Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms

2006 ◽  
Vol 65 (3) ◽  
pp. 607-622 ◽  
Author(s):  
Peter Block ◽  
Juri Paern ◽  
Eyke Hüllermeier ◽  
Paul Sanschagrin ◽  
Christoph A. Sotriffer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Protein Interactions ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Protein Protein Interactions ◽  
Physicochemical Descriptors

Targeting Virus-host Protein Interactions: Feature Extraction and Machine Learning Approaches

2019 ◽  
Vol 20 (3) ◽  
pp. 177-184 ◽  
Author(s):  
Nantao Zheng ◽  
Kairou Wang ◽  
Weihua Zhan ◽  
Lei Deng
Keyword(s):  
Machine Learning ◽  
Computational Methods ◽  
Protein Interactions ◽  
Prediction Models ◽  
Learning Algorithms ◽  
Biological Data ◽  
Machine Learning Algorithms ◽  
Host Protein ◽  
Protein Protein Interactions ◽  
Protein Motifs

Background:Targeting critical viral-host Protein-Protein Interactions (PPIs) has enormous application prospects for therapeutics. Using experimental methods to evaluate all possible virus-host PPIs is labor-intensive and time-consuming. Recent growth in computational identification of virus-host PPIs provides new opportunities for gaining biological insights, including applications in disease control. We provide an overview of recent computational approaches for studying virus-host PPI interactions.Methods:In this review, a variety of computational methods for virus-host PPIs prediction have been surveyed. These methods are categorized based on the features they utilize and different machine learning algorithms including classical and novel methods.Results:We describe the pivotal and representative features extracted from relevant sources of biological data, mainly include sequence signatures, known domain interactions, protein motifs and protein structure information. We focus on state-of-the-art machine learning algorithms that are used to build binary prediction models for the classification of virus-host protein pairs and discuss their abilities, weakness and future directions.Conclusion:The findings of this review confirm the importance of computational methods for finding the potential protein-protein interactions between virus and host. Although there has been significant progress in the prediction of virus-host PPIs in recent years, there is a lot of room for improvement in virus-host PPI prediction.

scholarly journals Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach

Open Biology ◽  
2016 ◽  
Vol 6 (9) ◽  
pp. 160183 ◽  
Author(s):  
Ashley J. Waardenberg ◽  
Bernou Homan ◽  
Stephanie Mohamed ◽  
Richard P. Harvey ◽  
Romaric Bouveret
Keyword(s):  
Machine Learning ◽  
Dna Binding ◽  
Protein Interactions ◽  
Heart Development ◽  
Machine Learning Algorithms ◽  
Protein Protein Interactions ◽  
Knowledge Based ◽  
Genome Wide ◽  
Binding Data ◽  
Gene Regulatory

The ability to accurately predict the DNA targets and interacting cofactors of transcriptional regulators from genome-wide data can significantly advance our understanding of gene regulatory networks. NKX2-5 is a homeodomain transcription factor that sits high in the cardiac gene regulatory network and is essential for normal heart development. We previously identified genomic targets for NKX2-5 in mouse HL-1 atrial cardiomyocytes using DNA-adenine methyltransferase identification (DamID). Here, we apply machine learning algorithms and propose a knowledge-based feature selection method for predicting NKX2-5 protein : protein interactions based on motif grammar in genome-wide DNA-binding data. We assessed model performance using leave-one-out cross-validation and a completely independent DamID experiment performed with replicates. In addition to identifying previously described NKX2-5-interacting proteins, including GATA, HAND and TBX family members, a number of novel interactors were identified, with direct protein : protein interactions between NKX2-5 and retinoid X receptor (RXR), paired-related homeobox (PRRX) and Ikaros zinc fingers (IKZF) validated using the yeast two-hybrid assay. We also found that the interaction of RXRα with NKX2-5 mutations found in congenital heart disease (Q187H, R189G and R190H) was altered. These findings highlight an intuitive approach to accessing protein–protein interaction information of transcription factors in DNA-binding experiments.

