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Crystal structure prediction has been a subject of topical interest, but remains a substantial challenge, especially for complex structures as it deals with the global minimization of the extremely rugged high-dimensional potential energy…

Materials Science · Physics 2022-01-26 Xuecheng Shao , Jian Lv , Peng Liu , Sen Shao , Pengyue Gao , Hanyu Liu , Yanchao Wang , Yanming Ma

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…

Biological Physics · Physics 2009-11-07 Erik van Nimwegen , Mihaela Zavolan , Nikolaus Rajewsky , Eric D. Siggia

Crystal-graph attention networks have emerged recently as remarkable tools for the prediction of thermodynamic stability and materials properties from unrelaxed crystal structures. Previous networks trained on two million materials…

In this work, we foresee the structure of a new class of borophenes with smaller 2D densities of atoms than those explored so far for 2D boron crystals. Boron atoms in the porous borophenes tend to be $5$-coordinated in contrast to commonly…

Materials Science · Physics 2021-11-25 T. Tarkowski , M. Marchwiany , N. Gonzalez Szwacki

We present a universal method for the large-scale prediction of the atomic structure of clusters. Our algorithm performs the joint evolutionary search for all clusters in a given area of the compositional space and takes advantage of…

Materials Science · Physics 2018-12-18 S. V. Lepeshkin , V. S. Baturin , Yu. A. Uspenskii , Artem R. Oganov

The de novo design of molecular structures using deep learning generative models introduces an encouraging solution to drug discovery in the face of the continuously increased cost of new drug development. From the generation of original…

Biomolecules · Quantitative Biology 2021-02-08 Yuemin Bian , Xiang-Qun Xie

Traditional approaches to Bayes net structure learning typically assume little regularity in graph structure other than sparseness. However, in many cases, we expect more systematicity: variables in real-world systems often group into…

Machine Learning · Computer Science 2012-07-02 Vikash Mansinghka , Charles Kemp , Thomas Griffiths , Joshua Tenenbaum

The discovery of small organic compounds for inducing stem cell differentiation is a time- and resource-intensive process. While data science could, in principle, facilitate the discovery of these compounds, novel approaches are required…

The traditional display of elements in the periodic table is convenient for the study of chemistry and physics. However, the atomic number alone is insufficient for training statistical machine learning models to describe and extract…

Materials Science · Physics 2023-08-25 Anthony Onwuli , Ashish V. Hegde , Kevin Nguyen , Keith T. Butler , Aron Walsh

Anticipating the low energy arrangements of atoms in space is an indispensable scientific task. Modern stochastic approaches to searching for these configurations depend on the optimisation of structures to nearby local minima in the energy…

Materials Science · Physics 2019-02-07 Chris J. Pickard

Recognition of structure prototypes from tremendous known inorganic crystal structures has been an important subject beneficial for material science research and new materials design. The existing databases of inorganic crystal structure…

In this letter we propose a new methodology for crystal structure prediction, which is based on the evolutionary algorithm USPEX and the machine-learning interatomic potentials actively learning on-the-fly. Our methodology allows for an…

Materials Science · Physics 2019-03-06 Evgeny V. Podryabinkin , Evgeny V. Tikhonov , Alexander V. Shapeev , Artem R. Oganov

This paper proposes a new paradigm and computational framework for identification of correspondences between sub-structures of distinct composite systems. For this, we define and investigate a variant of traditional data clustering, termed…

Machine Learning · Computer Science 2007-05-23 Zvika Marx , Ido Dagan , Joachim Buhmann

Metastable materials are abundant in nature and technology, showcasing remarkable properties that inspire innovative materials design. However, traditional crystal structure prediction methods, which rely solely on energetic factors to…

Materials Science · Physics 2023-11-27 Busheng Wang , Katerina P. Hilleke , Samad Hajinazar , Gilles Frapper , Eva Zurek

X-ray crystallography rarely captures chemical bonding between atoms of a structure in question. Most of the time distance-based heuristics are applied to establish the pairs of bonded atoms. One class of such heuristics depends on a set of…

With the availability of extensive databases of inorganic materials, data-driven approaches leveraging machine learning have gained prominence in materials science research. In this study, we propose an innovative adaptation of data-driven…

Materials Science · Physics 2023-06-30 Elton Ogoshi , Henrique Ferreira , João N. B. Rodrigues , Gustavo M. Dalpian

We present new automatic methods of search for star clusters using the data available in new huge stellar catalogues. Using 2MASS catalogue we have discovered over ten new open clusters in the region of Galaxy anticenter and determined…

Astrophysics · Physics 2007-05-23 Sergey Koposov , Elena Glushkova , Ivan Zolotukhin

We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable…

Materials Science · Physics 2009-11-18 A. R. Oganov , C. W. Glass

We present a new algorithm to search for distant clusters of galaxies on catalogues deriving from imaging data, as those of the ESO Imaging Survey. Our algorithm is a matched filter one, similar to that adopted by Postman et al. (1996),…

Astrophysics · Physics 2007-05-23 C. Lobo , A. Iovino , D. Lazzati , G. Chincarini

Causal structure discovery from observational data is fundamental to the causal understanding of autonomous systems such as medical decision support systems, advertising campaigns and self-driving cars. This is essential to solve well-known…