scholarly journals Improving AlphaFold modeling using implicit information from experimental density maps

2022 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Billy K Poon ◽  
Pavel Afonine ◽  
Christopher J Schlicksup ◽  
Tristan I Croll ◽  
...  
Keyword(s):  
Machine Learning ◽  
Experimental Data ◽  
Iterative Procedure ◽  
Experimental Information ◽  
Implicit Information ◽  
Prediction Algorithms ◽  
Map Interpretation ◽  
Density Maps ◽  
Protein Models ◽  
Experimental Density

Machine learning prediction algorithms such as AlphaFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including experimental information, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt based on experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We find that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for crystallographic and electron cryo-microscopy map interpretation.

scholarly journals Smart Design Nano-Hybrid Formulations by Machine Learning

Proceedings ◽  
2020 ◽  
Vol 78 (1) ◽  
pp. 5
Author(s):  
Raquel de Melo Barbosa ◽  
Fabio Fonseca de Oliveira ◽  
Gabriel Bezerra Motta Câmara ◽  
Tulio Flavio Accioly de Lima e Moura ◽  
Fernanda Nervo Raffin ◽  
...  
Keyword(s):  
Machine Learning ◽  
Experimental Data ◽  
Water Solubility ◽  
Inorganic Materials ◽  
Fine Tuning ◽  
Support Vector ◽  
Drug Solubility ◽  
Physical Behavior ◽  
Best Fit

Nano-hybrid formulations combine organic and inorganic materials in self-assembled platforms for drug delivery. Laponite is a synthetic clay, biocompatible, and a guest of compounds. Poloxamines are amphiphilic four-armed compounds and have pH-sensitive and thermosensitive properties. The association of Laponite and Poloxamine can be used to improve attachment to drugs and to increase the solubility of β-Lapachone (β-Lap). β-Lap has antiviral, antiparasitic, antitumor, and anti-inflammatory properties. However, the low water solubility of β-Lap limits its clinical and medical applications. All samples were prepared by mixing Tetronic 1304 and LAP in a range of 1–20% (w/w) and 0–3% (w/w), respectively. The β-Lap solubility was analyzed by UV-vis spectrophotometry, and physical behavior was evaluated across a range of temperatures. The analysis of data consisted of response surface methodology (RMS), and two kinds of machine learning (ML): multilayer perceptron (MLP) and support vector machine (SVM). The ML techniques, generated from a training process based on experimental data, obtained the best correlation coefficient adjustment for drug solubility and adequate physical classifications of the systems. The SVM method presented the best fit results of β-Lap solubilization. In silico tools promoted fine-tuning, and near-experimental data show β-Lap solubility and classification of physical behavior to be an excellent strategy for use in developing new nano-hybrid platforms.

On the bursting mechanism in rotating rings

1993 ◽  
Vol 28 (3) ◽  
pp. 153-162 ◽  
Author(s):  
C Bandera ◽  
M Nicolich ◽  
A Strozzi
Keyword(s):  
Experimental Data ◽  
Correction Factor ◽  
Static Loading ◽  
Experimental Information ◽  
Theoretical Interpretation ◽  
Dynamic Correction

The bursting mechanism in roatating, bored discs is theoretically reviewed in the light of published experimental information. In particlar, the segmentation sequence in bursting wheels is analysed according to a curved bar modelling and to a quasi-static loading, where a dynamic correction factor is introduced which reconciles theory with experiments. Finally, a diagram reporting the number of wheel fragmented pieces in terms of the ratio of ring inner to outer radii is presented, based upon available experimental data and theoretical interpretation.

Risk-Controlled Wellbore Stability Criterion Based on Machine Learning Assisted Finite Element Model

2021 ◽  
Author(s):  
Hussain AlBahrani ◽  
Nobuo Morita
Keyword(s):  
Machine Learning ◽  
Experimental Data ◽  
Finite Element ◽  
Finite Element Model ◽  
Stability Criterion ◽  
Element Model ◽  
Rock Failure ◽  
Wellbore Stability ◽  
Wellbore Instability ◽  
Conventional Methods

Abstract In many drilling scenarios that include deep wells and highly stressed environments, the mud weight required to completely prevent wellbore instability can be impractically high. In such cases, what is known as risk-controlled wellbore stability criterion is introduced. This criterion allows for a certain level of wellbore instability to take place. This means that the mud weight calculated using this criterion will only constrain wellbore instability to a certain manageable level, hence the name risk-controlled. Conventionally, the allowable level of wellbore instability in this type of models has always been based on the magnitude of the breakout angle. However, wellbore enlargements, as seen in calipers and image logs, can be highly irregular in terms of its distribution around the wellbore. This irregularity means that risk-controlling the wellbore instability through the breakout angle might not be always sufficient. Instead, the total volume of cavings is introduced as the risk control parameter for wellbore instability. Unlike the breakout angle, the total volume of cavings can be coupled with a suitable hydraulics model to determine the threshold of manageable instability. The expected total volume of cavings is determined using a machine learning (ML) assisted 3D elasto-plastic finite element model (FEM). The FEM works to model the interval of interest, which eventually provides a description of the stress distribution around the wellbore. The ML algorithm works to learn the patterns and limits of rock failure in a supervised training manner based on the wellbore enlargement seen in calipers and image logs from nearby offset wells. Combing the FEM output with the ML algorithm leads to an accurate prediction of shear failure zones. The model is able to predict both the radial and circumferential distribution of enlargements at any mud weight and stress regime, which leads to a determination of the expected total volume of cavings. The model implementation is first validated through experimental data. The experimental data is based on true-triaxial tests of bored core samples. Next, a full dataset from offset wells is used to populate and train the model. The trained model is then used to produce estimations of risk-controlled stability mud weights for different drilling scenarios. The model results are compared against those produced by conventional methods. Finally, both the FEM-ML model and the conventional methods results are compared against the drilling experience of the offset wells. This methodology provides a more comprehensive and new solution to risk controlling wellbore instability. It relies on a novel process which learns rock failure from calipers and image logs.

