InstaNovo
algorithm · Transformer (AR)
InstaNovo: algorithm · Transformer (AR). Knapsack beam search
Knapsack beam search
| Kind | algorithm |
| Deep learning | yes |
| Acquisition | DDA |
| Family | Transformer (AR) |
Code
Live stars, open issues and last-push figures are on the Code activity chart.
Benchmarks
- denovo_benchmarks: median peptide-level average precision 0.853 over 86 datasets, median rank 1 of 14 (version 1.2.2).
Both are mass-based matches on the tool’s most recent run. What these numbers mean.
Papers describing it (2)
- De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023, bioRxiv, preprint)
- InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025, Nature Machine Intelligence, peer-reviewed)
Papers using it (6)
Applications and evaluations that ran this method. They are not counted among its authors below.
- Can we Confidently Sequence the „Peptide Dark Matter“? Reaching a Consensus for De Novo Peptide Sequencing (2026, Proceedings of the 38th European Peptide Symposium, presentation)
- INSearch: AI-native framework for large scale proteomic database search via contrastive joint embeddings and transformer-based scoring function (2026, thesis)
- Sparse Autoencoders for Interpretability of InstaNovo (2026, thesis)
- Generalizable Direct Protein Sequencing With InstaNexus (2026, Molecular & Cellular Proteomics, peer-reviewed)
- Generalizable direct protein sequencing with InstaNexus (2025, bioRxiv, preprint)
- Advancing De Novo Glycopeptide Sequencing with InstaNovo in Glycoproteomics (2025, thesis)