Evidence map›Paper›PMID 34589181›Full record

ReviewComputational and structural biotechnology journal2021

Machine learning and deep learning methods that use omics data for metastasis prediction.

Somayah Albaradei, Maha Thafar, Asim Alsaedi, Christophe Van Neste, Takashi Gojobori, Magbubah Essack, Xin Gao

Abstract readReview
In one paragraph

Review in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
92citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

92 citing papers in PubMed, 1 synthesis or guideline pooled it.

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32 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Somayah AlbaradeiComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Maha ThafarComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Asim AlsaediKing Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.
Christophe Van NesteComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Takashi GojoboriComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Magbubah EssackComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
Xin GaoComputational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Knowing metastasis is the primary cause of cancer-related deaths, incentivized research directed towards unraveling the complex cellular processes that drive the metastasis. Advancement in technology and specifically the advent of high-throughput sequencing provides knowledge of such processes. This knowledge led to the development of therapeutic and clinical applications, and is now being used to predict the onset of metastasis to improve diagnostics and disease therapies. In this regard, predicting metastasis onset has also been explored using artificial intelligence approaches that are machine learning, and more recently, deep learning-based. This review summarizes the different machine learning and deep learning-based metastasis prediction methods developed to date. We also detail the different types of molecular data used to build the models and the critical signatures derived from the different methods. We further highlight the challenges associated with using machine learning and deep learning methods, and provide suggestions to improve the predictive performance of such methods.

Indexed as

Acc, AccuracyAE, autoencoderANN, Artificial Neural NetworkArtificial intelligenceAUC, area under the curveBC, Betweenness centralityBH, Benjamini-HochbergBioGRID, Biological General Repository for Interaction DatasetsCancerCCP, compound covariate predictorCEA, Carcinoembryonic antigenCNN, convolution neural networksCV, cross-validationDBN, deep belief networkDDBN, discriminative deep belief networkDeep learningDEGs, differentially expressed genesDIP, Database of Interacting ProteinsDNN, Deep neural networkDT, Decision TreeEMT, epithelial-mesenchymal transitionFC, fully connectedGA, Genetic AlgorithmGANs, generative adversarial networksGEO, Gene Expression OmnibusHCC, hepatocellular carcinomaHPRD, Human Protein Reference Databasek-CV, k-fold cross validationKNN, K-nearest neighborLIMMA, linear models for microarray dataLOOCV, Leave-one-out cross-validationLR, Logistic RegressionL-SVM, linear SVMMachine learningMCCV, Monte Carlo cross-validationMetastasisMLP, multilayer perceptronmRMR, minimum redundancy maximum relevanceNPV, negative predictive valuePCA, Principal component analysisPPI, protein-protein interactionPPV, positive predictive valueRC, ridge classifierRFE, recursive feature eliminationRF, Random ForestRMA, robust multi‐array averageRNN, recurrent neural networksSe, sensitivitySGD, stochastic gradient descentSMOTE, synthetic minority over-sampling techniqueSp, specificitySVM, Support Vector MachineTCGA, The Cancer Genome Atlas

Identifiers

PMID34589181
PMCPMC8450182

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.