Related papers: A methodology for determining amino-acid substitut…
Rough sets were proposed to deal with the vagueness and incompleteness of knowledge in information systems. There are may optimization issues in this field such as attribute reduction. Matroids generalized from matrices are widely used in…
An optimization technique is used to determine the pairwise interactions between amino acids in globular proteins. A numerical strategy is applied to a set of proteins for maximizing the native fold stability with respect to alternative…
Table structure recognition is a challenging task due to the various structures and complicated cell spanning relations. Previous methods handled the problem starting from elements in different granularities (rows/columns, text regions),…
We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium…
In this paper, we introduce a Model-based Algorithm Turning Engine, namely MATE, where the parameters of an algorithm are represented as expressions of the features of a target optimisation problem. In contrast to most static…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
In this paper, we consider dynamic matroids, where elements can be inserted to or deleted from the ground set over time. The independent sets change to reflect the current ground set. As matroids are central to the study of many…
Analysis of multivariate data sets from e.g. microarray studies frequently results in lists of genes which are associated with some response of interest. The biological interpretation is often complicated by the statistical instability of…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
We study a class of rearrangement problems under a novel pick-n-swap prehensile manipulation model, in which a robotic manipulator, capable of carrying an item and making item swaps, is tasked to sort items stored in lattices of variable…
Alternating minimization represents a widely applicable and empirically successful approach for finding low-rank matrices that best fit the given data. For example, for the problem of low-rank matrix completion, this method is believed to…
The problem of covering the ground set of two matroids by a minimum number of common independent sets is notoriously hard even in very restricted settings, i.e.\ when the goal is to decide if two common independent sets suffice or not.…
In phylogenetics it is of interest for rate matrix sets to satisfy closure under matrix multiplication as this makes finding the set of corresponding transition matrices possible without having to compute matrix exponentials. It is also…
The theory part of this paper is sketched as follows. Based on column stochastic average matrix $T_n$ selected as a basic substitution matrix, the method of advanced successive difference substitution is established. Then, a set of…
Alternating Minimization is a widely used and empirically successful heuristic for matrix completion and related low-rank optimization problems. Theoretical guarantees for Alternating Minimization have been hard to come by and are still…
We present a new method to extract distance and orientation dependent potentials between amino acid side chains using a database of protein structures and the standard Boltzmann device. The importance of orientation dependent interactions…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
This paper addresses optimal feedback selection for generic arbitrary pole placement of structured systems when each feedback edge is associated with a cost. Given a structured system and a feedback cost matrix, our aim is to find a…