Machine learning-based approaches for ubiquitination site prediction in human proteins

BMC Bioinformatics

Table 8 Hybrid results for the LSTM model based on the macro-F1 score on the test set. The bold values show the best results

Window size	Seq	Seq + PSSM	Seq + AAC	Seq + DPC	Seq + PCP	Seq + All
5	0.530 ± 0.003	0.518 ± 0.003	0.490 ± 0.001	0.502 ± 0.001	0.499 ± 0.019	0.522 ± 0.002
7	0.520 ± 0.002	0.528 ± 0.004	0.519 ± 0.002	0.523 ± 0.001	0.518 ± 0.01	0.525 ± 0.002
9	0.530 ± 0.001	0.534 ± 0.002	0.529 ± 0.001	0.528 ± 0.002	0.527 ± 0.006	0.531 ± 0.001
15	0.545 ± 0	0.55 ± 0.005	0.543 ± 0.002	0.539 ± 0.002	0.544 ± 0.006	0.543 ± 0.003
21	0.555 ± 0.003	0.559 ± 0.003	0.553 ± 0.002	0.542 ± 0.001	0.554 ± 0.003	0.549 ± 0.005
27	0.563 ± 0.003	0.568 ± 0.001	0.559 ± 0.002	0.551 ± 0.002	0.562 ± 0.002	0.558 ± 0.007
33	0.563 ± 0.004	0.571 ± 0.002	0.562 ± 0.002	0.557 ± 0.001	0.569 ± 0.004	0.561 ± 0.006
45	0.570 ± 0.002	0.576 ± 0.007	0.566 ± 0.002	0.562 ± 0.002	0.570 ± 0.003	0.566 ± 0.003
55	0.572 ± 0.003	0.572 ± 0.006	0.569 ± 0.002	0.565 ± 0.004	0.573 ± 0.003	0.566 ± 0.002
77	0.574 ± 0.004	0.576 ± 0.004	0.572 ± 0.003	0.567 ± 0.004	0.572 ± 0.003	0.569 ± 0.003
99	0.573 ± 0.002	0.576 ± 0.002	0.571 ± 0.002	0.569 ± 0.003	0.574 ± 0.002	0.566 ± 0.002
Avg (5–99)	0.554 ± 0.009	0.557 ± 0.013	0.548 ± 0.006	0.546 ± 0.008	0.551 ± 0.025	0.551 ± 0.013
Avg (7–99)	0.557 ± 0.008	0.561 ± 0.013	0.554 ± 0.006	0.550 ± 0.008	0.556 ± 0.016	0.553 ± 0.013

ISSN: 1471-2105