scholarly journals In Silico Prediction of siRNA Ionizable-Lipid Nanoparticles in vivo Efficacy: Machine Learning Modeling Based on Formulation and Molecular Descriptors

2021 ◽  
Author(s):  
Abdelkader A Metwally ◽  
Amira A Nayel ◽  
Rania M Hathout
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
In Silico ◽  
Molecular Descriptors ◽  
Lipid Nanoparticles ◽  
Data Set ◽  
In Vivo Efficacy ◽  
Artificial Neural

In silico prediction of the in vivo efficacy of siRNA ionizable-lipid nanoparticles is desirable yet never achieved before. This study aims to computationally predict siRNA nanoparticles in vivo efficacy, which saves time and resources. A data set containing 120 entries was prepared by combining molecular descriptors of the ionizable lipids together with two nanoparticles formulation characteristics. Input descriptor combinations were selected by an evolutionary algorithm. Artificial neural networks, support vector machines and partial least squares regression were used for QSAR modeling. Depending on how the data set is split, two training sets and two external validation sets were prepared. Training and validation sets contained 90 and 30 entries respectively. The results showed the successful predictions of validation set log(dose) with R2val = 0.86 – 0.89 and 0.75 – 80 for validation sets one and two respectively. Artificial neural networks resulted in the best R2val for both validation sets. For predictions that have high bias, improvement of R2val from 0.47 to 0.96 was achieved by selecting the training set lipids lying within the applicability domain. In conclusion, in vivo performance of siRNA nanoparticles was successfully predicted by combining cheminformatics with machine learning techniques.

scholarly journals Automatic Lithofacies Classification with t-SNE and K-Nearest Neighbors Algorithm

2021 ◽  
Vol 44 ◽  
Author(s):  
Guilherme Loriato Potratz ◽  
Smith Washington Arauco Canchumuni ◽  
Jose David Bermudez Castro ◽  
Júlia Potratz ◽  
Marco Aurélio C. Pacheco
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Unsupervised Classification ◽  
Machine Learning Algorithms ◽  
Hydrocarbon Exploration ◽  
Data Set ◽  
Log Data ◽  
Hidden Patterns ◽  
Artificial Neural

One of the critical processes in the exploration of hydrocarbons is the identification and prediction of lithofacies that constitute the reservoir. One of the cheapest and most efficient ways to carry out that process is from the interpretation of well log data, which are often obtained continuously and in the majority of drilled wells. The main methodologies used to correlate log data to data obtained in well cores are based on statistical analyses, machine learning models and artificial neural networks. This study aims to test an algorithm of dimension reduction of data together with an unsupervised classification method of predicting lithofacies automatically. The performance of the methodology presented was compared to predictions made with artificial neural networks. We used the t-Distributed Stochastic Neighbor Embedding (t-SNE) as an algorithm for mapping the wells logging data in a smaller feature space. Then, the predictions of facies are performed using a KNN algorithm. The method is assessed in the public dataset of the Hugoton and Panoma fields. Prediction of facies through traditional artificial neural networks obtained an accuracy of 69%, where facies predicted through the t-SNE + K-NN algorithm obtained an accuracy of 79%. Considering the nature of the data, which have high dimensionality and are not linearly correlated, the efficiency of t SNE+KNN can be explained by the ability of the algorithm to identify hidden patterns in a fuzzy boundary in data set. It is important to stress that the application of machine learning algorithms offers relevant benefits to the hydrocarbon exploration sector, such as identifying hidden patterns in high-dimensional datasets, searching for complex and non-linear relationships, and avoiding the need for a preliminary definition of mathematic relations among the model’s input data.

scholarly journals A Machine Learning Approach as a Surrogate for a Finite Element Analysis: Status of Research and Application to One Dimensional Systems

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1654
Author(s):  
Poojitha Vurtur Badarinath ◽  
Maria Chierichetti ◽  
Fatemeh Davoudi Kakhki
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Finite Element Analysis ◽  
Finite Element ◽  
Artificial Neural Networks ◽  
Stress Distribution ◽  
Maintenance Scheduling ◽  
Element Analysis ◽  
One Dimensional ◽  
Artificial Neural

Current maintenance intervals of mechanical systems are scheduled a priori based on the life of the system, resulting in expensive maintenance scheduling, and often undermining the safety of passengers. Going forward, the actual usage of a vehicle will be used to predict stresses in its structure, and therefore, to define a specific maintenance scheduling. Machine learning (ML) algorithms can be used to map a reduced set of data coming from real-time measurements of a structure into a detailed/high-fidelity finite element analysis (FEA) model of the same system. As a result, the FEA-based ML approach will directly estimate the stress distribution over the entire system during operations, thus improving the ability to define ad-hoc, safe, and efficient maintenance procedures. The paper initially presents a review of the current state-of-the-art of ML methods applied to finite elements. A surrogate finite element approach based on ML algorithms is also proposed to estimate the time-varying response of a one-dimensional beam. Several ML regression models, such as decision trees and artificial neural networks, have been developed, and their performance is compared for direct estimation of the stress distribution over a beam structure. The surrogate finite element models based on ML algorithms are able to estimate the response of the beam accurately, with artificial neural networks providing more accurate results.

scholarly journals Predicting Absorption-Distribution Properties of Neuroprotective Phosphine-Borane Compounds Using In Silico Modeling and Machine Learning

