RankNovo
post-processor · Transformer (AR)
Universal reranking
| Kind | post-processor |
| Deep learning | yes |
| Acquisition | both |
| 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 |
|---|---|---|---|---|---|---|
| shared with CrossNovo | — | Google Drive | MIT | 607 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.
Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Trained on
- MassIVE-KB (v1 30M-PSM split (Casanovo)) · 2024 preprint, 2025 preprint, 2025 ML conference
Evaluated on
- Nine-species benchmark (original (DeepNovo, 2017)) · 2024 preprint, 2025 preprint, 2025 ML conference
- Nine-species benchmark (revised (build not stated)) · 2024 preprint, 2025 preprint, 2025 ML conference
Reported comparisons (3)
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.
Table1
Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing, page 7: Evaluation of RankNovo in comparison to baseline and base models on the 9-species-V1 and 9-species-V2 test sets. Bolded entries indicate the best-performing models. The symbol “†” indicates that the model serves as both a baseline and a base model. “⋆” signifies that the base models were developed and trained by us. Here, ByNovo is the best base model. So the performance of three self-trained base models (R-Casa, R-Contra, R-By) is only provided in Appendix D.1.
| Nine-species benchmark | Amino acid precision | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| PEAKS | 0.719 | 0.586 | 0.633 | 0.639 | 0.673 | 0.600 | 0.644 | 0.728 | 0.748 | 0.663 |
| DeepNovo | 0.742 | 0.602 | 0.630 | 0.610 | 0.694 | 0.623 | 0.679 | 0.731 | 0.750 | 0.673 |
| PointNovo | 0.768 | 0.589 | 0.644 | 0.606 | 0.712 | 0.626 | 0.730 | 0.733 | 0.779 | 0.687 |
| Casanovo | 0.749 | 0.603 | 0.629 | 0.586 | 0.679 | 0.689 | 0.668 | 0.721 | 0.684 | 0.667 |
| Casanovo V2 · released | 0.888 | 0.791 | 0.823 | 0.872 | 0.877 | 0.813 | 0.891 | 0.891 | 0.915 | 0.862 |
| ContraNovo · released | 0.901 | 0.807 | 0.848 | 0.920 | 0.896 | 0.839 | 0.913 | 0.898 | 0.919 | 0.882 |
| ByNovo | 0.920 | 0.823 | 0.876 | 0.917 | 0.914 | 0.841 | 0.932 | 0.912 | 0.934 | 0.897 |
| RankNovo | 0.926 | 0.838 | 0.885 | 0.929 | 0.920 | 0.860 | 0.938 | 0.918 | 0.938 | 0.906 |
| Nine-species benchmark | Peptide recall | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| PEAKS | 0.387 | 0.203 | 0.287 | 0.277 | 0.356 | 0.197 | 0.362 | 0.403 | 0.428 | 0.322 |
| DeepNovo | 0.449 | 0.253 | 0.330 | 0.293 | 0.422 | 0.286 | 0.436 | 0.454 | 0.462 | 0.376 |
| PointNovo | 0.518 | 0.298 | 0.396 | 0.351 | 0.478 | 0.355 | 0.511 | 0.513 | 0.534 | 0.439 |
| Casanovo | 0.537 | 0.330 | 0.406 | 0.341 | 0.478 | 0.426 | 0.506 | 0.521 | 0.490 | 0.448 |
| Casanovo V2 · released | 0.793 | 0.558 | 0.669 | 0.712 | 0.754 | 0.555 | 0.772 | 0.783 | 0.837 | 0.714 |
| ContraNovo · released | 0.815 | 0.575 | 0.711 | 0.820 | 0.780 | 0.616 | 0.799 | 0.794 | 0.854 | 0.752 |
| ByNovo | 0.833 | 0.582 | 0.731 | 0.789 | 0.799 | 0.596 | 0.814 | 0.807 | 0.871 | 0.758 |
| RankNovo | 0.851 | 0.620 | 0.752 | 0.820 | 0.813 | 0.629 | 0.836 | 0.822 | 0.885 | 0.781 |
RankNovo reranks the candidates of six base models. Casanovo V2 and ContraNovo are the released models; ByNovo is RankNovo's own in-house model, with an auxiliary b/y ion-annotation head (its Appendix B.4); R-Casanovo, R-ContraNovo and R-ByNovo are reverse-decoding versions of the three, trained by RankNovo's authors and recorded as the 'reverse decoding' variant. All six were trained on MassIVE-KB and evaluated zero-shot. '†' marks a model that is both baseline and base model, '⋆' one the authors trained. The plain Casanovo row repeats the values other papers print for Casanovo (0.749 and 0.537 on Bacillus) and the paper does not say where they come from. THE TEXT AND THE TABLE DISAGREE on V1: the prose gives RankNovo an amino-acid precision of 0.829 and a peptide recall '6.1%' above ByNovo; the table prints 0.824, and 0.660 against ByNovo's 0.623. The table's values are recorded.
