相关论文: Carbon--The First Frontier of Information Processi…

An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…

Quantum systems carry information. Quantum theory supports at least two distinct kinds of information (classical and quantum), and a variety of different ways to encode and preserve information in physical systems. A system's ability to…

The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to…

In recent years, the rise of deep learning and automation requirements in the software industry has elevated Intelligent Software Engineering to new heights. The number of approaches and applications in code understanding is growing, with…

While coding regions in the genome have a direct interpretation in terms of protein products, significant fractions are non-coding and yet control essential biological functions. Unlike the genetic code, there is no "lookup table" that…

Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…

Computational protein design facilitates discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories:…

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these…

This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…

Learning an encoding of feature vectors in terms of an over-complete dictionary or a information geometric (Fisher vectors) construct is wide-spread in statistical signal processing and computer vision. In content based information…

Atomic ions trapped in ultra-high vacuum form an especially well-understood and useful physical system for quantum information processing. They provide excellent shielding of quantum information from environmental noise, while strong,…

Color and structure are the two pillars that construct an image. Usually, the structure is well expressed through a rich spectrum of colors, allowing objects in an image to be recognized by neural networks. However, under extreme…

Tensor data with rich structural information becomes increasingly important in process modeling, monitoring, and diagnosis. Here structural information is referred to structural properties such as sparsity, smoothness, low-rank, and…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

A framework is presented for a computational theory of probabilistic argument. The Probabilistic Reasoning Environment encodes knowledge at three levels. At the deepest level are a set of schemata encoding the system's domain knowledge.…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

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…

Dense prediction tasks have enjoyed a growing complexity of encoder architectures, decoders, however, have remained largely the same. They rely on individual blocks decoding intermediate feature maps sequentially. We introduce banks, shared…

This paper attempts a more formal approach to the legibility of text based programming languages, presenting, with proof, minimum possible ways of representing structure in text interleaved with information. This presumes that a minimalist…

An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…