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2505
Author(s):  
Raheem Remtulla ◽  
Sanjoy Kumar Das ◽  
Leonard A. Levin
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
In Silico ◽  
Disulfide Bonds ◽  
Oral Absorption ◽  
In Vivo Studies ◽  
Drug Candidates ◽  
In Silico Methods

Phosphine-borane complexes are novel chemical entities with preclinical efficacy in neuronal and ophthalmic disease models. In vitro and in vivo studies showed that the metabolites of these compounds are capable of cleaving disulfide bonds implicated in the downstream effects of axonal injury. A difficulty in using standard in silico methods for studying these drugs is that most computational tools are not designed for borane-containing compounds. Using in silico and machine learning methodologies, the absorption-distribution properties of these unique compounds were assessed. Features examined with in silico methods included cellular permeability, octanol-water partition coefficient, blood-brain barrier permeability, oral absorption and serum protein binding. The resultant neural networks demonstrated an appropriate level of accuracy and were comparable to existing in silico methodologies. Specifically, they were able to reliably predict pharmacokinetic features of known boron-containing compounds. These methods predicted that phosphine-borane compounds and their metabolites meet the necessary pharmacokinetic features for orally active drug candidates. This study showed that the combination of standard in silico predictive and machine learning models with neural networks is effective in predicting pharmacokinetic features of novel boron-containing compounds as neuroprotective drugs.

General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks.

ChemInform ◽  
2005 ◽  
Vol 36 (32) ◽  
Author(s):  
M. Karthikeyan ◽  
Robert C. Glen ◽  
Andreas Bender
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Melting Point ◽  
Data Set ◽  
Artificial Neural

Artificial neural networks in tandem with molecular descriptors as predictive tools for continuous liposome manufacturing

2021 ◽  
pp. 120713
Author(s):  
Sameera Sansare ◽  
Tibo Duran ◽  
Hossein Mohammadiarani ◽  
Manish Goyal ◽  
Gowtham Yenduri ◽  
...  
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Molecular Descriptors ◽  
Predictive Tools ◽  
Artificial Neural

scholarly journals Opportunities and Constraints in Applying Artificial Neural Networks (ANNs) in Food Authentication. Honey—A Case Study

2021 ◽  
Vol 11 (15) ◽  
pp. 6723
Author(s):  
Ariana Raluca Hategan ◽  
Romulus Puscas ◽  
Gabriela Cristea ◽  
Adriana Dehelean ◽  
Francois Guyon ◽  
...  
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Training Sample ◽  
Training Data ◽  
Elemental Content ◽  
Neural Structure ◽  
Food Authentication ◽  
Data Set ◽  
Artificial Neural

The present work aims to test the potential of the application of Artificial Neural Networks (ANNs) for food authentication. For this purpose, honey was chosen as the working matrix. The samples were originated from two countries: Romania (50) and France (53), having as floral origins: acacia, linden, honeydew, colza, galium verum, coriander, sunflower, thyme, raspberry, lavender and chestnut. The ANNs were built on the isotope and elemental content of the investigated honey samples. This approach conducted to the development of a prediction model for geographical recognition with an accuracy of 96%. Alongside this work, distinct models were developed and tested, with the aim of identifying the most suitable configurations for this application. In this regard, improvements have been continuously performed; the most important of them consisted in overcoming the unwanted phenomenon of over-fitting, observed for the training data set. This was achieved by identifying appropriate values for the number of iterations over the training data and for the size and number of the hidden layers and by introducing of a dropout layer in the configuration of the neural structure. As a conclusion, ANNs can be successfully applied in food authenticity control, but with a degree of caution with respect to the “over optimization” of the correct classification percentage for the training sample set, which can lead to an over-fitted model.

Adaptive kinetic structural behavior through machine learning: Optimizing the process of kinematic transformation using artificial neural networks

2015 ◽  
Vol 29 (4) ◽  
pp. 371-391 ◽  
Author(s):  
Odysseas Kontovourkis ◽  
Marios C. Phocas ◽  
Ifigenia Lamprou
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Adaptive Behavior ◽  
Physical Environment ◽  
Transformation Process ◽  
Artificial Neural ◽  
Kinematic Transformation ◽  
Alternative Solutions ◽  
Digital Or

AbstractNowadays, on the basis of significant work carried out, architectural adaption structures are considered to be intelligent entities, able to react to various internal or external influences. Their adaptive behavior can be examined in a digital or physical environment, generating a variety of alternative solutions or structural transformations. These are controlled through different computational approaches, ranging from interactive exploration ones, producing alternative emergent results, to automate optimization ones, resulting in acceptable fitting solutions. This paper examines the adaptive behavior of a kinetic structure, aiming to explore suitable solutions resulting in final appropriate shapes during the transformation process. A machine learning methodology that implements an artificial neural networks algorithm is integrated to the suggested structure. The latter is formed by units articulated together in a sequential composition consisting of primary soft mechanisms and secondary rigid components that are responsible for its reconfiguration and stiffness. A number of case studies that respond to unstructured environments are set as examples, to test the effectiveness of the proposed methodology to be used for handling a large number of input data and to optimize the complex and nonlinear transformation behavior of the kinetic system at the global level, as a result of the units’ local activation that influences nearby units in a chaotic and unpredictable manner.

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