Comparison of Group-Contribution and Machine Learning-based Property Prediction Models with Uncertainty Quantification

2021 ◽  
pp. 755-760
Author(s):  
Adem R.N. Aouichaoui ◽  
Resul Al ◽  
Jens Abildskov ◽  
Gürkan Sin
Keyword(s):  
Machine Learning ◽  
Uncertainty Quantification ◽  
Prediction Models ◽  
Group Contribution ◽  
Property Prediction

scholarly journals Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy

2022 ◽  
Author(s):  
Yunsie Chung ◽  
Florence H. Vermeire ◽  
Haoyang Wu ◽  
Pierre J. Walker ◽  
Michael H. Abraham ◽  
...  
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Prediction Models ◽  
Solvation Energy ◽  
Solvation Free Energy ◽  
Learning Model ◽  
Group Contribution ◽  
Group Contribution Method ◽  
Solvation Enthalpy ◽  
Machine Learning Model

We present a group contribution method (SoluteGC) and a machine learning model (SoluteML) to predict the Abraham solute parameters, as well as a machine learning model (DirectML) to predict solvation free energy and enthalpy at 298 K. The proposed group contribution method uses atom-centered functional groups with corrections for ring and polycyclic strain whilst the machine learning models adopt a directed message passing neural network. The solute parameters predicted from SoluteGC and SoluteML are used to calculate solvation energy and enthalpy via linear free energy relationships. Extensive data sets containing 8366 solute parameters, 20253 solvation free energies, and 6322 solvation enthalpies are compiled in this work to train the models. The three models are each evaluated on the same test sets using both random and substructure-based solute splits for solvation energy and enthalpy predictions. The results show that the DirectML model is superior to the SoluteML and SoluteGC models for both predictions and can provide accuracy comparable to that of advanced quantum chemistry methods. Yet, even though the DirectML model performs better in general, all three models are useful for various purposes. Uncertain predicted values can be identified by comparing the 3 models, and when the 3 models are combined together, they can provide even more accurate predictions than any one of them individually. Finally, we present our compiled solute parameter, solvation energy, and solvation enthalpy databases (SoluteDB, dGsolvDBx, dHsolvDB) and provide public access to our final prediction models through a simple web-based tool, software package, and source code.

scholarly journals Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy

2021 ◽  
Author(s):  
Yunsie Chung ◽  
Florence H. Vermeire ◽  
Haoyang Wu ◽  
Pierre J. Walker ◽  
Michael H. Abraham ◽  
...  
Keyword(s):  
Machine Learning ◽  
Free Energy ◽  
Prediction Models ◽  
Solvation Energy ◽  
Solvation Free Energy ◽  
Learning Model ◽  
Group Contribution ◽  
Group Contribution Method ◽  
Solvation Enthalpy ◽  
Machine Learning Model

We present a group contribution method (SoluteGC) and a machine learning model (SoluteML) to predict the Abraham solute parameters, as well as a machine learning model (DirectML) to predict solvation free energy and enthalpy at 298 K. The proposed group contribution method uses atom-centered functional groups with corrections for ring and polycyclic strain whilst the machine learning models adopt a directed message passing neural network. The solute parameters predicted from SoluteGC and SoluteML are used to calculate solvation energy and enthalpy via linear free energy relationships. Extensive data sets containing 8366 solute parameters, 20253 solvation free energies, and 6322 solvation enthalpies are compiled in this work to train the models. The three models are each evaluated on the same test sets using both random and substructure-based solute splits for solvation energy and enthalpy predictions. The results show that the DirectML model is superior to the SoluteML and SoluteGC models for both predictions and can provide accuracy comparable to that of advanced quantum chemistry methods. Yet, even though the DirectML model performs better in general, all three models are useful for various purposes. Uncertain predicted values can be identified by comparing the 3 models, and when the 3 models are combined together, they can provide even more accurate predictions than any one of them individually. Finally, we present our compiled solute parameter, solvation energy, and solvation enthalpy databases (SoluteDB, dGsolvDBx, dHsolvDB) and provide public access to our final prediction models through a simple web-based tool, software package, and source code.

