scholarly journals The evolution of logic circuits for the purpose of protein contact map prediction

2016 ◽  
Author(s):  
Samuel D Chapman ◽  
Christoph Adami ◽  
Claus O Wilke ◽  
Dukka B KC
Keyword(s):  
Machine Learning ◽  
Logic Circuits ◽  
Contact Map ◽  
Protein Biochemistry ◽  
Residue Contact ◽  
Contact Maps ◽  
Contact Patterns ◽  
Unbiased Manner ◽  
Novel Method ◽  
Selection Of

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.

scholarly journals The evolution of logic circuits for the purpose of protein contact map prediction

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3139 ◽  
Author(s):  
Samuel D. Chapman ◽  
Christoph Adami ◽  
Claus O. Wilke ◽  
Dukka B KC
Keyword(s):  
Machine Learning ◽  
Logic Circuits ◽  
Contact Map ◽  
Protein Biochemistry ◽  
Residue Contact ◽  
Contact Maps ◽  
Contact Patterns ◽  
Unbiased Manner ◽  
Novel Method ◽  
Selection Of

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.

scholarly journals The evolution of logic circuits for the purpose of protein contact map prediction

2016 ◽  
Author(s):  
Samuel D Chapman ◽  
Christoph Adami ◽  
Claus O Wilke ◽  
Dukka B KC
Keyword(s):  
Machine Learning ◽  
Logic Circuits ◽  
Contact Map ◽  
Protein Biochemistry ◽  
Residue Contact ◽  
Contact Maps ◽  
Contact Patterns ◽  
Unbiased Manner ◽  
Novel Method ◽  
Selection Of

Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset.

A Novel Amino Acid Sequence-based Computational Approach to Predicting Cell-penetrating Peptides

2019 ◽  
Vol 15 (3) ◽  
pp. 206-211 ◽  
Author(s):  
Jihui Tang ◽  
Jie Ning ◽  
Xiaoyan Liu ◽  
Baoming Wu ◽  
Rongfeng Hu
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Amino Acid Position ◽  
Cell Penetrating Peptides ◽  
Support Vector ◽  
Cell Penetration ◽  
Drug Candidates ◽  
Machine Learning Model ◽  
Cell Penetrating ◽  
Novel Method

<P>Introduction: Machine Learning is a useful tool for the prediction of cell-penetration compounds as drug candidates. </P><P> Materials and Methods: In this study, we developed a novel method for predicting Cell-Penetrating Peptides (CPPs) membrane penetrating capability. For this, we used orthogonal encoding to encode amino acid and each amino acid position as one variable. Then a software of IBM spss modeler and a dataset including 533 CPPs, were used for model screening. </P><P> Results: The results indicated that the machine learning model of Support Vector Machine (SVM) was suitable for predicting membrane penetrating capability. For improvement, the three CPPs with the most longer lengths were used to predict CPPs. The penetration capability can be predicted with an accuracy of close to 95%. </P><P> Conclusion: All the results indicated that by using amino acid position as a variable can be a perspective method for predicting CPPs membrane penetrating capability.</P>

Deep Learning in Disease Diagnosis: Models and Datasets

2020 ◽  
Vol 15 ◽  
Author(s):  
Deeksha Saxena ◽  
Mohammed Haris Siddiqui ◽  
Rajnish Kumar
Keyword(s):  
Biological Sciences ◽  
Machine Learning ◽  
Deep Learning ◽  
Disease Diagnosis ◽  
Learning Models ◽  
Data Types ◽  
Related Data ◽  
Abstract Level ◽  
Experimental Validations ◽  
Selection Of

Background: Deep learning (DL) is an Artificial neural network-driven framework with multiple levels of representation for which non-linear modules combined in such a way that the levels of representation can be enhanced from lower to a much abstract level. Though DL is used widely in almost every field, it has largely brought a breakthrough in biological sciences as it is used in disease diagnosis and clinical trials. DL can be clubbed with machine learning, but at times both are used individually as well. DL seems to be a better platform than machine learning as the former does not require an intermediate feature extraction and works well with larger datasets. DL is one of the most discussed fields among the scientists and researchers these days for diagnosing and solving various biological problems. However, deep learning models need some improvisation and experimental validations to be more productive. Objective: To review the available DL models and datasets that are used in disease diagnosis. Methods: Available DL models and their applications in disease diagnosis were reviewed discussed and tabulated. Types of datasets and some of the popular disease related data sources for DL were highlighted. Results: We have analyzed the frequently used DL methods, data types and discussed some of the recent deep learning models used for solving different biological problems. Conclusion: The review presents useful insights about DL methods, data types, selection of DL models for the disease diagnosis.

