ArticleBMC bioinformatics2020
So you think you can PLS-DA?
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
156 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Rapid evaporative ionization mass spectrometry in surgery: a systematic review.The British journal of surgery · 2025Pooled it
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- Second-trimester multimetabolite panel for early preeclampsia rule-out.International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics · 2026Article
- Targeted Serum Organic-Acid Profiling Identifies Candidate Metabolic Signatures in Peripartum Cardiomyopathy: A Case-Control Study.International journal of molecular sciences · 2026Article
- Maternal Vitamin D Deficiency During Pregnancy Alters Hepatic Metabolism in Adult Female Offspring Without Overt Metabolic Dysfunction.Metabolites · 2026Article
- Effect biomonitoring in a controlled firefighting setting: an untargeted metabolomic pilot study.Archives of toxicology · 2026Article
- Influence of sire fertility on the metabolism of in vitro produced embryos.Reproduction & fertility · 2026Article
- Circulating Short-Chain Fatty Acid Profile Predicts Functional Outcome After Moderate-to-Severe Traumatic Brain Injury.Critical care explorations · 2026Article
- From fragrance wheel to functional genes: a multi-omics investigation into fragrance type formation in ornamentalHorticulture research · 2026Article
- Phenotype Classification of Intact Cells by NMR Spectroscopy through Machine Learning Approaches.Journal of the American Chemical Society · 2026Article
- Investigation of the cortical bone metabolome of C57BL/6J mice with adenine-induced kidney disease.JBMR plus · 2026Article
- A multi-omics analysis of gut bacteriome, virome, and serum metabolome in bipolar depression.Npj mental health research · 2026Article
- Single-cell vibration analysis for potential diagnostic applications.Biophysical reports · 2026Article
- Biological Signatures of Inflammation Biomarkers Identified Using Data Reduction Methods in Adult Population: A Scoping Review Protocol.Health science reports · 2026Article
- Postural test to differentiate primary aldosteronism from low-renin hypertension: a retrospective single-center study.Journal of endocrinological investigation · 2026Article
- Lipidomic profiles associated with treatment related hepatotoxicity in children with acute lymphoblastic leukemia.Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer · 2026Article
- Postharvest methyl jasmonate dipping modulates lipid composition and volatile profiles to alleviate chilling injury in yellow-fleshed peach fruit.BMC plant biology · 2026Article
- Urate-lowering effect of delphinidin-3-glucoside in red kidney beans via binding to the FAD site of the XO enzyme.Journal of advanced research · 2026Article
- Mineral content and potentially toxic elements inFood chemistry: X · 2026Article
96 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPartial Least-Squares Discriminant Analysis (PLS-DA) is a popular machine learning tool that is gaining increasing attention as a useful feature selector and classifier. In an effort to understand its strengths and weaknesses, we performed a series of experiments with synthetic data and compared its performance to its close relative from which it was initially invented, namely Principal Component Analysis (PCA).
resultsWe demonstrate that even though PCA ignores the information regarding the class labels of the samples, this unsupervised tool can be remarkably effective as a feature selector. In some cases, it outperforms PLS-DA, which is made aware of the class labels in its input. Our experiments range from looking at the signal-to-noise ratio in the feature selection task, to considering many practical distributions and models encountered when analyzing bioinformatics and clinical data. Other methods were also evaluated. Finally, we analyzed an interesting data set from 396 vaginal microbiome samples where the ground truth for the feature selection was available. All the 3D figures shown in this paper as well as the supplementary ones can be viewed interactively at http://biorg.cs.fiu.edu/plsda
conclusionsOur results highlighted the strengths and weaknesses of PLS-DA in comparison with PCA for different underlying data models.
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Registered trials
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.