ContraNovo

algorithm · Transformer (AR)

ContraNovo: algorithm · Transformer (AR). Contrastive learning

Contrastive learning

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.

Checkpoints

Version Trained on Host Licence Size Checked Backup
AAAI release — Google Drive MIT 275 MB verified 2026-10-02 copy

A host marked archival has a DOI and keeps what it is given. The others can move or disappear, which is why they are checked rather than merely listed. verified means the bytes were fetched and hashed on the date shown; live means only that the host answered when last asked. Where a copy is linked, it is a backup of someone else’s weights kept in case the original link goes stale; the original is the link to cite and to prefer.

Benchmarks

  • denovo_benchmarks: median peptide-level average precision 0.808 over 86 datasets, median rank 4 of 14 (version bm-1.0.0).
  • ProteoBench, on the nine-species benchmark, ProteoBench selection: peptide-level AUC 0.883; precision 0.670 at 98% coverage; amino-acid AUC 0.838 (version 1.0, beam search, submitted 2026-08-07).

Both are mass-based matches on the tool’s most recent run. What these numbers mean.

Reported comparisons (2)

The comparison tables this method’s own papers print, standardised: every value on a 0-1 scale, methods down the side, the measure and then the species across. These are numbers papers report about themselves and their baselines. They are not a leaderboard, and they do not compare across tables: each was produced by a different group, on the dataset named in its corner, with each baseline either retrained, run from released weights or quoted from another paper. Where the paper says which, it follows the method’s name (hover it for the sentence); most papers do not say. Bold is the best value in a column and underline the runner-up, our ranking rather than the paper’s own marks.

Table 1

ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing, page 6: Comparison of the performance of ContraNovo and five baseline methods on 9-species-V1 test set. The bold font indicates the best performance.

Nine-species benchmark
original (DeepNovo, 2017) 		Amino acid precision
Mus musculus Homo sapiens Saccharomyces cerevisiae Methanosarcina mazei Apis mellifera Solanum lycopersicum Vigna mungo Bacillus subtilis Candidatus Thiodiazotropha endoloripes Average
PEAKS 0.600 0.639 0.748 0.673 0.633 0.728 0.644 0.719 0.586 0.663
DeepNovo 0.623 0.610 0.750 0.694 0.630 0.731 0.679 0.742 0.602 0.673
PointNovo 0.626 0.606 0.779 0.712 0.644 0.733 0.730 0.768 0.589 0.687
Casanovo 0.689 0.586 0.684 0.679 0.629 0.721 0.668 0.749 0.603 0.667
Casanovo V2 0.760 0.676 0.752 0.755 0.706 0.785 0.748 0.790 0.681 0.739
ContraNovo 0.798 0.771 0.797 0.799 0.745 0.810 0.807 0.828 0.711 0.785
Nine-species benchmark
original (DeepNovo, 2017) 		Peptide precision
Mus musculus Homo sapiens Saccharomyces cerevisiae Methanosarcina mazei Apis mellifera Solanum lycopersicum Vigna mungo Bacillus subtilis Candidatus Thiodiazotropha endoloripes Average
PEAKS 0.197 0.277 0.428 0.356 0.287 0.403 0.362 0.387 0.203 0.322
DeepNovo 0.286 0.293 0.462 0.422 0.330 0.454 0.436 0.449 0.253 0.376
PointNovo 0.355 0.351 0.534 0.478 0.396 0.513 0.511 0.518 0.298 0.439
Casanovo 0.426 0.341 0.490 0.478 0.406 0.521 0.506 0.537 0.330 0.448
Casanovo V2 0.483 0.446 0.599 0.557 0.493 0.618 0.589 0.622 0.446 0.539
ContraNovo 0.567 0.622 0.674 0.630 0.576 0.672 0.677 0.688 0.486 0.621

Table2

ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide Sequencing, page 7: Comparison of the performance of ContraNovo and CasaNovoV2 methods on 9-species-V2 test set. The bold font indicates the best performance.

Nine-species benchmark
revised (main) 		Amino acid precision
Mus musculus Homo sapiens Saccharomyces cerevisiae Methanosarcina mazei Apis mellifera Solanum lycopersicum Vigna mungo Bacillus subtilis Candidatus Thiodiazotropha endoloripes Average
Casanovo V2 0.792 0.836 0.851 0.828 0.759 0.823 0.858 0.852 0.760 0.818
ContraNovo 0.816 0.893 0.875 0.863 0.804 0.860 0.909 0.861 0.778 0.851
Nine-species benchmark
revised (main) 		Peptide precision
Mus musculus Homo sapiens Saccharomyces cerevisiae Methanosarcina mazei Apis mellifera Solanum lycopersicum Vigna mungo Bacillus subtilis Candidatus Thiodiazotropha endoloripes Average
Casanovo V2 0.520 0.651 0.729 0.675 0.572 0.692 0.702 0.717 0.505 0.640
ContraNovo 0.566 0.745 0.719 0.716 0.608 0.716 0.791 0.713 0.521 0.677

Paper describing it

Authors (9)

Zhi Jin, Sheng Xu, Xiang Zhang (Shanghai AI Lab), Tianze Ling, Nanqing Dong, Wanli Ouyang, Zhiqiang Gao, Cheng Chang, Siqi Sun

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