scholarly journals Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 95 ◽  
Author(s):  
Md. Mehedi Hasan ◽  
Mst. Shamima Khatun ◽  
Hiroyuki Kurata
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Prediction Models ◽  
Cell Metabolism ◽  
Cost Effective ◽  
Learning Approaches ◽  
Large Scale Assessment ◽  
Current State ◽  
Lysine Succinylation ◽  
Essential Properties

Lysine succinylation is a form of posttranslational modification of the proteins that play an essential functional role in every aspect of cell metabolism in both prokaryotes and eukaryotes. Aside from experimental identification of succinylation sites, there has been an intense effort geared towards the development of sequence-based prediction through machine learning, due to its promising and essential properties of being highly accurate, robust and cost-effective. In spite of these advantages, there are several problems that are in need of attention in the design and development of succinylation site predictors. Notwithstanding of many studies on the employment of machine learning approaches, few articles have examined this bioinformatics field in a systematic manner. Thus, we review the advancements regarding the current state-of-the-art prediction models, datasets, and online resources and illustrate the challenges and limitations to present a useful guideline for developing powerful succinylation site prediction tools.

Development of Rainfall Prediction Models Using Machine Learning Approaches for Different Agro-Climatic Zones

2021 ◽  
pp. 72-94
Author(s):  
Diwakar Naidu ◽  
Babita Majhi ◽  
Surendra Kumar Chandniha
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Large Scale ◽  
Prediction Models ◽  
Machine Learning Algorithms ◽  
Learning Approaches ◽  
Learning Models ◽  
Climatic Zones ◽  
Environmental Prediction ◽  
Machine Learning Models

This study focuses on modelling the changes in rainfall patterns in different agro-climatic zones due to climate change through statistical downscaling of large-scale climate variables using machine learning approaches. Potential of three machine learning algorithms, multilayer artificial neural network (MLANN), radial basis function neural network (RBFNN), and least square support vector machine (LS-SVM) have been investigated. The large-scale climate variable are obtained from National Centre for Environmental Prediction (NCEP) reanalysis product and used as predictors for model development. Proposed machine learning models are applied to generate projected time series of rainfall for the period 2021-2050 using the Hadley Centre coupled model (HadCM3) B2 emission scenario data as predictors. An increasing trend in anticipated rainfall is observed during 2021-2050 in all the ACZs of Chhattisgarh State. Among the machine learning models, RBFNN found as more feasible technique for modeling of monthly rainfall in this region.

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.

Application of Machine Learning Approaches for the Design and Study of Anticancer Drugs

2019 ◽  
Vol 20 (5) ◽  
pp. 488-500 ◽  
Author(s):  
Yan Hu ◽  
Yi Lu ◽  
Shuo Wang ◽  
Mengying Zhang ◽  
Xiaosheng Qu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Design ◽  
Anticancer Drugs ◽  
Nearest Neighbor ◽  
Cost Effective ◽  
Support Vector ◽  
Learning Approaches ◽  
K Nearest Neighbor ◽  
Activity Prediction ◽  
Linear Discriminant

Background: Globally the number of cancer patients and deaths are continuing to increase yearly, and cancer has, therefore, become one of the world&#039;s highest causes of morbidity and mortality. In recent years, the study of anticancer drugs has become one of the most popular medical topics. </P><P> Objective: In this review, in order to study the application of machine learning in predicting anticancer drugs activity, some machine learning approaches such as Linear Discriminant Analysis (LDA), Principal components analysis (PCA), Support Vector Machine (SVM), Random forest (RF), k-Nearest Neighbor (kNN), and Naïve Bayes (NB) were selected, and the examples of their applications in anticancer drugs design are listed. </P><P> Results: Machine learning contributes a lot to anticancer drugs design and helps researchers by saving time and is cost effective. However, it can only be an assisting tool for drug design. </P><P> Conclusion: This paper introduces the application of machine learning approaches in anticancer drug design. Many examples of success in identification and prediction in the area of anticancer drugs activity prediction are discussed, and the anticancer drugs research is still in active progress. Moreover, the merits of some web servers related to anticancer drugs are mentioned.

Recent Progress in Machine Learning-based Prediction of Peptide Activity for Drug Discovery

2019 ◽  
Vol 19 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Qihui Wu ◽  
Hanzhong Ke ◽  
Dongli Li ◽  
Qi Wang ◽  
Jiansong Fang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Large Scale ◽  
Recent Progress ◽  
High Specificity ◽  
Learning Approaches ◽  
Anticancer Peptides ◽  
The Past ◽  
Traditional Approaches ◽  
Large Scale Screening

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.

