CrossNovo

algorithm · Transformer (NAR)

CrossNovo: algorithm · Transformer (NAR). AR + NAR hybrid

AR + NAR hybrid

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

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 RankNovo — 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

Evaluated on

Reported comparisons (6)

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

Distilling Non-Autoregressive Model Knowledge for Autoregressive De Novo Peptide Sequencing, page 7: Comparison of the performance of CrossNovo and 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
π-PrimeNovo 0.784 0.729 0.802 0.801 0.763 0.815 0.822 0.846 0.734 0.788
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
CrossNovo 0.816 0.800 0.814 0.826 0.785 0.830 0.831 0.856 0.740 0.811
Nine-species benchmark
original (DeepNovo, 2017) 		Peptide recall
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
π-PrimeNovo 0.567 0.574 0.697 0.650 0.603 0.697 0.702 0.721 0.531 0.638
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
CrossNovo 0.596 0.661 0.698 0.660 0.610 0.695 0.716 0.726 0.518 0.654

In the paper: column peptide recall, Mouse: the original table only underlined ContraNovo (Contra.) (0.567); π-PrimeNovo (Prime.) (0.567) ties with it and is underlined here too.

Table1

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation, page 8: Comparison of the performance of CROSSNOVO and baseline methods on the 9-species-v1 test set.

The same table is also printed in Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (Table1, page 8).

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
π-PrimeNovo 0.784 0.729 0.802 0.801 0.763 0.815 0.822 0.846 0.734 0.788
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
InstaNovo 0.703 0.636 0.691 0.712 0.660 0.732 0.711 0.739 0.619 0.689
Casanovo V2 0.760 0.676 0.752 0.755 0.706 0.785 0.748 0.790 0.681 0.739
π-HelixNovo 0.765 0.665 0.768 0.784 0.757 0.721 0.793 0.816 0.681 0.750
ContraNovo 0.798 0.771 0.797 0.799 0.745 0.810 0.807 0.828 0.711 0.785
CrossNovo 0.816 0.800 0.814 0.826 0.785 0.830 0.831 0.856 0.740 0.811
Nine-species benchmark
original (DeepNovo, 2017) 		Peptide recall
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
π-PrimeNovo 0.567 0.574 0.697 0.650 0.603 0.697 0.702 0.721 0.531 0.638
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
InstaNovo 0.471 0.455 0.559 0.528 0.466 0.732 0.564 0.576 0.416 0.530
Casanovo V2 0.483 0.446 0.599 0.557 0.493 0.618 0.589 0.622 0.446 0.539
π-HelixNovo 0.483 0.392 0.568 0.560 0.473 0.560 0.623 0.596 0.388 0.517
ContraNovo 0.567 0.622 0.674 0.630 0.576 0.672 0.677 0.688 0.486 0.621
CrossNovo 0.596 0.661 0.698 0.660 0.610 0.695 0.716 0.726 0.518 0.654

In the paper: column peptide recall, Mouse: the original table only underlined ContraNovo (Contra.) (0.567); π-PrimeNovo (Prime.) (0.567) ties with it and is underlined here too.
In the paper: column peptide recall, Tomato: the original table bolded π-PrimeNovo (Prime.) (0.697), InstaNovo (Insta) (0.732) and underlined CrossNovo (Ours) (0.695).

Table2

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation, page 8: Comparison of the performance of CROSSNOVO and baseline methods on 9-species-v2 test set. The bold font indicates the best performance.

The same table is also printed in Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (Table2, page 8), Distilling Non-Autoregressive Model Knowledge for Autoregressive De Novo Peptide Sequencing (Table2, page 8).

Nine-species benchmark
revised (build not stated) 		Amino acid precision
Mus musculus Homo sapiens Saccharomyces cerevisiae Methanosarcina mazei Apis mellifera Solanum lycopersicum Vigna mungo Bacillus subtilis Candidatus Thiodiazotropha endoloripes Average
π-PrimeNovo 0.839 0.893 0.932 0.908 0.862 0.909 0.931 0.921 0.827 0.891
Casanovo V2 0.813 0.872 0.915 0.877 0.823 0.891 0.891 0.888 0.791 0.862
ContraNovo 0.839 0.920 0.919 0.896 0.848 0.898 0.913 0.901 0.807 0.882
CrossNovo 0.857 0.937 0.939 0.920 0.880 0.914 0.939 0.927 0.837 0.906
Nine-species benchmark
revised (build not stated) 		Peptide recall
Mus musculus Homo sapiens Saccharomyces cerevisiae Methanosarcina mazei Apis mellifera Solanum lycopersicum Vigna mungo Bacillus subtilis Candidatus Thiodiazotropha endoloripes Average
π-PrimeNovo 0.627 0.795 0.884 0.812 0.742 0.824 0.837 0.849 0.626 0.777
Casanovo V2 0.555 0.712 0.837 0.754 0.669 0.783 0.772 0.793 0.558 0.714
ContraNovo 0.616 0.820 0.854 0.780 0.711 0.794 0.799 0.815 0.575 0.752
CrossNovo 0.651 0.850 0.885 0.819 0.751 0.816 0.847 0.850 0.607 0.786

