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

https://github.com/BEAM-Labs/denovo

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.

Reported comparisons (5)

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
Nine-species benchmark original (DeepNovo, 2017)	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
Nine-species benchmark original (DeepNovo, 2017)	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.

Nine-species benchmark original (DeepNovo, 2017)	Amino acid precision
Nine-species benchmark original (DeepNovo, 2017)	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
Nine-species benchmark original (DeepNovo, 2017)	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 Distilling Non-Autoregressive Model Knowledge for Autoregressive De Novo Peptide Sequencing (Table2, page 8).

Nine-species benchmark revised (main)	Amino acid precision
Nine-species benchmark revised (main)	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 (main)	Peptide recall
Nine-species benchmark revised (main)	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.

WIgG1-Mouse antibody (CrossNovo); no accession stated	Amino acid precision					Peptide recall
WIgG1-Mouse antibody (CrossNovo); no accession stated	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.

IgG1-Human antibody (CrossNovo); no accession stated	Amino acid precision
IgG1-Human antibody (CrossNovo); no accession stated	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

IgG1-Human antibody (CrossNovo); no accession stated	Peptide recall
IgG1-Human antibody (CrossNovo); no accession stated	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

Papers describing it (3)

Distilling Non-Autoregressive Model Knowledge for Autoregressive De Novo Peptide Sequencing (2025, OpenReview, preprint)
Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025, arXiv, preprint)
Bidirectional Representations Augmented Autoregressive Biological Sequence Generation (2025, NeurIPS 2025, ML conference)

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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