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.

scholarly journals Machine Learning Methods Applied to the Prediction of Pseudo-nitzschia spp. Blooms in the Galician Rias Baixas (NW Spain)

2021 ◽  
Vol 10 (4) ◽  
pp. 199
Author(s):  
Francisco M. Bellas Aláez ◽  
Jesus M. Torres Palenzuela ◽  
Evangelos Spyrakos ◽  
Luis González Vilas
Keyword(s):  
Machine Learning ◽  
Performance Metrics ◽  
Prediction Models ◽  
Support Vector ◽  
False Alarms ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Rías Baixas ◽  
New Algorithms

This work presents new prediction models based on recent developments in machine learning methods, such as Random Forest (RF) and AdaBoost, and compares them with more classical approaches, i.e., support vector machines (SVMs) and neural networks (NNs). The models predict Pseudo-nitzschia spp. blooms in the Galician Rias Baixas. This work builds on a previous study by the authors (doi.org/10.1016/j.pocean.2014.03.003) but uses an extended database (from 2002 to 2012) and new algorithms. Our results show that RF and AdaBoost provide better prediction results compared to SVMs and NNs, as they show improved performance metrics and a better balance between sensitivity and specificity. Classical machine learning approaches show higher sensitivities, but at a cost of lower specificity and higher percentages of false alarms (lower precision). These results seem to indicate a greater adaptation of new algorithms (RF and AdaBoost) to unbalanced datasets. Our models could be operationally implemented to establish a short-term prediction system.

57 Precision neoantigen discovery using novel algorithms and expanded HLA-ligandome datasets

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A62-A62
Author(s):  
Dattatreya Mellacheruvu ◽  
Rachel Pyke ◽  
Charles Abbott ◽  
Nick Phillips ◽  
Sejal Desai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cell Lines ◽  
Antigen Processing ◽  
Large Scale ◽  
Prediction Models ◽  
K562 Cells ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
High Quality ◽  
Tissue Samples

BackgroundAccurately identified neoantigens can be effective therapeutic agents in both adjuvant and neoadjuvant settings. A key challenge for neoantigen discovery has been the availability of accurate prediction models for MHC peptide presentation. We have shown previously that our proprietary model based on (i) large-scale, in-house mono-allelic data, (ii) custom features that model antigen processing, and (iii) advanced machine learning algorithms has strong performance. We have extended upon our work by systematically integrating large quantities of high-quality, publicly available data, implementing new modelling algorithms, and rigorously testing our models. These extensions lead to substantial improvements in performance and generalizability. Our algorithm, named Systematic HLA Epitope Ranking Pan Algorithm (SHERPA™), is integrated into the ImmunoID NeXT Platform®, our immuno-genomics and transcriptomics platform specifically designed to enable the development of immunotherapies.MethodsIn-house immunopeptidomic data was generated using stably transfected HLA-null K562 cells lines that express a single HLA allele of interest, followed by immunoprecipitation using W6/32 antibody and LC-MS/MS. Public immunopeptidomics data was downloaded from repositories such as MassIVE and processed uniformly using in-house pipelines to generate peptide lists filtered at 1% false discovery rate. Other metrics (features) were either extracted from source data or generated internally by re-processing samples utilizing the ImmunoID NeXT Platform.ResultsWe have generated large-scale and high-quality immunopeptidomics data by using approximately 60 mono-allelic cell lines that unambiguously assign peptides to their presenting alleles to create our primary models. Briefly, our primary ‘binding’ algorithm models MHC-peptide binding using peptide and binding pockets while our primary ‘presentation’ model uses additional features to model antigen processing and presentation. Both primary models have significantly higher precision across all recall values in multiple test data sets, including mono-allelic cell lines and multi-allelic tissue samples. To further improve the performance of our model, we expanded the diversity of our training set using high-quality, publicly available mono-allelic immunopeptidomics data. Furthermore, multi-allelic data was integrated by resolving peptide-to-allele mappings using our primary models. We then trained a new model using the expanded training data and a new composite machine learning architecture. The resulting secondary model further improves performance and generalizability across several tissue samples.ConclusionsImproving technologies for neoantigen discovery is critical for many therapeutic applications, including personalized neoantigen vaccines, and neoantigen-based biomarkers for immunotherapies. Our new and improved algorithm (SHERPA) has significantly higher performance compared to a state-of-the-art public algorithm and furthers this objective.

Machine learning identifies an immunological pattern associated with multiple juvenile idiopathic arthritis subtypes

2019 ◽  
Vol 78 (5) ◽  
pp. 617-628 ◽  
Author(s):  
Erika Van Nieuwenhove ◽  
Vasiliki Lagou ◽  
Lien Van Eyck ◽  
James Dooley ◽  
Ulrich Bodenhofer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Juvenile Idiopathic Arthritis ◽  
Large Scale ◽  
Inflammatory Diseases ◽  
Adaptive Immune System ◽  
Healthy Children ◽  
Learning Approaches ◽  
Data Set ◽  
Immune Signature ◽  
Systemic Jia