Software-in-the-Loop Combined Machine Learning for Dynamic Responses Analysis of Floating Offshore Wind Turbines

2021 ◽  
Author(s):  
Peng Chen ◽  
Changhong Hu ◽  
Zhiqiang Hu
Keyword(s):  
Machine Learning ◽  
Experimental Data ◽  
Wind Turbines ◽  
Dynamic Responses ◽  
Offshore Wind ◽  
Learning Technology ◽  
Mean Values ◽  
Offshore Wind Turbines ◽  
Floating Offshore Wind Turbines ◽  
Brute Force Method

Abstract Artificial intelligence (AI) brings a new solution to overcome the challenges of Floating offshore wind turbines (FOWTs) to better predict the dynamic responses with intelligent strategies. A new AI-based software-in-the-loop method, named SADA is introduced in this paper for the prediction of dynamic responses of FOWTs, which is proposed based on an in-house programme DARwind. DARwind is a coupled aero-hydro-servo-elastic in-house program for FOWTs, and a reinforcement learning method with exhaust algorithm and deep deterministic policy gradient (DDPG) are embedded in DARwind as an AI module. Firstly, the methodology is introduced with the selection of Key Disciplinary Parameters (KDPs). Secondly, Brute-force Method and DDPG algorithms are adopted to changes the KDPs’ values according to the feedback of 6DOF motions of Hywind Spar-type platform through comparing the DARwind simulation results and those of basin experimental data. Therefore, many other dynamic responses that cannot be measured in basin experiment can be predicted in good accuracy with SADA method. Finally, the case study of SADA method was conducted and the results demonstrated that the mean values of the platform’s motions can be predicted with higher accuracy. This proposed SADA method takes advantage of numerical-experimental method, basin experimental data and the machine learning technology, which brings a new and promising solution for overcoming the handicap impeding direct use of conventional basin experimental way to analyze FOWT’s dynamic responses during the design phase.

Simulation and prediction of optical characterization of casting (Adamantan-Fulgide) thin films using (CTANNs) approach

2019 ◽  
Vol 33 (11) ◽  
pp. 1950093 ◽  
Author(s):  
A. M. A. EL-Barry ◽  
D. M. Habashy
Keyword(s):  
Experimental Data ◽  
Thin Films ◽  
Back Propagation ◽  
Optical Characterization ◽  
Experimental Information ◽  
Training Algorithm ◽  
Energy Gaps ◽  
Resilient Back Propagation ◽  
Good Agreement

For reinforcement, the photochromic field and the cooperation between the theoretical and experimental branches of physics, the computational, theoretical artificial neural networks (CTANNs) and the resilient back propagation (R[Formula: see text]) training algorithm were used to model optical characterizations of casting (Admantan-Fulgide) thin films with different concentrations. The simulated values of ANN are in good agreement with the experimental data. The model was also used to predict values, which were not included in the training. The high precision of the model has been constructed. Moreover, the concentration dependence of both the energy gaps and Urbach’s tail were, also tested. The capability of the technique to simulate the experimental information with best accuracy and the foretelling of some concentrations which is not involved in the experimental data recommends it to dominate the modeling technique in casting (Admantan-Fulgide) thin films.

scholarly journals Discovering Business Processes from Email Logs using fastText and Process Mining

2020 ◽  
Author(s):  
Yaghoub rashnavadi ◽  
Sina Behzadifard ◽  
Reza Farzadnia ◽  
sina zamani
Keyword(s):  
Machine Learning ◽  
Business Processes ◽  
Oil And Gas ◽  
Process Mining ◽  
The Body ◽  
Process Models ◽  
Supervised Machine Learning ◽  
Implicit Information ◽  
Oil And Gas Sector