In the paper: column amino acid precision, Average: the original table bolded RankNovo (0.824), RankNovo (0.906).
In the paper: column amino acid precision, Bacillus: the original table bolded RankNovo (0.874), RankNovo (0.926).
In the paper: column amino acid precision, C. bacteria: the original table bolded RankNovo (0.746), RankNovo (0.838).
In the paper: column amino acid precision, Honeybee: the original table bolded RankNovo (0.810), RankNovo (0.885).
In the paper: column amino acid precision, Human: the original table bolded RankNovo (0.802), RankNovo (0.929).
In the paper: column amino acid precision, M. mazei: the original table bolded RankNovo (0.840), RankNovo (0.920).
In the paper: column amino acid precision, Mouse: the original table bolded RankNovo (0.828), RankNovo (0.860).
In the paper: column amino acid precision, Ricebean: the original table bolded RankNovo (0.859), RankNovo (0.938).
In the paper: column amino acid precision, Tomato: the original table bolded RankNovo (0.844), RankNovo (0.918).
In the paper: column amino acid precision, Yeast: the original table bolded RankNovo (0.816), RankNovo (0.938).
In the paper: column peptide recall, Average: the original table bolded RankNovo (0.660), RankNovo (0.781).
In the paper: column peptide recall, Bacillus: the original table bolded RankNovo (0.738), RankNovo (0.851).
In the paper: column peptide recall, C. bacteria: the original table bolded RankNovo (0.539), RankNovo (0.620).
In the paper: column peptide recall, Honeybee: the original table bolded RankNovo (0.630), RankNovo (0.752).
In the paper: column peptide recall, Human: the original table bolded RankNovo (0.642), RankNovo (0.820).
In the paper: column peptide recall, M. mazei: the original table bolded RankNovo (0.672), RankNovo (0.813).
In the paper: column peptide recall, Mouse: the original table bolded RankNovo (0.583), RankNovo (0.629).
In the paper: column peptide recall, Ricebean: the original table bolded RankNovo (0.733), RankNovo (0.836).
In the paper: column peptide recall, Tomato: the original table bolded RankNovo (0.691), RankNovo (0.822).
In the paper: column peptide recall, Yeast: the original table bolded RankNovo (0.703), RankNovo (0.885).
Table6
Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing, page 17: Evaluation of RankNovo in comparison to baseline and base methods on the 9-species-V1 test set. Bolded entries indicate the best-performing models. The symbol “†” indicates that the model serves as both a baseline and a base model. “⋆” signifies that the base models were developed and trained by us.
The same table is also printed in RankNovo: A Universal Reranking Approach for Robust De Novo Peptide Sequencing (Table1, page 8).
