CausalNovo

algorithm · Transformer (AR)

CausalNovo: algorithm · Transformer (AR). Causality-informed framework

Causality-informed framework

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

Code

Not tracked on the Code activity chart: those figures come from the GitHub API, and this link is not a GitHub repository.

Reported comparisons (8)

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 (HC-PT)

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Comparison with state-of-the-art models in amino acid-level and peptide-level performance. † denotes our retrained results, and others are provided by NovoBench. The best results are marked in bold, and the second-best results are underlined.

ProteomeTools
HC-PT (NovoBench) 		Amino acid precision Amino acid recall Peptide precision Peptide AUC
DeepNovo · quoted 0.531 0.534 0.313 0.255
PointNovo · quoted 0.623 0.622 0.419 0.373
InstaNovo · quoted 0.289 0.285 0.057 0.034
SearchNovo · quoted 0.652 0.658 0.447 0.413
Casanovo · quoted 0.442 0.453 0.211 0.177
Casanovo · retrained 0.525 0.530 0.324 0.290
CausalNovo on †CasaNovo 0.635 0.639 0.459 0.426
AdaNovo · quoted 0.442 0.451 0.212 0.178
AdaNovo · retrained 0.492 0.496 0.289 0.254
CausalNovo on †AdaNovo 0.634 0.637 0.453 0.420
π-HelixNovo · quoted 0.588 0.582 0.356 0.318
π-HelixNovo · retrained 0.532 0.537 0.301 0.261
CausalNovo on †π-HelixNovo 0.656 0.658 0.450 0.415

Table1 (Nine-species)

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Comparison with state-of-the-art models in amino acid-level and peptide-level performance. † denotes our retrained results, and others are provided by NovoBench. The best results are marked in bold, and the second-best results are underlined.

Nine-species benchmark Amino acid precision Amino acid recall Peptide precision Peptide AUC
PEAKS · quoted 0.748 0.428
DeepNovo · quoted 0.696 0.638 0.428 0.376
PointNovo · quoted 0.740 0.671 0.480 0.436
InstaNovo · quoted 0.420 0.395 0.164 0.123
SearchNovo · quoted 0.748 0.746 0.550 0.489
Casanovo · quoted 0.697 0.696 0.481 0.439
Casanovo · retrained 0.741 0.740 0.529 0.493
CausalNovo on †CasaNovo 0.765 0.766 0.564 0.528
AdaNovo · quoted 0.698 0.709 0.505 0.469
AdaNovo · retrained 0.681 0.681 0.473 0.439
CausalNovo on †AdaNovo 0.744 0.746 0.542 0.507
π-HelixNovo · quoted 0.765 0.758 0.517 0.453
π-HelixNovo · retrained 0.765 0.752 0.509 0.431
CausalNovo on †π-HelixNovo 0.787 0.784 0.543 0.483

Table1 (Seven-species)

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Comparison with state-of-the-art models in amino acid-level and peptide-level performance. † denotes our retrained results, and others are provided by NovoBench. The best results are marked in bold, and the second-best results are underlined.

Seven-species benchmark Amino acid precision Amino acid recall Peptide precision Peptide AUC
DeepNovo · quoted 0.492 0.433 0.204 0.136
PointNovo · quoted 0.196 0.169 0.022 0.007
InstaNovo · quoted 0.192 0.176 0.031 0.009
SearchNovo · quoted 0.489 0.488 0.259 0.174
Casanovo · quoted 0.322 0.327 0.119 0.084
Casanovo · retrained 0.357 0.366 0.159 0.119
CausalNovo on †CasaNovo 0.477 0.478 0.245 0.200
AdaNovo · quoted 0.379 0.385 0.174 0.135
AdaNovo · retrained 0.403 0.405 0.189 0.149
CausalNovo on †AdaNovo 0.453 0.453 0.233 0.192
π-HelixNovo · quoted 0.481 0.472 0.234 0.173
π-HelixNovo · retrained 0.465 0.462 0.218 0.156
CausalNovo on †π-HelixNovo 0.536 0.534 0.282 0.229

Table2 (HC-PT)

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Comparison with state-of-the-art models in PTM-level performance. † denotes our retrained results, and others are given by NovoBench. The best is marked in bold.

ProteomeTools
HC-PT (NovoBench) 		Ptm precision Ptm recall
DeepNovo · quoted 0.626 0.615
PointNovo · quoted 0.676 0.740
InstaNovo · quoted 0.350 0.261
SearchNovo · quoted 0.715 0.772
Casanovo · quoted 0.501 0.460
Casanovo · retrained 0.550 0.582
CausalNovo on †CasaNovo 0.671 0.741
AdaNovo · quoted 0.552 0.482
AdaNovo · retrained 0.562 0.532
CausalNovo on †AdaNovo 0.652 0.743
π-HelixNovo · quoted 0.568 0.667
π-HelixNovo · retrained 0.632 0.566
CausalNovo on †π-HelixNovo 0.737 0.746

Table2 (Nine-species)

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Comparison with state-of-the-art models in PTM-level performance. † denotes our retrained results, and others are given by NovoBench. The best is marked in bold.

