SEAOP : a statistical ensemble approach for outlier detection in quantitative proteomics data
© The Author(s) 2024. Published by Oxford University Press..
Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann-Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2024 |
|---|---|
| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:25 |
|---|---|
| Enthalten in: |
Briefings in bioinformatics - 25(2024), 3 vom: 27. März |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Huang, Jinze [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Ensemble |
|---|
| Anmerkungen: |
Date Completed 03.04.2024 Date Revised 26.04.2024 published: Print Citation Status MEDLINE |
|---|
| doi: |
10.1093/bib/bbae129 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM370471768 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM370471768 | ||
| 003 | DE-627 | ||
| 005 | 20240426234059.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 240403s2024 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1093/bib/bbae129 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1388.xml |
| 035 | |a (DE-627)NLM370471768 | ||
| 035 | |a (NLM)38557674 | ||
| 035 | |a (PII)bbae129 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Huang, Jinze |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a SEAOP |b a statistical ensemble approach for outlier detection in quantitative proteomics data |
| 264 | 1 | |c 2024 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 03.04.2024 | ||
| 500 | |a Date Revised 26.04.2024 | ||
| 500 | |a published: Print | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © The Author(s) 2024. Published by Oxford University Press. | ||
| 520 | |a Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann-Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Python | |
| 650 | 4 | |a ensemble | |
| 650 | 4 | |a outlier detection | |
| 650 | 4 | |a proteomics | |
| 650 | 4 | |a quality control | |
| 700 | 1 | |a Zhao, Yang |e verfasserin |4 aut | |
| 700 | 1 | |a Meng, Bo |e verfasserin |4 aut | |
| 700 | 1 | |a Lu, Ao |e verfasserin |4 aut | |
| 700 | 1 | |a Wei, Yaoguang |e verfasserin |4 aut | |
| 700 | 1 | |a Dong, Lianhua |e verfasserin |4 aut | |
| 700 | 1 | |a Fang, Xiang |e verfasserin |4 aut | |
| 700 | 1 | |a An, Dong |e verfasserin |4 aut | |
| 700 | 1 | |a Dai, Xinhua |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Briefings in bioinformatics |d 2000 |g 25(2024), 3 vom: 27. März |w (DE-627)NLM11366883X |x 1477-4054 |7 nnns |
| 773 | 1 | 8 | |g volume:25 |g year:2024 |g number:3 |g day:27 |g month:03 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1093/bib/bbae129 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 25 |j 2024 |e 3 |b 27 |c 03 | ||