Related papers: Binary Assignments of Amino Acids from Pattern Con…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Binary optimization, a representative subclass of discrete optimization, plays an important role in mathematical optimization and has various applications in computer vision and machine learning. Usually, binary optimization problems are…
Binary optimisation tasks are ubiquitous in areas ranging from logistics to cryptography. The exponential complexity of such problems means that the performance of traditional computational methods decreases rapidly with increasing problem…
We propose an optimized parameter set for protein secondary structure prediction using three layer feed forward back propagation neural network. The methodology uses four parameters viz. encoding scheme, window size, number of neurons in…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
We consider an experiment with two qualitative factors at 2 levels each and a binary response, that follows a generalized linear model. In Mandal, Yang and Majumdar (2010) we obtained basic results and characterizations of locally D-optimal…
Binary concepts are empirically used by humans to generalize efficiently. And they are based on Bernoulli distribution which is the building block of information. These concepts span both low-level and high-level features such as "large vs…
In supervised binary hashing, one wants to learn a function that maps a high-dimensional feature vector to a vector of binary codes, for application to fast image retrieval. This typically results in a difficult optimization problem,…
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…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
Networks of neurons in the brain encode preferred patterns of neural activity via their synaptic connections. Despite receiving considerable attention, the precise relationship between network connectivity and encoded patterns is still…
We develop efficient binary (i.e., 1-bit) and multi-bit coding schemes for estimating the scale parameter of $\alpha$-stable distributions. The work is motivated by the recent work on one scan 1-bit compressed sensing (sparse signal…
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…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
In this paper, a virus optimization algorithm, which is one of the metaheuristic optimization technique, is employed for the first time to the problem of finding extremal binary self-dual codes. We present a number of generator matrices of…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
This article shows that any type of binary data can be defined as a collection from codewords of variable length. This feature helps us to define an Injective and surjective function from the suggested codewords to the required codewords.…
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that…
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…