Predictors of remission from body dysmorphic disorder after internet-delivered cognitive behavior therapy: a machine learning approach

2019 ◽  
Author(s):  
Oskar Flygare ◽  
Jesper Enander ◽  
Erik Andersson ◽  
Brjánn Ljótsson ◽  
Volen Z Ivanov ◽  
...  
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Random Forests ◽  
Clinical Utility ◽  
Body Dysmorphic Disorder ◽  
Prediction Models ◽  
Behavioral Therapy ◽  
Learning Approach ◽  
Learning Approaches ◽  
Machine Learning Approach

**Background:** Previous attempts to identify predictors of treatment outcomes in body dysmorphic disorder (BDD) have yielded inconsistent findings. One way to increase precision and clinical utility could be to use machine learning methods, which can incorporate multiple non-linear associations in prediction models. **Methods:** This study used a random forests machine learning approach to test if it is possible to reliably predict remission from BDD in a sample of 88 individuals that had received internet-delivered cognitive behavioral therapy for BDD. The random forest models were compared to traditional logistic regression analyses. **Results:** Random forests correctly identified 78% of participants as remitters or non-remitters at post-treatment. The accuracy of prediction was lower in subsequent follow-ups (68%, 66% and 61% correctly classified at 3-, 12- and 24-month follow-ups, respectively). Depressive symptoms, treatment credibility, working alliance, and initial severity of BDD were among the most important predictors at the beginning of treatment. By contrast, the logistic regression models did not identify consistent and strong predictors of remission from BDD. **Conclusions:** The results provide initial support for the clinical utility of machine learning approaches in the prediction of outcomes of patients with BDD. **Trial registration:** ClinicalTrials.gov ID: NCT02010619.

COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina Faizollahzadeh Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to SIR and SEIR models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

In silico Prediction of Inhibitory Constant of Thrombin Inhibitors Using Machine Learning

2019 ◽  
Vol 21 (9) ◽  
pp. 662-669 ◽  
Author(s):  
Junnan Zhao ◽  
Lu Zhu ◽  
Weineng Zhou ◽  
Lingfeng Yin ◽  
Yuchen Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Regression Tree ◽  
Large Data ◽  
Thrombin Inhibitors ◽  
Coagulation Cascade ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Descriptor Selection

Background: Thrombin is the central protease of the vertebrate blood coagulation cascade, which is closely related to cardiovascular diseases. The inhibitory constant Ki is the most significant property of thrombin inhibitors. Method: This study was carried out to predict Ki values of thrombin inhibitors based on a large data set by using machine learning methods. Taking advantage of finding non-intuitive regularities on high-dimensional datasets, machine learning can be used to build effective predictive models. A total of 6554 descriptors for each compound were collected and an efficient descriptor selection method was chosen to find the appropriate descriptors. Four different methods including multiple linear regression (MLR), K Nearest Neighbors (KNN), Gradient Boosting Regression Tree (GBRT) and Support Vector Machine (SVM) were implemented to build prediction models with these selected descriptors. Results: The SVM model was the best one among these methods with R2=0.84, MSE=0.55 for the training set and R2=0.83, MSE=0.56 for the test set. Several validation methods such as yrandomization test and applicability domain evaluation, were adopted to assess the robustness and generalization ability of the model. The final model shows excellent stability and predictive ability and can be employed for rapid estimation of the inhibitory constant, which is full of help for designing novel thrombin inhibitors.

A Review of Statistical and Machine Learning Techniques for Microvascular Complications in Type 2 Diabetes

2020 ◽  
Vol 16 ◽  
Author(s):  
Nitigya Sambyal ◽  
Poonam Saini ◽  
Rupali Syal
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Clinical Medicine ◽  
Microvascular Complications ◽  
Descriptive Analysis ◽  
Machine Learning Techniques ◽  
World Health ◽  
Public Health Issue ◽  
Learning Techniques ◽  
Health Organization

Background and Introduction: Diabetes mellitus is a metabolic disorder that has emerged as a serious public health issue worldwide. According to the World Health Organization (WHO), without interventions, the number of diabetic incidences is expected to be at least 629 million by 2045. Uncontrolled diabetes gradually leads to progressive damage to eyes, heart, kidneys, blood vessels and nerves. Method: The paper presents a critical review of existing statistical and Artificial Intelligence (AI) based machine learning techniques with respect to DM complications namely retinopathy, neuropathy and nephropathy. The statistical and machine learning analytic techniques are used to structure the subsequent content review. Result: It has been inferred that statistical analysis can help only in inferential and descriptive analysis whereas, AI based machine learning models can even provide actionable prediction models for faster and accurate diagnose of complications associated with DM. Conclusion: The integration of AI based analytics techniques like machine learning and deep learning in clinical medicine will result in improved disease management through faster disease detection and cost reduction for disease treatment.

