RASCAL: calculation of graph similarity using maximum common edge subgraphs

A new graph similarity calculation procedure is introduced for comparing labeled graphs. Given a minimum similarity threshold, the procedure consists of an initial screening process to determine whether it is possible for the measure of similarity between the two graphs to exceed the minimum threshold, followed by a rigorous maximum common edge subgraph (MCES) detection algorithm to compute the exact degree and composition of similarity. The proposed MCES algorithm is based on a maximum clique formulation of the problem and is a significant improvement over other published algorithms. It presents new approaches to both lower and upper bounding as well as vertex selection

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

Measurement cost of metric-aware variational quantum algorithms

Variational quantum algorithms are promising tools for near-term quantum computers as their shallow circuits are robust to experimental imperfections. Their practical applicability, however, strongly depends on how many times their circuits need to be executed for sufficiently reducing shot-noise. We consider metric-aware quantum algorithms: variational algorithms that use a quantum computer to efficiently estimate both a matrix and a vector object. For example, the recently introduced quantum natural gradient approach uses the quantum Fisher information matrix as a metric tensor to correct the gradient vector for the co-dependence of the circuit parameters. We rigorously characterise and upper bound the number of measurements required to determine an iteration step to a fixed precision, and propose a general approach for optimally distributing samples between matrix and vector entries. Finally, we establish that the number of circuit repetitions needed for estimating the quantum Fisher information matrix is asymptotically negligible for an increasing number of iterations and qubits.Comment: 17 pages, 3 figure

Machine learning reveals orbital interaction in crystalline materials

We propose a novel representation of crystalline materials named orbital-field matrix (OFM) based on the distribution of valence shell electrons. We demonstrate that this new representation can be highly useful in mining material data. Our experiment shows that the formation energies of crystalline materials, the atomization energies of molecular materials, and the local magnetic moments of the constituent atoms in transition metal--rare-earth metal bimetal alloys can be predicted with high accuracy using the OFM. Knowledge regarding the role of coordination numbers of transition-metal and rare-earth metal elements in determining the local magnetic moment of transition metal sites can be acquired directly from decision tree regression analyses using the OFM.Comment: 10 page

Tricritical scaling at the N_t=6 chiral phase transition for 2 flavour lattice QCD with staggered quarks

We have simulated lattice QCD directly in the chiral limit of zero quark mass by adding an additional, irrelevant 4-fermion interaction to the standard action. Using lattices having temporal extent of six and spatial extents of twelve and eighteen, we find that the theory with 2 massless staggered quark flavors has a second order finite temperature phase transition. The critical exponents $\beta_{mag}$, $\delta$ and $\nu$ are measured and favour tricritical behaviour over that expected by universality arguments. The pion screening mass is consistent with zero below the transition, but is degenerate with the nonzero $\sigma(f_0)$ mass above the transition, indicating the restoration of chiral symmetry.Comment: 12 pages, 3 postscript figures Letter has been rewritten to reflect a reinterpretation of our results as indicating tricritical critical indices rather than those predicted by standard universality arguments. Some additional analysis which supports this interpretation is included. The comparison of our methods with those of others has been expande