InstaNovo

algorithm · Transformer (AR)

InstaNovo: algorithm · Transformer (AR). Knapsack beam search

Knapsack beam search

Kind	algorithm
Family	Transformer (AR)
Deep learning	yes
Acquisition	DDA

Code

• https://github.com/instadeepai/instanovo

Live stars, open issues and last-push figures are on the Code activity chart.

Papers

• 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)
• InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments (2025, Nature Machine Intelligence, peer-reviewed)
• De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments (2023, bioRxiv, preprint)

Authors (31)

Kevin Eloff, Konstantinos Kalogeropoulos, Oliver Morell, Amandla Mabona, Jakob Berg Jespersen, Wesley Williams, Sam P. B. van Beljouw, Marcin J. Skwark, Andreas Hougaard Laustsen, Stan J. J. Brouns, Anne Ljungars, Erwin M. Schoof, Jeroen Van Goey, Ulrich auf dem Keller, Karim Beguir, Nicolas Lopez Carranza, Timothy P. Jenkins, Rachel Catzel, Esperanza Rivera-de-Torre, Isaac H.J. Houngue, Marco Reverenna, Maike Wennekers Nielsen, Darian Stephan Wolff, Elpida Lytra, Pasquale D. Colaianni, Marie V. Lukassen, Alberto Santos, Jemma Daniel, Suthimon Thumtecho, Mohammed Esameldin Adam Nagi, Tasneem Midhat Mustafa Attaallah

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