|
Nine-species benchmark original (DeepNovo, 2017) |
Amino acid precision | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| PEAKS | 0.719 | 0.586 | 0.633 | 0.639 | 0.673 | 0.600 | 0.644 | 0.728 | 0.748 | 0.663 |
| DeepNovo | 0.742 | 0.602 | 0.630 | 0.610 | 0.694 | 0.623 | 0.679 | 0.731 | 0.750 | 0.673 |
| PointNovo | 0.768 | 0.589 | 0.644 | 0.606 | 0.712 | 0.626 | 0.730 | 0.733 | 0.779 | 0.687 |
| Casanovo | 0.749 | 0.603 | 0.629 | 0.586 | 0.679 | 0.689 | 0.668 | 0.721 | 0.684 | 0.667 |
| Casanovo V2 · released | 0.806 | 0.685 | 0.727 | 0.69 | 0.774 | 0.768 | 0.769 | 0.799 | 0.762 | 0.753 |
| ContraNovo · released | 0.828 | 0.706 | 0.761 | 0.771 | 0.798 | 0.799 | 0.804 | 0.808 | 0.782 | 0.784 |
| ByNovo | 0.858 | 0.723 | 0.791 | 0.767 | 0.823 | 0.803 | 0.836 | 0.828 | 0.804 | 0.804 |
| Casanovo reverse decoding · retrained | 0.804 | 0.699 | 0.728 | 0.719 | 0.769 | 0.776 | 0.782 | 0.795 | 0.762 | 0.759 |
| ContraNovo reverse decoding · retrained | 0.839 | 0.716 | 0.775 | 0.782 | 0.806 | 0.811 | 0.816 | 0.822 | 0.798 | 0.796 |
| ByNovo reverse decoding | 0.855 | 0.724 | 0.794 | 0.762 | 0.821 | 0.81 | 0.835 | 0.831 | 0.762 | 0.799 |
| RankNovo | 0.874 | 0.746 | 0.81 | 0.802 | 0.84 | 0.828 | 0.859 | 0.844 | 0.816 | 0.824 |
|
Nine-species benchmark original (DeepNovo, 2017) |
Peptide recall | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| PEAKS | 0.387 | 0.203 | 0.287 | 0.277 | 0.356 | 0.197 | 0.362 | 0.403 | 0.428 | 0.322 |
| DeepNovo | 0.449 | 0.253 | 0.330 | 0.293 | 0.422 | 0.286 | 0.436 | 0.454 | 0.462 | 0.376 |
| PointNovo | 0.518 | 0.298 | 0.396 | 0.351 | 0.478 | 0.355 | 0.511 | 0.513 | 0.534 | 0.439 |
| Casanovo | 0.537 | 0.330 | 0.406 | 0.341 | 0.478 | 0.426 | 0.506 | 0.521 | 0.490 | 0.448 |
| Casanovo V2 · released | 0.646 | 0.46 | 0.527 | 0.492 | 0.592 | 0.493 | 0.628 | 0.637 | 0.629 | 0.567 |
| ContraNovo · released | 0.684 | 0.487 | 0.576 | 0.624 | 0.628 | 0.563 | 0.676 | 0.655 | 0.669 | 0.618 |
| ByNovo | 0.708 | 0.499 | 0.597 | 0.584 | 0.639 | 0.545 | 0.696 | 0.667 | 0.676 | 0.623 |
| Casanovo reverse decoding · retrained | 0.628 | 0.467 | 0.515 | 0.511 | 0.57 | 0.505 | 0.611 | 0.611 | 0.601 | 0.558 |
| ContraNovo reverse decoding · retrained | 0.682 | 0.499 | 0.583 | 0.606 | 0.621 | 0.566 | 0.673 | 0.654 | 0.664 | 0.616 |
| ByNovo reverse decoding | 0.703 | 0.493 | 0.59 | 0.554 | 0.637 | 0.543 | 0.685 | 0.659 | 0.629 | 0.610 |
| RankNovo | 0.738 | 0.539 | 0.63 | 0.642 | 0.672 | 0.583 | 0.733 | 0.691 | 0.703 | 0.660 |
RankNovo reranks the candidates of six base models. Casanovo V2 and ContraNovo are the released models; ByNovo is RankNovo's own in-house model, with an auxiliary b/y ion-annotation head (its Appendix B.4); R-Casanovo, R-ContraNovo and R-ByNovo are reverse-decoding versions of the three, trained by RankNovo's authors and recorded as the 'reverse decoding' variant. All six were trained on MassIVE-KB and evaluated zero-shot. '†' marks a model that is both baseline and base model, '⋆' one the authors trained. The plain Casanovo row repeats the values other papers print for Casanovo (0.749 and 0.537 on Bacillus) and the paper does not say where they come from. THE TEXT AND THE TABLE DISAGREE on V1: the prose gives RankNovo an amino-acid precision of 0.829 and a peptide recall '6.1%' above ByNovo; the table prints 0.824, and 0.660 against ByNovo's 0.623. The table's values are recorded.
Table7
Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing, page 17: Evaluation of RankNovo in comparison to baseline and base methods on the 9-species-V2 test set. Bolded entries indicate the best-performing models. The symbol “†” indicates that the model serves as both a baseline and a base model. “⋆” signifies that the base models were developed and trained by us.
