Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

Searching the solution space in constructive geometric constraint solving with genetic algorithms

Geometric problems defined by constraints have an exponential number of solution instances in the number of geometric elements involved. Generally, the user is only interested in one instance such that besides fulfilling the geometric constraints, exhibits some additional properties. Selecting a solution instance amounts to selecting a given root every time the geometric constraint solver needs to compute the zeros of a multi valuated function. The problem of selecting a given root is known as the Root Identification Problem. In this paper we present a new technique to solve the root identification problem. The technique is based on an automatic search in the space of solutions performed by a genetic algorithm. The user specifies the solution of interest by defining a set of additional constraints on the geometric elements which drive the search of the genetic algorithm. The method is extended with a sequential niche technique to compute multiple solutions. A number of case studies illustrate the performance of the method.Postprint (published version

High-speed detection of emergent market clustering via an unsupervised parallel genetic algorithm

We implement a master-slave parallel genetic algorithm (PGA) with a bespoke log-likelihood fitness function to identify emergent clusters within price evolutions. We use graphics processing units (GPUs) to implement a PGA and visualise the results using disjoint minimal spanning trees (MSTs). We demonstrate that our GPU PGA, implemented on a commercially available general purpose GPU, is able to recover stock clusters in sub-second speed, based on a subset of stocks in the South African market. This represents a pragmatic choice for low-cost, scalable parallel computing and is significantly faster than a prototype serial implementation in an optimised C-based fourth-generation programming language, although the results are not directly comparable due to compiler differences. Combined with fast online intraday correlation matrix estimation from high frequency data for cluster identification, the proposed implementation offers cost-effective, near-real-time risk assessment for financial practitioners.Comment: 10 pages, 5 figures, 4 tables, More thorough discussion of implementatio

The Design and Implementation of a Bayesian CAD Modeler for Robotic Applications

We present a Bayesian CAD modeler for robotic applications. We address the problem of taking into account the propagation of geometric uncertainties when solving inverse geometric problems. The proposed method may be seen as a generalization of constraint-based approaches in which we explicitly model geometric uncertainties. Using our methodology, a geometric constraint is expressed as a probability distribution on the system parameters and the sensor measurements, instead of a simple equality or inequality. To solve geometric problems in this framework, we propose an original resolution method able to adapt to problem complexity. Using two examples, we show how to apply our approach by providing simulation results using our modeler

Incorporating characteristics of human creativity into an evolutionary art algorithm

A perceived limitation of evolutionary art and design algorithms is that they rely on human intervention; the artist selects the most aesthetically pleasing variants of one generation to produce the next. This paper discusses how computer generated art and design can become more creatively human-like with respect to both process and outcome. As an example of a step in this direction, we present an algorithm that overcomes the above limitation by employing an automatic fitness function. The goal is to evolve abstract portraits of Darwin, using our 2nd generation fitness function which rewards genomes that not just produce a likeness of Darwin but exhibit certain strategies characteristic of human artists. We note that in human creativity, change is less choosing amongst randomly generated variants and more capitalizing on the associative structure of a conceptual network to hone in on a vision. We discuss how to achieve this fluidity algorithmically