We present a solution to scale spectral algorithms for learning sequence functions. We are interested in the case where these functions are sparse (that is, for most sequences they return 0). Spectral algorithms reduce the learning problem to the task of computing an SVD decomposition over a special type of matrix called the Hankel matrix. This matrix is designed to capture the relevant statist...

We demonstrate a method for reducing the number of arithmetic operations within a (0, 1)matrix vector product. We employ an algorithm, SEQUITUR, developed for lossless text compression, which generates a context free grammar derived from an inherent hierarchy of repeated sequences. In this context, the sequences are composed of bit patterns for a set of adjacent columns. This grammar will repre...

Following Petoukhov and his collaborators, we use two length n zero-one sequences, alpha and beta, to represent a length n genetic sequence (alpha/beta) so that the columns of (alpha/beta) have the following correspondence with the nucleotides: C ~ (0/0), U ~ (1/0), G ~ (1/1), A ~ (0/1). Using the Gray code ordering to arrange alpha and beta, we build a 2(n) x 2(n) matrix C(n) including all the...

We present a solution to scale spectral algorithms for learning sequence functions. We are interested in the case where these functions are sparse (that is, for most sequences they return 0). Spectral algorithms reduce the learning problem to the task of computing an SVD decomposition over a special type of matrix called the Hankel matrix. This matrix is designed to capture the relevant statist...

Correlated mutation analysis (CMA) is a sequence-based approach for ab initio protein contact map prediction. The basis of this approach is the observed correlation between mutations in interacting amino acid residues. These correlations are often estimated by either calculating the Pearson's correlation coefficient (PCC) or the mutual information (MI) between columns in a multiple sequence ali...

This paper presents the retrofit of five conventional distillation trains for the separation of quaternary mixtures of hydrocarbons for feed compositions with high or low content of intermediate components. The retrofit implies the incorporation of liquid or vapour recycle streams among the conventional distillation columns. Each recycle stream removes one condenser or one reboiler. The introdu...

Knowledge of droplet behavior is one of the most important criteria for determination of mass transfer kinetics for choosing the type of liquid-liquid extraction columns. Mean drop size data of dispersed phase droplets in continuous phase have been obtained for Various Rotary Agitated Liquid-Liquid Extraction Columns . The effects of operational variables such as mass transfer directions with a...

Installing stone columns in the ground is an effective improvement technique to increase the load bearing capacity and reduce the consolidation settlement of the loose or weak cohesive soils. In addition to the increase in the bearing capacity and reduction in the settlement, stone columns can accelerate the dissipation rate of the excess pore water pressure generated by the surcharge, which ex...

There can be many reasons for engineers to place the footings near a slope such as leakage of suitable sites or architectural considerations. One of the approaches to increase the amount of bearing capacity, especially in soft soils, is adding stone columns to the soil. In this research, the behavior of a strip footing placed near a stone column reinforced clayey slope was investigated. For thi...

BACKGROUND Cysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions. RESULTS Here we present an alignment method that ensures homologous cysteines align by assigning a unique 10 amino acid barcode to those identified as structurally homologous by the DALI webserver. The free inter-cysteine regions of the barcoded sequ...