The same table is also printed in RankNovo: A Universal Reranking Approach for Robust De Novo Peptide Sequencing (Table2, page 8).
|
Nine-species benchmark revised (build not stated) |
Amino acid precision | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| Casanovo V2 · released | 0.888 | 0.791 | 0.823 | 0.872 | 0.877 | 0.813 | 0.891 | 0.891 | 0.915 | 0.862 |
| ContraNovo · released | 0.901 | 0.807 | 0.848 | 0.920 | 0.896 | 0.839 | 0.913 | 0.898 | 0.919 | 0.882 |
| ByNovo | 0.92 | 0.823 | 0.876 | 0.917 | 0.914 | 0.841 | 0.932 | 0.912 | 0.934 | 0.897 |
| Casanovo reverse decoding · retrained | 0.876 | 0.804 | 0.814 | 0.891 | 0.867 | 0.821 | 0.881 | 0.891 | 0.898 | 0.860 |
| ContraNovo reverse decoding · retrained | 0.909 | 0.815 | 0.865 | 0.923 | 0.901 | 0.849 | 0.919 | 0.907 | 0.925 | 0.890 |
| ByNovo reverse decoding | 0.919 | 0.822 | 0.879 | 0.912 | 0.912 | 0.843 | 0.932 | 0.913 | 0.936 | 0.897 |
| RankNovo | 0.926 | 0.838 | 0.885 | 0.929 | 0.920 | 0.860 | 0.938 | 0.918 | 0.938 | 0.906 |
|
Nine-species benchmark revised (build not stated) |
Peptide recall | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| Casanovo V2 · released | 0.793 | 0.558 | 0.669 | 0.712 | 0.754 | 0.555 | 0.772 | 0.783 | 0.837 | 0.714 |
| ContraNovo · released | 0.815 | 0.575 | 0.711 | 0.820 | 0.780 | 0.616 | 0.799 | 0.794 | 0.854 | 0.752 |
| ByNovo | 0.833 | 0.582 | 0.731 | 0.789 | 0.799 | 0.596 | 0.814 | 0.807 | 0.871 | 0.758 |
| Casanovo reverse decoding · retrained | 0.759 | 0.558 | 0.643 | 0.732 | 0.723 | 0.558 | 0.721 | 0.768 | 0.799 | 0.696 |
| ContraNovo reverse decoding · retrained | 0.821 | 0.581 | 0.719 | 0.815 | 0.779 | 0.620 | 0.804 | 0.798 | 0.861 | 0.755 |
| ByNovo reverse decoding | 0.831 | 0.585 | 0.729 | 0.781 | 0.794 | 0.589 | 0.815 | 0.803 | 0.873 | 0.756 |
| RankNovo | 0.851 | 0.620 | 0.752 | 0.820 | 0.813 | 0.629 | 0.836 | 0.822 | 0.885 | 0.781 |
RankNovo reranks the candidates of six base models. Casanovo V2 and ContraNovo are the released models; ByNovo is RankNovo's own in-house model, with an auxiliary b/y ion-annotation head (its Appendix B.4); R-Casanovo, R-ContraNovo and R-ByNovo are reverse-decoding versions of the three, trained by RankNovo's authors and recorded as the 'reverse decoding' variant. All six were trained on MassIVE-KB and evaluated zero-shot. '†' marks a model that is both baseline and base model, '⋆' one the authors trained. The plain Casanovo row repeats the values other papers print for Casanovo (0.749 and 0.537 on Bacillus) and the paper does not say where they come from.
In the paper: column peptide recall, Human: the original table only bolded RankNovo (0.820); ContraNovo (ContraNovo†) (0.820) ties with it and is bolded here too.
Compared against in other papers (1)
2 tables from 1 paper that report this method as a baseline, newest first. The caveats of the comparisons above hold twice over: each paper ran, retrained or quoted this method its own way, so its number here is that paper’s claim, not a measurement of the method. Where a paper says which it did, the word follows the method’s name.
ScopeNovo: a De Novo Peptide Sequencing Method Using Spectrum-Spectrum Similarity to Refine the Prediction Accuracy (2026) · 2 tables
Table 1 (Nine-species · revised (build not stated))
ScopeNovo: a De Novo Peptide Sequencing Method Using Spectrum-Spectrum Similarity to Refine the Prediction Accuracy, page 5: Comparison of de novo peptide sequencing methods on 9-species-V1 and 9-species-V2 benchmarks. For ScopeNovo we report two operating regimes: Setting 1 (External Library, spectrum-consistency reranking against a curated external spectral library), which characterizes the upper-bound performance attainable when high-quality external spectral resources are available; and Setting 2 (Self-Constructed Library), in which the reference library is bootstrapped entirely from high-confidence in-batch de novo predictions on the test data itself, placing ScopeNovo under the same resource assumptions as the baselines and yielding a direct comparison. In each column, the best value among the baselines and ScopeNovo (Setting 2) is in bold; ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.
