ArticleNAR genomics and bioinformatics2023
GraphPart: homology partitioning for biological sequence analysis.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- QMAP: a benchmark for standardized evaluation of antimicrobial peptide MIC and hemolytic activity regression.Scientific reports · 2026Article
- Optimizing genomic language models for promoter prediction: a comparative study of tokenization and cross-species learning.NAR genomics and bioinformatics · 2026Article
- How to build machine learning models able to extrapolate from standard to modified peptides.Journal of cheminformatics · 2025Article
- Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.Briefings in bioinformatics · 2025Review
- NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.BMC bioinformatics · 2025Article
- ProtAlign-ARG: antibiotic resistance gene characterization integrating protein language models and alignment-based scoring.Scientific reports · 2025Article
- Beyond the leaderboard: leveraging predictive modeling for protein-ligand insights and discovery.Bioinformatics (Oxford, England) · 2025Article
- ProDualNet: dual-target protein sequence design method based on protein language model and structure model.Briefings in bioinformatics · 2025Article
- Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data.Briefings in bioinformatics · 2025Article
- Data splitting to avoid information leakage with DataSAIL.Nature communications · 2025Article
- Ayu: a machine intelligence tool for identification of extracellular proteins in the marine secretome.Nature communications · 2025Article
- Predicting the subcellular location of prokaryotic proteins with DeepLocPro.Bioinformatics (Oxford, England) · 2024Article
- AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors.Bioinformatics (Oxford, England) · 2024Article
- SpanSeq: similarity-based sequence data splitting method for improved development and assessment of deep learning projects.NAR genomics and bioinformatics · 2024Article
- Guiding questions to avoid data leakage in biological machine learning applications.Nature methods · 2024Review
- DeepLoc 2.1: multi-label membrane protein type prediction using protein language models.Nucleic acids research · 2024Article
- SpecGMM: Integrating Spectral analysis and Gaussian Mixture Models for taxonomic classification and identification of discriminative DNA regions.Bioinformatics advances · 2024Article
- SignalP: The Evolution of a Web Server.Methods in molecular biology (Clifton, N.J.) · 2024Article
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Authors and funding
6 authors.
Funding
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Abstract
When splitting biological sequence data for the development and testing of predictive models, it is necessary to avoid too-closely related pairs of sequences ending up in different partitions. If this is ignored, performance of prediction methods will tend to be overestimated. Several algorithms have been proposed for homology reduction, where sequences are removed until no too-closely related pairs remain. We present GraphPart, an algorithm for homology partitioning that divides the data such that closely related sequences always end up in the same partition, while keeping as many sequences as possible in the dataset. Evaluation of GraphPart on Protein, DNA and RNA datasets shows that it is capable of retaining a larger number of sequences per dataset, while providing homology separation on a par with reduction approaches.
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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.