相关论文: Simplified amino acid alphabets based on deviation…

The anisotropic feature of charge transfer reactions in realistic proteins cannot be ignored, due to the highly complex chemical structure of bio-molecules. In this work, we have performed the first large-scale quantitative assessment of…

Sparse Code Division Multiple Access (CDMA), a variation on the standard CDMA method in which the spreading (signature) matrix contains only a relatively small number of non-zero elements, is presented and analysed using methods of…

Dependency distance minimization (DDm) is a well-established principle of word order. It has been predicted theoretically that DDm implies compression, namely the minimization of word lengths. This is a second order prediction because it…

Four natural boundary statistics and two natural bulk statistics are considered for alternating sign matrices (ASMs). Specifically, these statistics are the positions of the 1's in the first and last rows and columns of an ASM, and the…

A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…

In this paper a variant of the classical hierarchical cluster analysis is reported. This agglomerative (bottom-up) cluster technique is referred to as the Adaptive Mean-Linkage Algorithm. It can be interpreted as a linkage algorithm where…

Lexical ambiguity, a challenging phenomenon in all natural languages, is particularly prevalent for languages with diacritics that tend to be omitted in writing, such as Arabic. Omitting diacritics leads to an increase in the number of…

Clustering of proteins is of interest in cancer cell biology. This article proposes a hierarchical Bayesian model for protein (variable) clustering hinging on correlation structure. Starting from a multivariate normal likelihood, we enforce…

In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…

In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…

Minimum Bayes-risk (MBR) decoding has recently gained renewed attention in text generation. MBR decoding considers texts sampled from a model as pseudo-references and selects the text with the highest similarity to the others. Therefore,…

Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…

Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…

Dictionary learning aims at seeking a dictionary under which the training data can be sparsely represented. Methods in the literature typically formulate the dictionary learning problem as an optimization w.r.t. two variables, i.e.,…

The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…

Recent advances in weakly supervised text classification mostly focus on designing sophisticated methods to turn high-level human heuristics into quality pseudo-labels. In this paper, we revisit the seed matching-based method, which is…

In many applications of natural language processing it is necessary to determine the likelihood of a given word combination. For example, a speech recognizer may need to determine which of the two word combinations ``eat a peach'' and ``eat…

Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…

Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…

The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…