ObjectivesJuvenile idiopathic arthritis (JIA) is the most common class of childhood rheumatic diseases, with distinct disease subsets that may have diverging pathophysiological origins. Both adaptive and innate immune processes have been proposed as primary drivers, which may account for the observed clinical heterogeneity, but few high-depth studies have been performed.MethodsHere we profiled the adaptive immune system of 85 patients with JIA and 43 age-matched controls with indepth flow cytometry and machine learning approaches.ResultsImmune profiling identified immunological changes in patients with JIA. This immune signature was shared across a broad spectrum of childhood inflammatory diseases. The immune signature was identified in clinically distinct subsets of JIA, but was accentuated in patients with systemic JIA and those patients with active disease. Despite the extensive overlap in the immunological spectrum exhibited by healthy children and patients with JIA, machine learning analysis of the data set proved capable of discriminating patients with JIA from healthy controls with ~90% accuracy.ConclusionsThese results pave the way for large-scale immune phenotyping longitudinal studies of JIA. The ability to discriminate between patients with JIA and healthy individuals provides proof of principle for the use of machine learning to identify immune signatures that are predictive to treatment response group.

45 Application of Machine Learning Models to Thermal Burn Patient Outcome Predictions in the Aftermath of a Nuclear Event

2021 ◽  
Vol 42 (Supplement_1) ◽  
pp. S33-S34
Author(s):  
Morgan A Taylor ◽  
Randy D Kearns ◽  
Jeffrey E Carter ◽  
Mark H Ebell ◽  
Curt A Harris
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Length Of Stay ◽  
Regression Models ◽  
Large Scale ◽  
Prediction Models ◽  
Burn Patients ◽  
Thermal Burn ◽  
Logistic Regression Models ◽  
Burn Patient

Abstract Introduction A nuclear disaster would generate an unprecedented volume of thermal burn patients from the explosion and subsequent mass fires (Figure 1). Prediction models characterizing outcomes for these patients may better equip healthcare providers and other responders to manage large scale nuclear events. Logistic regression models have traditionally been employed to develop prediction scores for mortality of all burn patients. However, other healthcare disciplines have increasingly transitioned to machine learning (ML) models, which are automatically generated and continually improved, potentially increasing predictive accuracy. Preliminary research suggests ML models can predict burn patient mortality more accurately than commonly used prediction scores. The purpose of this study is to examine the efficacy of various ML methods in assessing thermal burn patient mortality and length of stay in burn centers. Methods This retrospective study identified patients with fire/flame burn etiologies in the National Burn Repository between the years 2009 – 2018. Patients were randomly partitioned into a 67%/33% split for training and validation. A random forest model (RF) and an artificial neural network (ANN) were then constructed for each outcome, mortality and length of stay. These models were then compared to logistic regression models and previously developed prediction tools with similar outcomes using a combination of classification and regression metrics. Results During the study period, 82,404 burn patients with a thermal etiology were identified in the analysis. The ANN models will likely tend to overfit the data, which can be resolved by ending the model training early or adding additional regularization parameters. Further exploration of the advantages and limitations of these models is forthcoming as metric analyses become available. Conclusions In this proof-of-concept study, we anticipate that at least one ML model will predict the targeted outcomes of thermal burn patient mortality and length of stay as judged by the fidelity with which it matches the logistic regression analysis. These advancements can then help disaster preparedness programs consider resource limitations during catastrophic incidents resulting in burn injuries.

Forecasting the risk at infractions: an ensemble comparison of machine learning approach

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Lei Li ◽  
Desheng Wu
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Short Term Memory ◽  
Model Performance ◽  
Large Data ◽  
Support Vector ◽  
Learning Approaches ◽  
Content Type ◽  
Day To Day Operations ◽  
Prediction Approach

PurposeThe infraction of securities regulations (ISRs) of listed firms in their day-to-day operations and management has become one of common problems. This paper proposed several machine learning approaches to forecast the risk at infractions of listed corporates to solve financial problems that are not effective and precise in supervision.Design/methodology/approachThe overall proposed research framework designed for forecasting the infractions (ISRs) include data collection and cleaning, feature engineering, data split, prediction approach application and model performance evaluation. We select Logistic Regression, Naïve Bayes, Random Forest, Support Vector Machines, Artificial Neural Network and Long Short-Term Memory Networks (LSTMs) as ISRs prediction models.FindingsThe research results show that prediction performance of proposed models with the prior infractions provides a significant improvement of the ISRs than those without prior, especially for large sample set. The results also indicate when judging whether a company has infractions, we should pay attention to novel artificial intelligence methods, previous infractions of the company, and large data sets.Originality/valueThe findings could be utilized to address the problems of identifying listed corporates' ISRs at hand to a certain degree. Overall, results elucidate the value of the prior infraction of securities regulations (ISRs). This shows the importance of including more data sources when constructing distress models and not only focus on building increasingly more complex models on the same data. This is also beneficial to the regulatory authorities.

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