Nine-species benchmark Ptm precision Ptm recall
DeepNovo · quoted 0.576 0.529
PointNovo · quoted 0.629 0.546
InstaNovo · quoted 0.443 0.294
SearchNovo · quoted 0.764 0.599
Casanovo · quoted 0.706 0.566
Casanovo · retrained 0.755 0.601
CausalNovo on †CasaNovo 0.791 0.608
AdaNovo · quoted 0.652 0.570
AdaNovo · retrained 0.678 0.552
CausalNovo on †AdaNovo 0.769 0.607
π-HelixNovo · quoted 0.680 0.598
π-HelixNovo · retrained 0.723 0.593
CausalNovo on †π-HelixNovo 0.731 0.616

Table2 (Seven-species)

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Comparison with state-of-the-art models in PTM-level performance. † denotes our retrained results, and others are given by NovoBench. The best is marked in bold.

Seven-species benchmark Ptm precision Ptm recall
DeepNovo · quoted 0.391 0.373
PointNovo · quoted 0.117 0.094
InstaNovo · quoted 0.126 0.115
SearchNovo · quoted 0.472 0.447
Casanovo · quoted 0.360 0.251
Casanovo · retrained 0.368 0.292
CausalNovo on †CasaNovo 0.503 0.422
AdaNovo · quoted 0.448 0.321
AdaNovo · retrained 0.430 0.356
CausalNovo on †AdaNovo 0.469 0.398
π-HelixNovo · quoted 0.473 0.366
π-HelixNovo · retrained 0.362 0.370
CausalNovo on †π-HelixNovo 0.513 0.427

Table3

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 6: Cross-species validation on the Ninespecies dataset. † denotes our retrained results.

Nine-species benchmark Amino acid precision
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum
Casanovo · retrained 0.743 0.754 0.761 0.769 0.754 0.753 0.753 0.717
CausalNovo on †CasaNovo 0.773 0.772 0.772 0.780 0.773 0.784 0.763 0.748
Nine-species benchmark Amino acid recall
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum
Casanovo · retrained 0.745 0.752 0.757 0.770 0.754 0.752 0.755 0.716
CausalNovo on †CasaNovo 0.774 0.773 0.774 0.779 0.776 0.782 0.763 0.752
Nine-species benchmark Peptide precision
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum
Casanovo · retrained 0.559 0.544 0.554 0.575 0.558 0.558 0.549 0.506
CausalNovo on †CasaNovo 0.584 0.578 0.578 0.587 0.580 0.595 0.557 0.545
Nine-species benchmark Peptide AUC
Bacillus subtilis Candidatus Thiodiazotropha endoloripes Apis mellifera Homo sapiens Methanosarcina mazei Mus musculus Vigna mungo Solanum lycopersicum
Casanovo · retrained 0.523 0.509 0.519 0.540 0.532 0.521 0.510 0.464
CausalNovo on †CasaNovo 0.551 0.544 0.545 0.553 0.544 0.560 0.521 0.506

Table8

CausalNovo: Advancing De Novo Peptide Sequencing via a Causality-Informed Framework, page 16: Cross-species validation on the Seven-species dataset. † denotes our retrained results.

Seven-species benchmark Amino acid precision Amino acid recall
Celegans Ecoli. Fruitfly Homo sapiens Mus musculus Pseudomonas Celegans Ecoli. Fruitfly Homo sapiens Mus musculus Pseudomonas
Casanovo 0.436 0.407 0.435 0.418 0.496 0.425 0.439 0.412 0.438 0.421 0.496 0.437
CausalNovo on †CasaNovo 0.512 0.511 0.503 0.507 0.534 0.502 0.513 0.514 0.513 0.509 0.536 0.502
Seven-species benchmark Peptide precision Peptide AUC
Celegans Ecoli. Fruitfly Homo sapiens Mus musculus Pseudomonas Celegans Ecoli. Fruitfly Homo sapiens Mus musculus Pseudomonas
Casanovo 0.220 0.208 0.222 0.210 0.268 0.227 0.174 0.165 0.179 0.167 0.223 0.188
CausalNovo on †CasaNovo 0.284 0.285 0.293 0.292 0.299 0.281 0.234 0.241 0.250 0.247 0.256 0.242

Paper describing it

Authors (6)

Ye Du, Chen Yang, Yuanliang Zhang, Lequan Yu, Qian Zhao, Shujun Wang

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