Related papers: Recognizing Local and Global Structural Motifs at …

Methods of causal discovery aim to identify causal structures in a data driven way. Existing algorithms are known to be unstable and sensitive to statistical errors, and are therefore rarely used with biomedical or epidemiological data. We…

A structured variable selection problem is considered in which the covariates, divided into predefined groups, activate according to sparse patterns with few nonzero entries per group. Capitalizing on the concept of atomic norm, a composite…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…

A widely-used operation on graphs is local clustering, i.e., extracting a well-characterized community around a seed node without the need to process the whole graph. Recently local motif clustering has been proposed: it looks for a local…

This paper defines a new learning architecture, Layered Self-Organizing Maps (LSOMs), that uses the SOM and supervised-SOM learning algorithms. The architecture is validated with the MNIST database of hand-written digit images. LSOMs are…

This paper introduces a simple but highly efficient ensemble for robust texture classification, which can effectively deal with translation, scale and changes of significant viewpoint problems. The proposed method first inherits the spirit…

I present a strategy for unsupervised manifold learning on local atomic environments in molecular simulations based on simple rotation- and permutation-invariant three-body features. These features are highly descriptive, generalize to…

We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The…

Amorphous materials are coming within reach of realistic computer simulations, but new approaches are needed to fully understand their intricate atomic structures. Here, we show how machine-learning (ML)-based techniques can give new,…

Via computer simulations of the standard binary Lennard-Jones glass former we have obtained in a systematic way a large set of close-by pairs of minima on the potential energy landscape, i.e. double-well potentials (DWP). We analyze this…

Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe…

Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…

Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…

Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…

Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…

Single atomic sites often determine the functionality and performance of materials, such as catalysts, semi-conductors or enzymes. Computing and understanding the properties of such sites is therefore a crucial component of the rational…

Currently, identification of crystallization pathways in polymers is being carried out using molecular simulation-based data on a preset cut-off point on a single order parameter (OP) to define nucleated or crystallized regions. Aside from…

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…