|
Nine-species benchmark revised (build not stated) |
Amino acid precision | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| Casanovo | 0.923 | 0.787 | 0.776 | 0.856 | 0.828 | 0.806 | 0.854 | 0.874 | 0.865 | 0.881 |
| Casanovo V2 | 0.843 | 0.799 | 0.788 | 0.865 | 0.836 | 0.813 | 0.867 | 0.882 | 0.875 | 0.865 |
| InstaNovo | 0.852 | 0.751 | 0.799 | 0.847 | 0.848 | 0.634 | 0.894 | 0.864 | 0.877 | 0.850 |
| ContraNovo | 0.863 | 0.802 | 0.817 | 0.909 | 0.864 | 0.830 | 0.903 | 0.881 | 0.883 | 0.865 |
| AdaNovo | 0.792 | 0.816 | 0.756 | 0.800 | 0.804 | 0.757 | 0.759 | 0.831 | 0.801 | 0.794 |
| RankNovo | 0.836 | 0.836 | 0.891 | 0.836 | 0.879 | 0.920 | 0.896 | 0.893 | 0.879 | 0.880 |
| π-PrimeNovo | 0.874 | 0.806 | 0.824 | 0.870 | 0.869 | 0.808 | 0.921 | 0.885 | 0.891 | 0.866 |
| ScopeNovo Setting 1 | 0.885 | 0.822 | 0.839 | 0.884 | 0.882 | 0.841 | 0.931 | 0.897 | 0.900 | 0.885 |
| ScopeNovo Setting 2 | 0.877 | 0.814 | 0.829 | 0.879 | 0.874 | 0.821 | 0.926 | 0.889 | 0.892 | 0.868 |
|
Nine-species benchmark revised (build not stated) |
Peptide accuracy | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| Casanovo | 0.687 | 0.522 | 0.579 | 0.662 | 0.656 | 0.522 | 0.645 | 0.730 | 0.738 | 0.682 |
| Casanovo V2 | 0.693 | 0.532 | 0.587 | 0.670 | 0.661 | 0.531 | 0.654 | 0.737 | 0.743 | 0.683 |
| InstaNovo | 0.704 | 0.512 | 0.625 | 0.670 | 0.666 | 0.504 | 0.679 | 0.721 | 0.758 | 0.698 |
| ContraNovo | 0.709 | 0.533 | 0.615 | 0.759 | 0.698 | 0.567 | 0.722 | 0.729 | 0.725 | 0.701 |
| AdaNovo | 0.636 | 0.624 | 0.597 | 0.590 | 0.641 | 0.472 | 0.538 | 0.693 | 0.653 | 0.635 |
| RankNovo | 0.713 | 0.603 | 0.617 | 0.717 | 0.712 | 0.559 | 0.744 | 0.724 | 0.680 | 0.682 |
| π-PrimeNovo | 0.712 | 0.572 | 0.612 | 0.710 | 0.714 | 0.548 | 0.766 | 0.719 | 0.684 | 0.697 |
| ScopeNovo Setting 1 | 0.748 | 0.664 | 0.669 | 0.762 | 0.772 | 0.664 | 0.816 | 0.771 | 0.702 | 0.737 |
| ScopeNovo Setting 2 | 0.728 | 0.619 | 0.641 | 0.750 | 0.743 | 0.611 | 0.788 | 0.745 | 0.691 | 0.716 |
The paper bolds the best of the baselines and ScopeNovo (Setting 2) only: 'ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.' Bold and underline here rank every row, Setting 1 included; the paper's own marks were checked against its rule, and match it.
