18575731
Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint
We used the freely available Chemistry Development Kit (CDK) fingerprint to classify 5235 representative molecules taken from ten banned classes in the 2005 World Anti-Doping Agency’s (WADA) prohibited list, including molecules taken from the corresponding activity classes in the MDL Drug Data Report (MDDR). We used both Random Forest and k-Nearest Neighbours (kNN) algorithms to generate classifiers. The kNN classifiers withk = 1 gave a very slightly better Matthews Correlation Coefficient than the Random Forest classifiers; the latter, however, predicted fewer false positives. The performance of kNN classifiers tended to decline with increasing k. The performance of the CDK fingerprint is essentially equivalent to that of Unity 2D. Our results suggest that it will be possible to use freely available chemoinformatics tools to aid the fight against drugs in sport, while minimising the risk of wrongfully penalising innocent athletes.
1936302
Communication and re-use of chemical information in bioscience
The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.
6478208
Chemistry in Bioinformatics
AbstractChemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.
18750819
Abstract types have existential types
data type declarations appear in typed programming languages like Ada, Alphard, CLU and ML. This form of declaration binds a list of identifiers to a type with associated operations, a composite "value" we call a data algebra. We use a second-order typed lambda calculus SOL to show how data algebras may be given types, passed as parameters, and returned as results of function calls. In the process, we discuss the semantics of abstract data type declarations and review a connection between typed programming languages and constructive logic.
8247618
An efficiently computable metric for comparing polygonal shapes
Abstract : Model-based recognition is concerned with comparing a shape A, which is stored as a model for some particular object, with a shape B, which is found to exist in an image. If A and B are close to being the same shape, then a vision system should report a match and return a measure of how good that match is. To be useful this measure should satisfy a number of properties, including: (1) it should be a metric, (2) it should be invariant under translation, rotation, and change-of-scale, (3) it should be reasonably easy to compute, and (4) it should match our intuition (i.e., answers should be similar to those that a person might give). We develop a method for comparing polygons that has these properties. The method works for both convex and nonconvex polygons and runs in time O(mn log mn) where m is the number of vertices in one polygon and n is the number of vertices in the other. Some examples are presented that show the method produces answers that are intuitively reasonable.
1836645
Computing the visibility graph of points within a polygon
We study the problem of computing the visibility graph defined by a set <i>P</i> of <i>n</i> points inside a polygon <i>Q</i>: two points <i>p</i>,<i>q</i> ε <i>P</i> are joined by an edge if the segment ‾<i><sub>pq</sub></i> ⊂ <i>Q</i>. Efficient output-sensitive algorithms are known for the case in which <i>P</i> is the set of all vertices of <i>Q</i>. We examine the general case in which <i>P</i> is an arbitrary set of points, interior or on the boundary of <i>Q</i> and study a variety of algorithmic questions. We give an output-sensitive algorithm, which is nearly optimal, when <i>Q</i> is a simple polygon. We introduce a notion of "fat" or "robust" visibility, and give a nearly optimal algorithm for computing visibility graphs according to it, in polygons <i>Q</i> that may have holes. Other results include an algorithm to detect if there are any visible pairs among <i>P</i>, and algorithms for output-sensitive computation of visibility graphs with distance restrictions, <i>invisibility</i> graphs, and rectangle visibility graphs.
52847645
Standard ML-NJ Weak Polymorphism and Imperative Constructs
Standard ML of New Jersey (SML-NJ) uses weak-type variables to restrict the polymorphic use of functions that may allocate reference cells, manipulate continuations, or use exceptions. However, the type system used in the SML-NJ compiler has not been presented in a form other than source code and has not been proved correct. A type system, in the form of typing rules and an equivalent algorithm, that appears to subsume the implemented algorithm is presented. Both use type variables of only a slightly more general nature than the compiler. One insight in the analysis is that the indexed type of a free variable is used in two ways, once in describing the applicative behavior of the variable itself and once in describing the larger term containing the variable. Taking this into account, an application rule that is more general than SML-NJ is formulated for applications of polymorphic functions to imperative arguments. The soundness of the type system is proved for imperative code using operational semantics. >
7753820
Approximate Geometric Pattern Matching Under Rigid Motions
We present techniques for matching point-sets in two and three dimensions under rigid-body transformations. We prove bounds on the worst-case performance of these algorithms to be within a small constant factor of optimal and conduct experiments to show that the average performance of these matching algorithms is often better than that predicted by the worst-case bounds.