MemNovo

algorithm · Transformer (AR)

MemNovo: algorithm · Transformer (AR). Autoregressive transformer de novo sequencer with a memory mechanism that lets the decoder revisit the input spectrum at each step to balance error accumulation.

Autoregressive transformer de novo sequencer with a memory mechanism that lets the decoder revisit the input spectrum at each step to balance error accumulation.

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

Code

https://github.com/AIMS-Lab-HKUSTGZ/MemNovo

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

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.

Table2

MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry, page 7: Performance comparison on the Nine Species benchmark. We report amino acid precision (AA) and peptide precision (Pep.) for each method. For Casanovo and InstaNovo, we additionally show results with MemNovo applied and the corresponding relative improvement (Rel. Imp.). Best results for each species are shown in bold. Results marked with † are reported from original publications, which may use different model versions and evaluation protocols; direct numerical comparison with our evaluation should be interpreted with caution.

Nine-species benchmark revised (balanced)	Amino acid precision
Nine-species benchmark revised (balanced)	Mus musculus	Homo sapiens	Saccharomyces cerevisiae	Methanosarcina mazei	Apis mellifera	Solanum lycopersicum	Vigna mungo	Bacillus subtilis	Candidatus Thiodiazotropha endoloripes	Average
DeepNovo · quoted	0.6230	0.6100	0.7500	0.6940	0.6300	0.7310	0.6790	0.7420	0.6020	0.6734
PointNovo · quoted	0.6260	0.6060	0.7790	0.7120	0.6440	0.7330	0.7300	0.7680	0.5890	0.6874
Casanovo	0.6352	0.6885	0.7672	0.7253	0.6730	0.7302	0.7446	0.7701	0.6895	0.7137
AdaNovo · quoted	0.6460	0.6180	0.7930	0.7280	0.6500	0.7400	0.7190	0.7390	0.6420	0.6972
InstaNovo	0.7351	0.7934	0.8447	0.8214	0.7754	0.8181	0.8450	0.8367	0.7631	0.8037
MemNovo on Casanovo	0.6524	0.7031	0.7688	0.7287	0.7749	0.7442	0.7469	0.7941	0.7055	0.7354
MemNovo on InstaNovo	0.7614	0.8130	0.8553	0.8350	0.7934	0.8324	0.8566	0.8504	0.7912	0.8210

Nine-species benchmark revised (balanced)	Peptide precision
Nine-species benchmark revised (balanced)	Mus musculus	Homo sapiens	Saccharomyces cerevisiae	Methanosarcina mazei	Apis mellifera	Solanum lycopersicum	Vigna mungo	Bacillus subtilis	Candidatus Thiodiazotropha endoloripes	Average
DeepNovo · quoted	0.2860	0.2930	0.4620	0.4220	0.3300	0.4540	0.4360	0.4490	0.2530	0.3761
PointNovo · quoted	0.3550	0.3510	0.5340	0.4780	0.3960	0.5130	0.5110	0.5180	0.2980	0.4393
Casanovo	0.2404	0.3105	0.4089	0.3254	0.2875	0.3873	0.3314	0.3585	0.2274	0.3197
AdaNovo · quoted	0.4670	0.3730	0.5930	0.4960	0.4310	0.5300	0.5460	0.5280	0.3720	0.4818
InstaNovo	0.3485	0.4562	0.5559	0.4927	0.4318	0.5116	0.5177	0.5185	0.3435	0.4640
MemNovo on Casanovo	0.3372	0.4541	0.4968	0.4295	0.5226	0.5250	0.3530	0.5309	0.3529	0.4447
MemNovo on InstaNovo	0.3522	0.4675	0.5981	0.5051	0.4419	0.5305	0.5481	0.5298	0.3668	0.4822

Table 6

MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry, page 10: Complete four-metric comparison on the Nine Species benchmark for InstaNovo and InstaNovo + MemNovo.

Nine-species benchmark revised (balanced)	Amino acid precision
Nine-species benchmark revised (balanced)	Bacillus subtilis	Saccharomyces cerevisiae	Methanosarcina mazei	Apis mellifera	Solanum lycopersicum	Vigna mungo	Homo sapiens	Mus musculus	Candidatus Thiodiazotropha endoloripes	Average
InstaNovo	0.7307	0.7665	0.7410	0.6740	0.7862	0.7851	0.7186	0.6767	0.6242	0.7226
MemNovo on InstaNovo	0.7372	0.7798	0.7383	0.6775	0.7945	0.7912	0.7314	0.6739	0.6433	0.7308

Nine-species benchmark revised (balanced)	Amino acid recall
Nine-species benchmark revised (balanced)	Bacillus subtilis	Saccharomyces cerevisiae	Methanosarcina mazei	Apis mellifera	Solanum lycopersicum	Vigna mungo	Homo sapiens	Mus musculus	Candidatus Thiodiazotropha endoloripes	Average
InstaNovo	0.7124	0.7482	0.7281	0.6542	0.7710	0.7623	0.7010	0.6608	0.6028	0.7045
MemNovo on InstaNovo	0.7109	0.7441	0.7334	0.6590	0.7704	0.7553	0.6990	0.6686	0.6053	0.7051

Nine-species benchmark revised (balanced)	Peptide precision
Nine-species benchmark revised (balanced)	Bacillus subtilis	Saccharomyces cerevisiae	Methanosarcina mazei	Apis mellifera	Solanum lycopersicum	Vigna mungo	Homo sapiens	Mus musculus	Candidatus Thiodiazotropha endoloripes	Average
InstaNovo	0.6366	0.6877	0.6096	0.5526	0.6904	0.6425	0.6138	0.4922	0.4660	0.5991
MemNovo on InstaNovo	0.6357	0.6925	0.6036	0.5477	0.6904	0.6419	0.6146	0.4843	0.4698	0.5978

Nine-species benchmark revised (balanced)	Peptide recall
Nine-species benchmark revised (balanced)	Bacillus subtilis	Saccharomyces cerevisiae	Methanosarcina mazei	Apis mellifera	Solanum lycopersicum	Vigna mungo	Homo sapiens	Mus musculus	Candidatus Thiodiazotropha endoloripes	Average
InstaNovo	0.6249	0.6772	0.5997	0.5384	0.6821	0.6293	0.6031	0.4823	0.4555	0.5881
MemNovo on InstaNovo	0.6259	0.6780	0.6015	0.5408	0.6824	0.6303	0.6026	0.4834	0.4567	0.5891

Paper describing it

MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry (2026, arXiv, preprint)

Authors (5)

Dongxin Lyu, Jingbo Zhou, Hongxin Xiang, Yuqiang Li, Jun Xia

Seen in the charts

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