Forecasting US movies box office performances in Turkey using machine learning algorithms

2020 ◽  
Vol 39 (5) ◽  
pp. 6579-6590
Author(s):  
Sandy Çağlıyor ◽  
Başar Öztayşi ◽  
Selime Sezgin
Keyword(s):  
Machine Learning ◽  
Global Economy ◽  
Learning Algorithms ◽  
Forecast Model ◽  
Machine Learning Algorithms ◽  
Gradient Boosting ◽  
High Stakes ◽  
Box Office ◽  
Industry Forecast ◽  
The Impact

The motion picture industry is one of the largest industries worldwide and has significant importance in the global economy. Considering the high stakes and high risks in the industry, forecast models and decision support systems are gaining importance. Several attempts have been made to estimate the theatrical performance of a movie before or at the early stages of its release. Nevertheless, these models are mostly used for predicting domestic performances and the industry still struggles to predict box office performances in overseas markets. In this study, the aim is to design a forecast model using different machine learning algorithms to estimate the theatrical success of US movies in Turkey. From various sources, a dataset of 1559 movies is constructed. Firstly, independent variables are grouped as pre-release, distributor type, and international distribution based on their characteristic. The number of attendances is discretized into three classes. Four popular machine learning algorithms, artificial neural networks, decision tree regression and gradient boosting tree and random forest are employed, and the impact of each group is observed by compared by the performance models. Then the number of target classes is increased into five and eight and results are compared with the previously developed models in the literature.

Intelligent system of English composition scoring model based on improved machine learning algorithm

2020 ◽  
pp. 1-11
Author(s):  
Jie Liu ◽  
Lin Lin ◽  
Xiufang Liang
Keyword(s):  
Machine Learning ◽  
Evaluation System ◽  
Intelligent System ◽  
Learning Algorithm ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Assessment System ◽  
English Composition ◽  
Region Extraction ◽  
Constraint Model

The online English teaching system has certain requirements for the intelligent scoring system, and the most difficult stage of intelligent scoring in the English test is to score the English composition through the intelligent model. In order to improve the intelligence of English composition scoring, based on machine learning algorithms, this study combines intelligent image recognition technology to improve machine learning algorithms, and proposes an improved MSER-based character candidate region extraction algorithm and a convolutional neural network-based pseudo-character region filtering algorithm. In addition, in order to verify whether the algorithm model proposed in this paper meets the requirements of the group text, that is, to verify the feasibility of the algorithm, the performance of the model proposed in this study is analyzed through design experiments. Moreover, the basic conditions for composition scoring are input into the model as a constraint model. The research results show that the algorithm proposed in this paper has a certain practical effect, and it can be applied to the English assessment system and the online assessment system of the homework evaluation system algorithm system.

The Unlearnable Checkerboard Pattern

2019 ◽  
Vol 1 (2) ◽  
pp. 78-80
Author(s):  
Eric Holloway
Keyword(s):  
Machine Learning ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Checkerboard Pattern ◽  
Simple Task

Detecting some patterns is a simple task for humans, but nearly impossible for current machine learning algorithms.  Here, the "checkerboard" pattern is examined, where human prediction nears 100% and machine prediction drops significantly below 50%.

1290-P: Gut Microbiota in New-Onset Pediatric Patients with Type 1 Diabetes: Machine Learning Algorithms to Classify Microorganisms Disease-Linked

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 1290-P
Author(s):  
GIUSEPPE D’ANNUNZIO ◽  
ROBERTO BIASSONI ◽  
MARGHERITA SQUILLARIO ◽  
ELISABETTA UGOLOTTI ◽  
ANNALISA BARLA ◽  
...  
Keyword(s):  
Machine Learning ◽  
Type 1 Diabetes ◽  
Gut Microbiota ◽  
Pediatric Patients ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
New Onset
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