Table 1 (Nine-species · original (DeepNovo, 2017))
ScopeNovo: a De Novo Peptide Sequencing Method Using Spectrum-Spectrum Similarity to Refine the Prediction Accuracy, page 5: Comparison of de novo peptide sequencing methods on 9-species-V1 and 9-species-V2 benchmarks. For ScopeNovo we report two operating regimes: Setting 1 (External Library, spectrum-consistency reranking against a curated external spectral library), which characterizes the upper-bound performance attainable when high-quality external spectral resources are available; and Setting 2 (Self-Constructed Library), in which the reference library is bootstrapped entirely from high-confidence in-batch de novo predictions on the test data itself, placing ScopeNovo under the same resource assumptions as the baselines and yielding a direct comparison. In each column, the best value among the baselines and ScopeNovo (Setting 2) is in bold; ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.
|
Nine-species benchmark original (DeepNovo, 2017) |
Amino acid precision | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| Casanovo | 0.788 | 0.676 | 0.708 | 0.676 | 0.754 | 0.765 | 0.761 | 0.792 | 0.756 | 0.743 |
| Casanovo V2 | 0.801 | 0.687 | 0.721 | 0.687 | 0.767 | 0.774 | 0.768 | 0.802 | 0.768 | 0.754 |
| InstaNovo | 0.802 | 0.656 | 0.718 | 0.691 | 0.756 | 0.742 | 0.794 | 0.774 | 0.767 | 0.745 |
| ContraNovo | 0.828 | 0.700 | 0.764 | 0.778 | 0.798 | 0.803 | 0.804 | 0.812 | 0.787 | 0.785 |
| AdaNovo | 0.858 | 0.798 | 0.767 | 0.690 | 0.804 | 0.778 | 0.878 | 0.818 | 0.791 | 0.798 |
| RankNovo | 0.807 | 0.771 | 0.880 | 0.784 | 0.838 | 0.823 | 0.876 | 0.846 | 0.828 | 0.827 |
| π-PrimeNovo | 0.840 | 0.715 | 0.767 | 0.725 | 0.799 | 0.797 | 0.823 | 0.822 | 0.795 | 0.789 |
| ScopeNovo Setting 1 | 0.849 | 0.715 | 0.778 | 0.729 | 0.811 | 0.809 | 0.816 | 0.825 | 0.796 | 0.797 |
| ScopeNovo Setting 2 | 0.844 | 0.722 | 0.774 | 0.732 | 0.806 | 0.809 | 0.829 | 0.828 | 0.798 | 0.795 |
|
Nine-species benchmark original (DeepNovo, 2017) |
Peptide accuracy | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus subtilis | Candidatus Thiodiazotropha endoloripes | Apis mellifera | Homo sapiens | Methanosarcina mazei | Mus musculus | Vigna mungo | Solanum lycopersicum | Saccharomyces cerevisiae | Average | |
| Casanovo | 0.621 | 0.437 | 0.494 | 0.446 | 0.568 | 0.485 | 0.593 | 0.622 | 0.601 | 0.551 |
| Casanovo V2 | 0.630 | 0.445 | 0.504 | 0.455 | 0.579 | 0.493 | 0.600 | 0.629 | 0.607 | 0.559 |
| InstaNovo | 0.652 | 0.459 | 0.535 | 0.515 | 0.595 | 0.525 | 0.635 | 0.635 | 0.618 | 0.582 |
| ContraNovo | 0.688 | 0.486 | 0.580 | 0.625 | 0.633 | 0.574 | 0.678 | 0.674 | 0.673 | 0.628 |
| AdaNovo | 0.753 | 0.638 | 0.620 | 0.494 | 0.671 | 0.546 | 0.797 | 0.684 | 0.660 | 0.660 |
| RankNovo | 0.765 | 0.592 | 0.642 | 0.621 | 0.688 | 0.595 | 0.765 | 0.720 | 0.726 | 0.687 |
| π-PrimeNovo | 0.725 | 0.532 | 0.602 | 0.575 | 0.654 | 0.572 | 0.701 | 0.701 | 0.703 | 0.650 |
| ScopeNovo Setting 1 | 0.789 | 0.610 | 0.665 | 0.628 | 0.731 | 0.660 | 0.755 | 0.752 | 0.744 | 0.711 |
| ScopeNovo Setting 2 | 0.749 | 0.572 | 0.643 | 0.624 | 0.690 | 0.637 | 0.733 | 0.732 | 0.721 | 0.684 |
The paper bolds the best of the baselines and ScopeNovo (Setting 2) only: 'ScopeNovo (Setting 1) is reported separately for reference and excluded from the bold comparison.' Bold and underline here rank every row, Setting 1 included; the paper's own marks were checked against its rule, and match it.
Papers describing it (3)
- RankNovo: A Universal Reranking Approach for Robust De Novo Peptide Sequencing (2024, OpenReview, preprint)
- Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing (2025, arXiv, preprint)
- Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing (2025, ICML 2025, ML conference)