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

This paper describes a new statistical parser which is based on probabilities of dependencies between head-words in the parse tree. Standard bigram probability estimation techniques are extended to calculate probabilities of dependencies…

This paper addresses image classification through learning a compact and discriminative dictionary efficiently. Given a structured dictionary with each atom (columns in the dictionary matrix) related to some label, we propose cross-label…

Explainable and interpretable unsupervised machine learning helps understand the underlying structure of data. We introduce an ensemble analysis of machine learning models to consolidate their interpretation. Its application shows that…

Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…

We present a Bayesian analysis of large-scale structure and cosmic microwave background data to constrain the form of the primordial power spectrum. We have extended the usual presumption of a scale invariant spectrum to include: (i) a…

One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation…

A Bloom filter is a method for reducing the space (memory) required for representing a set by allowing a small error probability. In this paper we consider a \emph{Sliding Bloom Filter}: a data structure that, given a stream of elements,…

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…

We present an introduction to some concepts of Bayesian data analysis in the context of atomic physics. Starting from basic rules of probability, we present the Bayes' theorem and its applications. In particular we discuss about how to…

Axion-like particles (ALPs) are predicted in many extensions of the Standard Model, and their masses can naturally be well below the electroweak scale. In the presence of couplings to electroweak bosons, these particles could be emitted in…

The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…

A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…

In this paper we consider Basis Pursuit De-Noising (BPDN) problems in which the sparse original signal is drawn from a finite alphabet. To solve this problem we propose an iterative message passing algorithm, which capitalises not only on…

A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…

To be cost-effective, biomedical proteins must be optimized with regard to many factors. Road maps are customary for large-scale projects, and here descriptive methods based on bioinformatic fractal thermodynamic scales are tested against…

Tree-adjoining grammars are a generalization of context-free grammars that are well suited to model human languages and are thus popular in computational linguistics. In the tree-adjoining grammar recognition problem, given a grammar…

Beyond identifying genetic variants, we introduce a set of Boolean relations that allows for a comprehensive classification of the relations for every pair of variants by taking all minimal alignments into account. We present an efficient…

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…

With the exponential increase of the protein sequence databases over time, multiple-sequence alignment (MSA) methods, like PSI-BLAST, perform exhaustive and time-consuming database search to retrieve evolutionary information. The resulting…

We introduce the notion of the stopping redundancy hierarchy of a linear block code as a measure of the trade-off between performance and complexity of iterative decoding for the binary erasure channel. We derive lower and upper bounds for…