Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Efficacy of PD-1/PD-L1 and LAG-3 immune checkpoint inhibitors in the treatment of patients with solid tumor.

Frontiers in immunology·2026

Same author

From Scarcity to Synthesis: Continual Learning Integrates Supervised and Unsupervised CT Image Recovery Models.

IEEE journal of biomedical and health informatics·2026

Same author

Correction for Cheng et al., "Simultaneous expression of three G genotypes of VP7 proteins in a recombinant porcine rotavirus confers protective immunity against multiple rotavirus infections".

Journal of virology·2026

Same author

Induction of mitochondrial fission and mtDNA leakage via the Smad3/Drp1 axis by PEDV infection activates the TLR9/NF-κB/IL-1β inflammatory pathway.

Virologica Sinica·2026

Same author

High-Performance Infrared Photodetectors Based on Graphene Nanoribbon Vertical Heterojunctions via Dissociated Double-Walled Carbon Nanotubes.

Nanomaterials (Basel, Switzerland)·2026

Same author

Synergistic effects of konjac glucomannan and ultrasound treatment on inhibiting retrogradation and modifying structural properties of quinoa starch gels.

Food chemistry·2026

Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026

Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026

Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 1, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

How to balance the bioinformatics data: pseudo-negative sampling.

Yongqing Zhang^1,2, Shaojie Qiao^3,4, Rongzhao Lu¹

¹School of Computer Science, Chengdu University of Information Technology, Chengdu, 610225, China.

BMC Bioinformatics

|December 26, 2019

Summary

This summary is machine-generated.

This study introduces pseudo-negative sampling to address imbalanced bioinformatics datasets, where negative samples vastly outnumber positive ones. This novel approach improves classification performance, particularly for the minority positive class.

Keywords:

Imbalanced data Max-relevance Min-redundancy Pearson correlation coefficients Pseudo-negative sampling

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Related Experiment Videos

Last Updated: Jan 1, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Area of Science:

Bioinformatics
Machine Learning
Data Science

Background:

Imbalanced datasets are prevalent in bioinformatics classification.
Data imbalance leads to underestimation of minority class performance.
Balancing bioinformatic data is a significant challenge.

Purpose of the Study:

To propose a novel data sampling approach for imbalanced datasets.
To effectively handle scenarios where negative samples dominate positive samples.
To improve the performance of minority class classification.

Main Methods:

Introduced pseudo-negative sampling.
Developed a supervised learning method using max-relevance min-redundancy criterion beyond Pearson correlation coefficient (MMPCC).
MMPCC selects pseudo-negative samples from negative samples and treats them as positive, using incremental searching for efficiency.

Main Results:

Pseudo-negative samples exhibit strong relevance to positive samples and low redundancy to negative ones.
MMPCC outperformed other sampling methods on UCI and bioinformatics datasets.
Improvements observed in Sensitivity, Specificity, Accuracy, and Mathew's Correlation Coefficient.

Conclusions:

Pseudo-negative sampling effectively addresses imbalanced datasets in bioinformatics.
The MMPCC method demonstrates superior performance compared to existing sampling techniques.
Increased Sensitivity in minority samples correlates with improved overall prediction accuracy.