Automated Identification and Classification of Stereochemistry: Chirality and Double Bond Stereoisomerism

Stereoisomers have the same molecular formula and the same atom connectivity and their existence can be related to the presence of different three-dimensional arrangements. Stereoisomerism is of great importance in many different fields since the molecular properties and biological effects of the stereoisomers are often significantly different. Most drugs for example, are often composed of a single stereoisomer of a compound, and while one of them may have therapeutic effects on the body, another may be toxic. A challenging task is the automatic detection of stereoisomers using line input specifications such as SMILES or InChI since it requires information about group theory (to distinguish stereoisomers using mathematical information about its symmetry), topology and geometry of the molecule. There are several software packages that include modules to handle stereochemistry, especially the ones to name a chemical structure and/or view, edit and generate chemical structure diagrams. However, there is a lack of software capable of automatically analyzing a molecule represented as a graph and generate a classification of the type of isomerism present in a given atom or bond. Considering the importance of stereoisomerism when comparing chemical structures, this report describes a computer program for analyzing and processing steric information contained in a chemical structure represented as a molecular graph and providing as output a binary classification of the isomer type based on the recommended conventions. Due to the complexity of the underlying issue, specification of stereochemical information is currently limited to explicit stereochemistry and to the two most common types of stereochemistry caused by asymmetry around carbon atoms: chiral atom and double bond. A Webtool to automatically identify and classify stereochemistry is available at http://nams.lasige.di.fc.ul.pt/tools.ph

Classes of Terminating Logic Programs

Termination of logic programs depends critically on the selection rule, i.e. the rule that determines which atom is selected in each resolution step. In this article, we classify programs (and queries) according to the selection rules for which they terminate. This is a survey and unified view on different approaches in the literature. For each class, we present a sufficient, for most classes even necessary, criterion for determining that a program is in that class. We study six classes: a program strongly terminates if it terminates for all selection rules; a program input terminates if it terminates for selection rules which only select atoms that are sufficiently instantiated in their input positions, so that these arguments do not get instantiated any further by the unification; a program local delay terminates if it terminates for local selection rules which only select atoms that are bounded w.r.t. an appropriate level mapping; a program left-terminates if it terminates for the usual left-to-right selection rule; a program exists-terminates if there exists a selection rule for which it terminates; finally, a program has bounded nondeterminism if it only has finitely many refutations. We propose a semantics-preserving transformation from programs with bounded nondeterminism into strongly terminating programs. Moreover, by unifying different formalisms and making appropriate assumptions, we are able to establish a formal hierarchy between the different classes.Comment: 50 pages. The following mistake was corrected: In figure 5, the first clause for insert was insert([],X,[X]

Finding unprecedentedly low-thermal-conductivity half-Heusler semiconductors via high-throughput materials modeling

The lattice thermal conductivity ({\kappa}{\omega}) is a key property for many potential applications of compounds. Discovery of materials with very low or high {\kappa}{\omega} remains an experimental challenge due to high costs and time-consuming synthesis procedures. High-throughput computational pre-screening is a valuable approach for significantly reducing the set of candidate compounds. In this article, we introduce efficient methods for reliably estimating the bulk {\kappa}{\omega} for a large number of compounds. The algorithms are based on a combination of machine-learning algorithms, physical insights, and automatic ab-initio calculations. We scanned approximately 79,000 half-Heusler entries in the AFLOWLIB.org database. Among the 450 mechanically stable ordered semiconductors identified, we find that {\kappa}{\omega} spans more than two orders of magnitude- a much larger range than that previously thought. {\kappa}{\omega} is lowest for compounds whose elements in equivalent positions have large atomic radii. We then perform a thorough screening of thermodynamical stability that allows to reduce the list to 77 systems. We can then provide a quantitative estimate of {\kappa}{\omega} for this selected range of systems. Three semiconductors having {\kappa}{\omega} < 5 W /(m K) are proposed for further experimental study.Comment: 9 pages, 4 figure

An Optimisation-Driven Prediction Method for Automated Diagnosis and Prognosis

open access articleThis article presents a novel hybrid classification paradigm for medical diagnoses and prognoses prediction. The core mechanism of the proposed method relies on a centroid classification algorithm whose logic is exploited to formulate the classification task as a real-valued optimisation problem. A novel metaheuristic combining the algorithmic structure of Swarm Intelligence optimisers with the probabilistic search models of Estimation of Distribution Algorithms is designed to optimise such a problem, thus leading to high-accuracy predictions. This method is tested over 11 medical datasets and compared against 14 cherry-picked classification algorithms. Results show that the proposed approach is competitive and superior to the state-of-the-art on several occasions