Dataset Information

Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers.

ABSTRACT: Applying the knowledge that methyltransferases and demethylases can modify adjacent cytosine-phosphorothioate-guanine (CpG) sites in the same DNA strand, we found that combining multiple CpGs into a single block may improve cancer diagnosis. However, survival prediction remains a challenge. In this study, we developed a pipeline named "stacked ensemble of machine learning models for methylation-correlated blocks" (EnMCB) that combined Cox regression, support vector regression (SVR), and elastic-net models to construct signatures based on DNA methylation-correlated blocks for lung adenocarcinoma (LUAD) survival prediction. We used methylation profiles from the Cancer Genome Atlas (TCGA) as the training set, and profiles from the Gene Expression Omnibus (GEO) as validation and testing sets. First, we partitioned the genome into blocks of tightly co-methylated CpG sites, which we termed methylation-correlated blocks (MCBs). After partitioning and feature selection, we observed different diagnostic capacities for predicting patient survival across the models. We combined the multiple models into a single stacking ensemble model. The stacking ensemble model based on the top-ranked block had the area under the receiver operating characteristic curve of 0.622 in the TCGA training set, 0.773 in the validation set, and 0.698 in the testing set. When stratified by clinicopathological risk factors, the risk score predicted by the top-ranked MCB was an independent prognostic factor. Our results showed that our pipeline was a reliable tool that may facilitate MCB selection and survival prediction.

SUBMITTER: Yu X

PROVIDER: S-EPMC7894106 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers.

Yu Xin X Yang Qian Q Wang Dong D Li Zhaoyang Z Chen Nianhang N Kong De-Xin DX

PeerJ 20210216

Applying the knowledge that methyltransferases and demethylases can modify adjacent cytosine-phosphorothioate-guanine (CpG) sites in the same DNA strand, we found that combining multiple CpGs into a single block may improve cancer diagnosis. However, survival prediction remains a challenge. In this study, we developed a pipeline named "stacked ensemble of machine learning models for methylation-correlated blocks" (EnMCB) that combined Cox regression, support vector regression (SVR), and elastic- ...[more]

PMID: 33628643

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Project description:BACKGROUND:In plants, long non-protein coding RNAs are believed to have essential roles in development and stress responses. However, relative to advances on discerning biological roles for long non-protein coding RNAs in animal systems, this RNA class in plants is largely understudied. With comparatively few validated plant long non-coding RNAs, research on this potentially critical class of RNA is hindered by a lack of appropriate prediction tools and databases. Supervised learning models trained on data sets of mostly non-validated, non-coding transcripts have been previously used to identify this enigmatic RNA class with applications largely focused on animal systems. Our approach uses a training set comprised only of empirically validated long non-protein coding RNAs from plant, animal, and viral sources to predict and rank candidate long non-protein coding gene products for future functional validation. RESULTS:Individual stochastic gradient boosting and random forest classifiers trained on only empirically validated long non-protein coding RNAs were constructed. In order to use the strengths of multiple classifiers, we combined multiple models into a single stacking meta-learner. This ensemble approach benefits from the diversity of several learners to effectively identify putative plant long non-coding RNAs from transcript sequence features. When the predicted genes identified by the ensemble classifier were compared to those listed in GreeNC, an established plant long non-coding RNA database, overlap for predicted genes from Arabidopsis thaliana, Oryza sativa and Eutrema salsugineum ranged from 51 to 83% with the highest agreement in Eutrema salsugineum. Most of the highest ranking predictions from Arabidopsis thaliana were annotated as potential natural antisense genes, pseudogenes, transposable elements, or simply computationally predicted hypothetical protein. Due to the nature of this tool, the model can be updated as new long non-protein coding transcripts are identified and functionally verified. CONCLUSIONS:This ensemble classifier is an accurate tool that can be used to rank long non-protein coding RNA predictions for use in conjunction with gene expression studies. Selection of plant transcripts with a high potential for regulatory roles as long non-protein coding RNAs will advance research in the elucidation of long non-protein coding RNA function.

Project description:In recent years, the number of vulnerabilities discovered and publicly disclosed has shown a sharp upward trend. However, the value of exploitation of vulnerabilities varies for attackers, considering that only a small fraction of vulnerabilities are exploited. Therefore, the realization of quick exclusion of the non-exploitable vulnerabilities and optimal patch prioritization on limited resources has become imperative for organizations. Recent works using machine learning techniques predict exploited vulnerabilities by extracting features from open-source intelligence (OSINT). However, in the face of explosive growth of vulnerability information, there is room for improvement in the application of past methods to multiple threat intelligence. A more general method is needed to deal with various threat intelligence sources. Moreover, in previous methods, traditional text processing methods were used to deal with vulnerability related descriptions, which only grasped the static statistical characteristics but ignored the context and the meaning of the words of the text. To address these challenges, we propose an exploit prediction model, which is based on a combination of fastText and LightGBM algorithm and called fastEmbed. We replicate key portions of the state-of-the-art work of exploit prediction and use them as benchmark models. Our model outperforms the baseline model whether in terms of the generalization ability or the prediction ability without temporal intermixing with an average overall improvement of 6.283% by learning the embedding of vulnerability-related text on extremely imbalanced data sets. Besides, in terms of predicting the exploits in the wild, our model also outperforms the baseline model with an F1 measure of 0.586 on the minority class (33.577% improvement over the work using features from darkweb/deepweb). The results demonstrate that the model can improve the ability to describe the exploitability of vulnerabilities and predict exploits in the wild effectively.

Dataset Information

Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers.

Publications

Predicting lung adenocarcinoma disease progression using methylation-correlated blocks and ensemble machine learning classifiers.

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