<p>Communication has never been more accessible than today. With the help of Instant messengers and Email Services, millions of people can transfer information with ease, and this trend has affected organizations as well. There are billions of organizational emails sent or received daily, and their main goal is to facilitate the daily operation of organizations. Behind this vast corpus of human-generated content, there is much implicit information that can be mined and used to improve or optimize the organizations’ operations. Business processes are one of those implicit knowledge areas that can be discovered from Email logs of an Organization, as most of the communications are followed inside Emails. The purpose of this research is to propose an approach to discover the process models in the Email log. In this approach, we combine two tools, supervised machine learning and process mining. With the help of supervised machine learning, fastText classifier, we classify the body text of emails to the activity-related. Then the generated log will be mined with process mining techniques to find process models. We illustrate the approach with a case study company from the oil and gas sector.</p>

scholarly journals Adaptive Intelligent Welding Manufacturing

2021 ◽  
Vol 100 (01) ◽  
pp. 63-83
Author(s):  
YUMING ZHANG ◽  
◽  
QIYUE WANG ◽  
YUKANG LIU
Keyword(s):  
Machine Learning ◽  
Experimental Data ◽  
Deep Learning ◽  
Welding Process ◽  
Welding Parameters ◽  
Weld Quality ◽  
Robotic Welding ◽  
Process Variables ◽  
Physical Constraints ◽  
Needed Information

Optimal design of the welding procedure gives the desired welding results under nominal welding conditions. During manufacturing, where the actual welding manufacturing conditions often deviate from the nominal ones used in the design, applying the designed procedure will produce welding results that are different from the desired ones. Adaption is needed to make corrections and adjust some of the welding parameters from those specified in the design. This is adaptive welding. While human welders can be adaptive to make corrections and adjustments, their performance is limited by their physical constraints and skill level. To be adaptive, automated and robotic welding systems require abilities in sensing the welding process, extracting the needed information from signals from the sensors, predicting the responses of the welding process to the adjustments on welding parameters, and optimizing the adjustments. This results in the application of classical sensing, modeling of process dynamics, and control system design. In many cases, the needed information for the weld quality and process variables of our concern is not easy to extract from the sensor’s data. Studies are needed to propose the phenomena to sense and establish the scientific foundation to correlate them to the weld quality or process variables of our concern. Such studies can be labor intensive, and a more automated approach is needed. Analysis suggests that artificial intelligence and machine learning, especially deep learning, can help automate the learning such that the needed intelligence for robotic welding adaptation can be directly and automatically learned from experimental data after the physical phenomena being represented by the experimental data has been appropriately selected to make sure they are fundamentally correlated to that with which we are concerned. Some adaptation abilities may also be learned from skilled human welders. In addition, human-robot collaborative welding may incorporate adaptations from humans with the welding robots. This paper analyzes and identifies the challenges in adaptive robotic welding, reviews efforts devoted to solve these challenges, analyzes the principles and nature of the methods behind these efforts, and introduces modern approaches, including machine learning/deep learning, learning from humans, and human-robot collaboration, to solve these challenges.

scholarly journals Prediction of drug-protein interaction and drug repositioning using machine learning model

2020 ◽  
Author(s):  
Yu-Ting Lin ◽  
Sheh-Yi Sheu ◽  
Chen-Ching Lin
Keyword(s):  
Machine Learning ◽  
Betweenness Centrality ◽  
Drug Repositioning ◽  
Protein Network ◽  
Training Data ◽  
Support Vector ◽  
Binding Interaction ◽  
Binding Strength ◽  
Edge Betweenness ◽  
Protein Models

AbstractBackgroundTraditional drug development is time-consuming and expensive, while computer-aided drug repositioning can improve efficiency and productivity. In this study, we proposed a machine learning pipeline to predict the binding interaction between proteins and marketed or studied drugs. We then extended the predicted interactions to construct a protein network that could be applied to discover the potentially shared drugs between proteins and thus predict drug repositioning.MethodsBinding information between proteins and drugs from the Binding Database and the physicochemical properties of drugs from the ChEMBL database were used to build the machine learning models, i.e. support vector regression. We further measured proportionalities between proteins by the predicted binding affinity and introduced edge betweenness centrality to construct a protein similarity network for drug repositioning.ResultsAs the proof of concept, we demonstrated our machine learning approach is capable of reflecting the binding strength between drugs and the target protein. When comparing coefficients of protein models, we found proteins SYUA and TAU that may share common ligand which were not in our training data. Using the edge betweenness centrality network based on the prediction proportionality of protein models, we found a potential target, AK1C2, of aspirin and of which the binding interaction had been validated.ConclusionsOur study could not only be applied to drug repositioning by comparing protein models or searching the protein-protein network, but also to predict the binding strength once the sufficient experimental data was provided to train the protein models.

scholarly journals A Temperature Variation of Debye-Waller Factor for Alkali and Noble Metals

1983 ◽  
Vol 38 (5) ◽  
pp. 503-508 ◽  
Author(s):  
A. R. Jani ◽  
V. B. Gohel
Keyword(s):  
Experimental Data ◽  
Temperature Variation ◽  
Phenomenological Model ◽  
Noble Metals ◽  
Experimental Information ◽  
Waller Factor ◽  
Critical Examination ◽  
Debye Waller Factor ◽  
Different Temperatures ◽  
Experimental Findings

Debye-Waller factors at different temperatures of four alkali and three noble metals have been computed on the basis of a screened shell phenomenological model. The theoretical values are compared with existing experimental data. Particularly for lithium and potassium, most recent experimental information has been included. A critical examination of the results reveals a satis­factory agreement between the theoretical and experimental findings.

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