ASlib: A Benchmark Library for Algorithm Selection

The task of algorithm selection involves choosing an algorithm from a set of algorithms on a per-instance basis in order to exploit the varying performance of algorithms over a set of instances. The algorithm selection problem is attracting increasing attention from researchers and practitioners in AI. Years of fruitful applications in a number of domains have resulted in a large amount of data, but the community lacks a standard format or repository for this data. This situation makes it difficult to share and compare different approaches effectively, as is done in other, more established fields. It also unnecessarily hinders new researchers who want to work in this area. To address this problem, we introduce a standardized format for representing algorithm selection scenarios and a repository that contains a growing number of data sets from the literature. Our format has been designed to be able to express a wide variety of different scenarios. Demonstrating the breadth and power of our platform, we describe a set of example experiments that build and evaluate algorithm selection models through a common interface. The results display the potential of algorithm selection to achieve significant performance improvements across a broad range of problems and algorithms.Comment: Accepted to be published in Artificial Intelligence Journa

Comparison of chemical clustering methods using graph- and fingerprint-based similarity measures

This paper compares several published methods for clustering chemical structures, using both graph- and fingerprint-based similarity measures. The clusterings from each method were compared to determine the degree of cluster overlap. Each method was also evaluated on how well it grouped structures into clusters possessing a non-trivial substructural commonality. The methods which employ adjustable parameters were tested to determine the stability of each parameter for datasets of varying size and composition. Our experiments suggest that both graph- and fingerprint-based similarity measures can be used effectively for generating chemical clusterings; it is also suggested that the CAST and Yin–Chen methods, suggested recently for the clustering of gene expression patterns, may also prove effective for the clustering of 2D chemical structures

Visual and computational analysis of structure-activity relationships in high-throughput screening data

Novel analytic methods are required to assimilate the large volumes of structural and bioassay data generated by combinatorial chemistry and high-throughput screening programmes in the pharmaceutical and agrochemical industries. This paper reviews recent work in visualisation and data mining that can be used to develop structure-activity relationships from such chemical/biological datasets

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