Intelligent Techniques Analysis for Glycosylation Site Prediction

2021 ◽  
Vol 15 ◽  
Author(s):  
Alhassan Alkuhlani ◽  
Walaa Gad ◽  
Mohamed Roushdy ◽  
Abdel-Badeeh M. Salem
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Cell Interaction ◽  
Glycosylation Site ◽  
Machine Learning Classification ◽  
Site Prediction ◽  
Glycosylation Sites ◽  
Wide Range ◽  
Feature Extraction And Selection ◽  
Computational Intelligent

Background: Glycosylation is one of the most common post-translation modifications (PTMs) in organism cells. It plays important roles in several biological processes including cell-cell interaction, protein folding, antigen’s recognition, and immune response. In addition, glycosylation is associated with many human diseases such as cancer, diabetes and coronaviruses. The experimental techniques for identifying glycosylation sites are time-consuming, extensive laboratory work, and expensive. Therefore, computational intelligence techniques are becoming very important for glycosylation site prediction. Objective: This paper is a theoretical discussion of the technical aspects of the biotechnological (e.g., using artificial intelligence and machine learning) to digital bioinformatics research and intelligent biocomputing. The computational intelligent techniques have shown efficient results for predicting N-linked, O-linked and C-linked glycosylation sites. In the last two decades, many studies have been conducted for glycosylation site prediction using these techniques. In this paper, we analyze and compare a wide range of intelligent techniques of these studies from multiple aspects. The current challenges and difficulties facing the software developers and knowledge engineers for predicting glycosylation sites are also included. Method: The comparison between these different studies is introduced including many criteria such as databases, feature extraction and selection, machine learning classification methods, evaluation measures and the performance results. Results and conclusions: Many challenges and problems are presented. Consequently, more efforts are needed to get more accurate prediction models for the three basic types of glycosylation sites.

Development of Prediction Models Using Machine Learning Algorithms for Girls with Suspected Central Precocious Puberty: Retrospective Study (Preprint)

2018 ◽  
Author(s):  
Liyan Pan ◽  
Guangjian Liu ◽  
Xiaojian Mao ◽  
Huixian Li ◽  
Jiexin Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Retrospective Study ◽  
Random Forest ◽  
Precocious Puberty ◽  
Prediction Models ◽  
Central Precocious Puberty ◽  
Machine Learning Algorithms ◽  
Stimulation Test ◽  
Gnrh Analogue ◽  
Prediction Probability

BACKGROUND Central precocious puberty (CPP) in girls seriously affects their physical and mental development in childhood. The method of diagnosis—gonadotropin-releasing hormone (GnRH)–stimulation test or GnRH analogue (GnRHa)–stimulation test—is expensive and makes patients uncomfortable due to the need for repeated blood sampling. OBJECTIVE We aimed to combine multiple CPP–related features and construct machine learning models to predict response to the GnRHa-stimulation test. METHODS In this retrospective study, we analyzed clinical and laboratory data of 1757 girls who underwent a GnRHa test in order to develop XGBoost and random forest classifiers for prediction of response to the GnRHa test. The local interpretable model-agnostic explanations (LIME) algorithm was used with the black-box classifiers to increase their interpretability. We measured sensitivity, specificity, and area under receiver operating characteristic (AUC) of the models. RESULTS Both the XGBoost and random forest models achieved good performance in distinguishing between positive and negative responses, with the AUC ranging from 0.88 to 0.90, sensitivity ranging from 77.91% to 77.94%, and specificity ranging from 84.32% to 87.66%. Basal serum luteinizing hormone, follicle-stimulating hormone, and insulin-like growth factor-I levels were found to be the three most important factors. In the interpretable models of LIME, the abovementioned variables made high contributions to the prediction probability. CONCLUSIONS The prediction models we developed can help diagnose CPP and may be used as a prescreening tool before the GnRHa-stimulation test.

scholarly journals The future is coming: promising perspectives regarding the use of machine learning in renal transplantation

2019 ◽  
Vol 41 (2) ◽  
pp. 284-287
Author(s):  
Pedro Guilherme Coelho Hannun ◽  
Luis Gustavo Modelli de Andrade
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Graft Function ◽  
Statistical Technique ◽  
Daily Routine ◽  
Learning Approaches ◽  
Post Transplantation ◽  
Chronic Allograft Rejection ◽  
Institutional Experience ◽  
Learning Principles

Abstract Introduction: The prediction of post transplantation outcomes is clinically important and involves several problems. The current prediction models based on standard statistics are very complex, difficult to validate and do not provide accurate prediction. Machine learning, a statistical technique that allows the computer to make future predictions using previous experiences, is beginning to be used in order to solve these issues. In the field of kidney transplantation, computational forecasting use has been reported in prediction of chronic allograft rejection, delayed graft function, and graft survival. This paper describes machine learning principles and steps to make a prediction and performs a brief analysis of the most recent applications of its application in literature. Discussion: There is compelling evidence that machine learning approaches based on donor and recipient data are better in providing improved prognosis of graft outcomes than traditional analysis. The immediate expectations that emerge from this new prediction modelling technique are that it will generate better clinical decisions based on dynamic and local practice data and optimize organ allocation as well as post transplantation care management. Despite the promising results, there is no substantial number of studies yet to determine feasibility of its application in a clinical setting. Conclusion: The way we deal with storage data in electronic health records will radically change in the coming years and machine learning will be part of clinical daily routine, whether to predict clinical outcomes or suggest diagnosis based on institutional experience.

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