Dataset Information

A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine.

ABSTRACT: RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA. Here, we present a data-driven model for RPI prediction using a gradient boosting classifier. Amino acids and nucleotides are classified based on the high-resolution structural data of RNA protein complexes. The minimum structural unit consisting of five residues is used as the descriptor. Comparative analysis of existing methods shows the consistently higher performance of our method irrespective of the length of RNA present in the RPI. The method has been successfully applied to map RPI networks involving both long noncoding RNA as well as TERRA RNA. The method is also shown to successfully predict RNA and protein hubs present in RPI networks of four different organisms. The robustness of this method will provide a way for predicting RPI networks of yet unknown interactions for both long noncoding RNA and microRNA.

SUBMITTER: Jain DS

PROVIDER: S-EPMC6015049 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine.

Jain Dharm Skandh DS Gupte Sanket Rajan SR Aduri Raviprasad R

Scientific reports 20180622 1

RNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA. Here, we present a data-driven model for RPI prediction using a g ...[more]

PMID: 29934510

Similar Datasets

Project description:BackgroundEmergency departments (ED) are becoming increasingly overwhelmed, increasing poor outcomes. Triage scores aim to optimize the waiting time and prioritize the resource usage. Artificial intelligence (AI) algorithms offer advantages for creating predictive clinical applications.ObjectiveEvaluate a state-of-the-art machine learning model for predicting mortality at the triage level and, by validating this automatic tool, improve the categorization of patients in the ED.DesignAn institutional review board (IRB) approval was granted for this retrospective study. Information of consecutive adult patients (ages 18-100) admitted at the emergency department (ED) of one hospital were retrieved (January 1, 2012-December 31, 2018). Features included the following: demographics, admission date, arrival mode, referral code, chief complaint, previous ED visits, previous hospitalizations, comorbidities, home medications, vital signs, and Emergency Severity Index (ESI). The following outcomes were evaluated: early mortality (up to 2 days post ED registration) and short-term mortality (2-30 days post ED registration). A gradient boosting model was trained on data from years 2012-2017 and examined on data from the final year (2018). The area under the curve (AUC) for mortality prediction was used as an outcome metric. Single-variable analysis was conducted to develop a nine-point triage score for early mortality.Key resultsOverall, 799,522 ED visits were available for analysis. The early and short-term mortality rates were 0.6% and 2.5%, respectively. Models trained on the full set of features yielded an AUC of 0.962 for early mortality and 0.923 for short-term mortality. A model that utilized the nine features with the highest single-variable AUC scores (age, arrival mode, chief complaint, five primary vital signs, and ESI) yielded an AUC of 0.962 for early mortality.ConclusionThe gradient boosting model shows high predictive ability for screening patients at risk of early mortality utilizing data available at the time of triage in the ED.

Project description:Circular RNA (circRNA) is a closed-loop structural non-coding RNA molecule which plays a significant role during the gene regulation processes. There are many previous studies shown that circRNAs can be regarded as the sponges of miRNAs. Thus, circRNA is also a key point for disease diagnosing, treating and inferring. However, traditional experimental approaches to verify the associations between the circRNA and disease are time-consuming and money-consuming. There are few computational models to predict potential circRNA-disease associations, which become our motivation to propose a new computational model. In this study, we propose a machine learning based computational model named Gradient Boosting Decision Tree with multiple biological data to predict circRNA-disease associations (GBDTCDA). The known circRNA-disease associations' data are downloaded from cricR2Disease database (http://bioinfo.snnu.edu.cn/CircR2Disease/). The feature vector of each circRNA-disease association pair is composed of four parts, which are the statistics information of different biological networks, the graph theory information of different biological networks, circRNA-disease associations' network information and circRNA nucleotide sequence information, respectively. Therefore, we use those feature vectors to train the gradient boosting decision tree regression model. Then, the leave one out cross validation (LOOCV) is adopted to evaluate the performance of our computational model. As for predicting some common diseases related circRNAs, our method GBDTCDA also obtains the better results. The Area under the ROC Curve (AUC) values of Basal cell carcinoma, Non-small cell lung cancer and cervical cancer are 95.8%, 88.3% and 93.5%, respectively. For further illustrating the performance of GBDTCDA, a case study of breast cancer is also supplemented in this study. Thus, our proposed method GBDTCDA is a powerful tool to predict potential circRNA-disease associations based on experimental results and analyses.

Dataset Information

A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine.

Publications

A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets