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Table 2 Per-segment performance for TMH (transmembrane helices). *

From: TMbed: transmembrane proteins predicted through language model embeddings

 

TMH (571/2936)

Recall (%)

Precision (%)

Qok (%)

Qnum (%)

Qtop (%)

TMbed

88.7 ± 0.6

88.7 ± 0.7

62.4 ± 3.7

86.0 ± 2.3

96.4 ± 2.7

DeepTMHMM

80.0 ± 2.4

80.5 ± 2.4

46.2 ± 4.8

85.7 ± 3.5

96.3 ± 2.2

TMSEG

74.5 ± 2.4

77.1 ± 1.7

35.6 ± 2.4

69.9 ± 2.7

83.8 ± 4.7

TOPCONS2

76.4 ± 1.5

78.4 ± 0.8

41.0 ± 3.1

74.4 ± 3.3

91.7 ± 3.1

OCTOPUS

71.6 ± 1.5

75.7 ± 1.4

36.0 ± 2.8

67.6 ± 3.4

87.5 ± 3.1

Philius

70.8 ± 2.2

73.7 ± 0.8

34.2 ± 3.7

66.9 ± 3.4

87.5 ± 2.9

PolyPhobius

76.0 ± 2.1

76.4 ± 1.1

40.3 ± 3.5

74.5 ± 2.8

86.8 ± 2.7

SPOCTOPUS

71.5 ± 1.2

75.8 ± 1.2

35.7 ± 3.3

67.4 ± 5.5

87.2 ± 3.4

SCAMPI2 (MSA)

72.3 ± 2.7

74.1 ± 1.5

33.5 ± 3.0

72.2 ± 4.5

90.6 ± 3.5

CCTOP1

77.0 ± 1.7

79.4 ± 1.0

41.9 ± 3.6

82.6 ± 2.7

92.6 ± 2.6

HMM-TM (MSA)2

73.3 ± 1.7

72.5 ± 1.2

33.5 ± 1.4

72.1 ± 3.0

88.3 ± 4.2

  1. *Segment performance for transmembrane helix (TMH) prediction based on 571 alpha helical TMPs (α-TMP) with a total of 2936 TMHs. Recall, Precision, Qok, Qnum, and Qtop were averaged over the five independent cross-validation test sets; error margins given for the 95% confidence interval (1.96*standard error); bold: best values for each column; italics: differences statistically significant with over 95% confidence (only computed between best and 2nd best).
  2. 1Evaluation missing for one of 571 α-TMPs.
  3. 2Evaluation includes only 552 of the 571 α-TMPs due to runtime errors of the method.