EU project GEMSS, which provides reliable, efficient, secure and lawful medical Grid services

The Effective Potential, the Renormalisation Group and Vacuum Stability

We review the calculation of the the effective potential with particular emphasis on cases when the tree potential or the renormalisation-group-improved, radiatively corrected potential exhibits non-convex behaviour. We illustrate this in a simple Yukawa model which exhibits a novel kind of dimensional transmutation. We also review briefly earlier work on the Standard Model. We conclude that, despite some recent claims to the contrary, it can be possible to infer reliably that the tree vacuum does not represent the true ground state of the theory.Comment: 23 pages; 5 figures; v2 includes minor changes in text and additional reference

Gauge invariant reduction to the light-front

The problem of constructing gauge invariant currents in terms of light-cone bound-state wave functions is solved by utilising the gauging of equations method. In particular, it is shown how to construct perturbative expansions of the electromagnetic current in the light-cone formalism, such that current conservation is satisfied at each order of the perturbation theory.Comment: 12 pages, revtex

A hybrid multiagent approach for global trajectory optimization

In this paper we consider a global optimization method for space trajectory design problems. The method, which actually aims at finding not only the global minimizer but a whole set of low-lying local minimizers(corresponding to a set of different design options), is based on a domain decomposition technique where each subdomain is evaluated through a procedure based on the evolution of a population of agents. The method is applied to two space trajectory design problems and compared with existing deterministic and stochastic global optimization methods

Anomaly Mediation, Fayet-Iliopoulos D-terms and the Renormalisation Group

We address renormalisation group evolution issues that arise in the Anomaly Mediated Supersymmetry Breaking scenario when the tachyonic slepton problem is resolved by Fayet-Iliopoulos term contributions. We present typical sparticle spectra both for the original formulation of this idea and an alternative using Fayet-Iliopoulos terms for a U(1) compatible with a straightforward GUT embedding.Comment: 20 pages, 2 figure

Thermal Stabilization of the HCP Phase in Titanium

We have used a tight-binding model that is fit to first-principles electronic-structure calculations for titanium to calculate quasi-harmonic phonons and the Gibbs free energy of the hexagonal close-packed (hcp) and omega crystal structures. We show that the true zero-temperature ground-state is the omega structure, although this has never been observed experimentally at normal pressure, and that it is the entropy from the thermal population of phonon states which stabilizes the hcp structure at room temperature. We present the first completely theoretical prediction of the temperature- and pressure-dependence of the hcp-omega phase transformation and show that it is in good agreement with experiment. The quasi-harmonic approximation fails to adequately treat the bcc phase because the zero-temperature phonons of this structure are not all stable

Efficient Recursion Method for Inverting Overlap Matrix

A new O(N) algorithm based on a recursion method, in which the computational effort is proportional to the number of atoms N, is presented for calculating the inverse of an overlap matrix which is needed in electronic structure calculations with the the non-orthogonal localized basis set. This efficient inverting method can be incorporated in several O(N) methods for diagonalization of a generalized secular equation. By studying convergence properties of the 1-norm of an error matrix for diamond and fcc Al, this method is compared to three other O(N) methods (the divide method, Taylor expansion method, and Hotelling's method) with regard to computational accuracy and efficiency within the density functional theory. The test calculations show that the new method is about one-hundred times faster than the divide method in computational time to achieve the same convergence for both diamond and fcc Al, while the Taylor expansion method and Hotelling's method suffer from numerical instabilities in most cases.Comment: 17 pages and 4 figure