Color Trend Analysis using Machine Learning with Fashion Collection Images

2021 ◽  
pp. 0887302X2199594
Author(s):  
Ahyoung Han ◽  
Jihoon Kim ◽  
Jaehong Ahn
Keyword(s):  
Machine Learning ◽  
Trend Analysis ◽  
Image Data ◽  
Fashion Industry ◽  
Color Palette ◽  
Web Scraping ◽  
Design Variables ◽  
Sales Organizations ◽  
Fashion Designers ◽  
Selection Of

Fashion color trends are an essential marketing element that directly affect brand sales. Organizations such as Pantone have global authority over professional color standards by annually forecasting color palettes. However, the question remains whether fashion designers apply these colors in fashion shows that guide seasonal fashion trends. This study analyzed image data from fashion collections through machine learning to obtain measurable results by web-scraping catwalk images, separating body and clothing elements via machine learning, defining a selection of color chips using k-means algorithms, and analyzing the similarity between the Pantone color palette (16 colors) and the analysis color chips. The gap between the Pantone trends and the colors used in fashion collections were quantitatively analyzed and found to be significant. This study indicates the potential of machine learning within the fashion industry to guide production and suggests further research expand on other design variables.

Machine learning approaches to understand and predict rate constants for organic processes in mixtures containing ionic liquids

2021 ◽  
Vol 23 (4) ◽  
pp. 2742-2752
Author(s):  
Tamar L. Greaves ◽  
Karin S. Schaffarczyk McHale ◽  
Raphael F. Burkart-Radke ◽  
Jason B. Harper ◽  
Tu C. Le
Keyword(s):  
Machine Learning ◽  
Ionic Liquids ◽  
Rate Constants ◽  
Learning Approaches ◽  
Learning Models ◽  
Organic Reaction ◽  
Machine Learning Models ◽  
Selection Of

Machine learning models were developed for an organic reaction in ionic liquids and validated on a selection of ionic liquids.

A novel method for the design and selection of neutron-attenuating media

2021 ◽  
Vol 160 ◽  
pp. 108368
Author(s):  
Abdullah G. Weiss ◽  
Moiz I. Butt ◽  
Pavel V. Tsvetkov ◽  
Mark L. Kimber ◽  
Sean M. McDeavitt
Keyword(s):  
Novel Method ◽  
Selection Of

Accelerating the optimization of enzyme-catalyzed synthesis conditions via machine learning and reactivity descriptors

2021 ◽  
Author(s):  
Zhongyu Wan ◽  
Quan-De Wang ◽  
Dongchang Liu ◽  
Jinhu Liang
Keyword(s):  
Machine Learning ◽  
Optimal Synthesis ◽  
Human Knowledge ◽  
Crucial Importance ◽  
Reactivity Descriptors ◽  
Synthesis Conditions ◽  
Wide Range ◽  
Synthesis Reactions ◽  
Selection Of

Enzyme-catalyzed synthesis reactions are of crucial importance for a wide range of applications. An accurate and rapid selection of optimal synthesis conditions is crucial and challenging for both human knowledge...

scholarly journals Selection of Suitable Machine Learning Algorithms for Classification Tasks in Reverse Logistics

Procedia CIRP ◽  
2021 ◽  
Vol 96 ◽  
pp. 272-277
Author(s):  
Hannah Lickert ◽  
Aleksandra Wewer ◽  
Sören Dittmann ◽  
Pinar Bilge ◽  
Franz Dietrich
Keyword(s):  
Machine Learning ◽  
Reverse Logistics ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Classification Tasks ◽  
Selection Of

scholarly journals Tuning of a Linear-Quadratic Stabilization System for an Anti-Aircraft Missile

Aerospace ◽  
2021 ◽  
Vol 8 (2) ◽  
pp. 48
Author(s):  
Witold Bużantowicz
Keyword(s):  
Analytical Solutions ◽  
Feedback Loop ◽  
Linear Quadratic Regulator ◽  
Added Value ◽  
Tuning Parameter ◽  
Stabilization System ◽  
Linear Quadratic ◽  
Quadratic Stabilization ◽  
Novel Method ◽  
Selection Of

A description is given of an application of a linear-quadratic regulator (LQR) for stabilizing the characteristics of an anti-aircraft missile, and an analytical method of selecting the weighting elements of the gain matrix in feedback loop is proposed. A novel method of LQR tuning via a single parameter ς was proposed and tested. The article supplements and develops the topics addressed in the author’s previous work. Its added value includes the observation that the solutions obtained are symmetric pairs, and that the tuning parameter ς proposed for the designed linear-quadratic regulator enables the selection of suitable parameters for the airframe stabilizing loop for the majority of the analytical solutions of the considered Riccati equation.

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