Table6

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation, page 26: Comparison of the performance of CROSSNOVO and baseline methods on WIgG1-Mouse. The bold font indicates the best performance.

The same table is also printed in Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (Table6, page 26).

Monoclonal antibody de novo assembly
as deposited 		Amino acid precision Peptide recall
HC AspN HC Chymotrypsin HC Trypsin LC AspN Average HC AspN HC Chymotrypsin HC Trypsin LC AspN Average
Casanovo V2 0.714 0.591 0.723 0.668 0.674 0.557 0.483 0.636 0.456 0.533
ContraNovo 0.750 0.612 0.650 0.649 0.665 0.649 0.545 0.671 0.519 0.596
CrossNovo 0.769 0.640 0.747 0.724 0.720 0.662 0.577 0.699 0.581 0.630

Table7

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation, page 26: Comparison of the performance of CROSSNOVO and baseline methods on IgG1-Human. Bold values indicate the best performance.

The same table is also printed in Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (Table7, page 26).

Monoclonal antibody de novo assembly
as deposited 		Amino acid precision
HC AspN HC Chymotrypsin HC GluC HC LysC HC Proteinase K HC Trypsin LC AspN LC LysC Average
Casanovo V2 0.520 0.472 0.605 0.757 0.354 0.759 0.666 0.778 0.642
ContraNovo 0.580 0.565 0.642 0.790 0.348 0.787 0.702 0.793 0.676
CrossNovo 0.613 0.617 0.694 0.814 0.367 0.803 0.719 0.807 0.702
Monoclonal antibody de novo assembly
as deposited 		Peptide recall
HC AspN HC Chymotrypsin HC GluC HC LysC HC Proteinase K HC Trypsin LC AspN LC LysC Average
Casanovo V2 0.265 0.274 0.399 0.569 0.206 0.595 0.325 0.625 0.446
ContraNovo 0.396 0.372 0.437 0.653 0.274 0.675 0.499 0.646 0.529
CrossNovo 0.415 0.421 0.512 0.701 0.275 0.699 0.544 0.676 0.560

Table 8

Bidirectional Representations Augmented Autoregressive Biological Sequence Generation, page 28: Performance comparison on five representative PTMs after fine-tuning on the 21-PTM dataset. Bold values indicate the best performance for each column.

The same table is also printed in Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (Table 8, page 28).

ProteomeTools
21-PTM subset 		Ptm accuracy Amino acid recall
Acetylation Biotinylation Crotonylation Butyrylation Dimethylation Acetylation Biotinylation Crotonylation Butyrylation Dimethylation
π-PrimeNovo 0.98 0.99 0.98 0.97 0.95 0.95 0.83 0.90 0.82 0.84
CrossNovo 0.98 0.98 0.98 0.98 0.97 0.96 0.83 0.86 0.85 0.85
ProteomeTools
21-PTM subset 		Peptide recall
Acetylation Biotinylation Crotonylation Butyrylation Dimethylation
π-PrimeNovo 0.89 0.70 0.79 0.65 0.66
CrossNovo 0.90 0.72 0.78 0.69 0.68

In the paper: column ptm accuracy, Acetylation: the original table only bolded CrossNovo (0.98); π-PrimeNovo (PrimeNovo) (0.98) ties with it and is bolded here too.
In the paper: column ptm accuracy, Crotonylation: the original table only bolded CrossNovo (0.98); π-PrimeNovo (PrimeNovo) (0.98) ties with it and is bolded here too.

Papers describing it (3)

Authors (8)

Xiang Zhang (Shanghai AI Lab), Jiaqi Wei, Zijie Qiu, Sheng Xu, Zhi Jin, Zhiqiang Gao, Nanqing Dong, Siqi Sun

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