Table 4 Open in new tab Macro F1 ( ⁠|$\%...

Method	Operons	ARG prediction	Virus	Enzyme	Pathogen	N-Cycle
RF	20.2	34.8	22.4	35.3	36.1	49.0	47.8	57.6	22.4	38.5	33.6	41.2	25.3	29.8	67.0	71.7
SVM	38.6	45.2	27.6	40.5	33.6	47.2	43.3	66.2	28.0	41.4	31.3	43.6	26.6	31.2	66.9	70.3
KNN	39.9	41.0	36.9	54.4	36.4	51.3	36.2	63.5	27.3	47.1	31.4	42.9	11.0	27.4	68.8	73.2
LSTM	40.4	42.5	47.1	60.3	39.1	62.3	47.5	84.2	36.7	66.3	42.8	51.0	41.3	49.7	71.9	81.2
BiLSTM	38.2	43.8	47.4	61.9	43.5	58.1	58.9	80.3	46.1	72.1	38.7	50.2	43.3	48.5	82.0	88.4
VT	43.3	47.8	57.1	70.0	49.8	68.1	55.7	86.4	58.0	81.0	68.2	75.8	49.8	57.3	84.5	90.7
HyenaDNA	42.4	47.1	50.9	68.2	53.6	78.1	66.2	88.1	61.0	70.4	79.6	83.6	51.1	57.6	92.4	96.0
ESM-2	38.2	42.5	57.2	71.4	56.0	82.1	68.2	90.0	60.7	84.4	92.5	96.7	56.0	67.5	95.8	96.1
NT	45.1	44.8	58.5	72.0	56.2	80.2	68.0	90.3	58.3	71.6	74.1	76.7	46.1	61.9	75.1	86.5
DNABERT2	51.7	52.4	65.2	79.8	51.5	78.7	61.2	88.6	58.2	82.3	85.4	85.2	52.9	60.6	88.6	95.7
Ours	61.8	65.4	78.6	90.1	57.4	85.2	69.4	91.4	75.7	90.2	99.1	98.8	99.3	99.0	99.5	99.2

Method

Operons

ARG prediction

Virus

Enzyme

Pathogen

N-Cycle

E-K12

CARD-A

CARD-D

CARD-R

VFDB

ENZYME

PATRIC

NCycDB

M.F1

W.F1

M.F1

W.F1

M.F1

W.F1

M.F1

W.F1

M.F1

W.F1

M.F1

W.F1

M.F1

W.F1

M.F1

W.F1

20.2

34.8

22.4

35.3

36.1

49.0

47.8

57.6

22.4

38.5

33.6

41.2

25.3

29.8

67.0

71.7

SVM

38.6

45.2

27.6

40.5

33.6

47.2

43.3

66.2

28.0

41.4

31.3

43.6

26.6

31.2

66.9

70.3

KNN

39.9

41.0

36.9

54.4

36.4

51.3

36.2

63.5

27.3

47.1

31.4

42.9

11.0

27.4

68.8

73.2

LSTM

40.4

42.5

47.1

60.3

39.1

62.3

47.5

84.2

36.7

66.3

42.8

51.0

41.3

49.7

71.9

81.2

BiLSTM

38.2

43.8

47.4

61.9

43.5

58.1

58.9

80.3

46.1

72.1

38.7

50.2

43.3

48.5

82.0

88.4

43.3

47.8

57.1

70.0

49.8

68.1

55.7

86.4

58.0

81.0

68.2

75.8

49.8

57.3

84.5

90.7

HyenaDNA

42.4

47.1

50.9

68.2

53.6

78.1

66.2

88.1

61.0

70.4

79.6

83.6

51.1

57.6

92.4

96.0

ESM-2

38.2

42.5

57.2

71.4

56.0

82.1

68.2

90.0

60.7

84.4

92.5

96.7

56.0

67.5

95.8

96.1

45.1

44.8

58.5

72.0

56.2

80.2

68.0

90.3

58.3

71.6

74.1

76.7

46.1

61.9

75.1

86.5

DNABERT2

51.7

52.4

65.2

79.8

51.5

78.7

61.2

88.6

58.2

82.3

85.4

85.2

52.9

60.6

88.6

95.7

Ours

61.8

65.4

78.6

90.1

57.4

85.2

69.4

91.4

75.7

90.2

99.1

98.8

99.3

99.0

99.5

99.2

Method	Operons	ARG prediction	Virus	Enzyme	Pathogen	N-Cycle
RF	20.2	34.8	22.4	35.3	36.1	49.0	47.8	57.6	22.4	38.5	33.6	41.2	25.3	29.8	67.0	71.7
SVM	38.6	45.2	27.6	40.5	33.6	47.2	43.3	66.2	28.0	41.4	31.3	43.6	26.6	31.2	66.9	70.3
KNN	39.9	41.0	36.9	54.4	36.4	51.3	36.2	63.5	27.3	47.1	31.4	42.9	11.0	27.4	68.8	73.2
LSTM	40.4	42.5	47.1	60.3	39.1	62.3	47.5	84.2	36.7	66.3	42.8	51.0	41.3	49.7	71.9	81.2
BiLSTM	38.2	43.8	47.4	61.9	43.5	58.1	58.9	80.3	46.1	72.1	38.7	50.2	43.3	48.5	82.0	88.4
VT	43.3	47.8	57.1	70.0	49.8	68.1	55.7	86.4	58.0	81.0	68.2	75.8	49.8	57.3	84.5	90.7
HyenaDNA	42.4	47.1	50.9	68.2	53.6	78.1	66.2	88.1	61.0	70.4	79.6	83.6	51.1	57.6	92.4	96.0
ESM-2	38.2	42.5	57.2	71.4	56.0	82.1	68.2	90.0	60.7	84.4	92.5	96.7	56.0	67.5	95.8	96.1
NT	45.1	44.8	58.5	72.0	56.2	80.2	68.0	90.3	58.3	71.6	74.1	76.7	46.1	61.9	75.1	86.5
DNABERT2	51.7	52.4	65.2	79.8	51.5	78.7	61.2	88.6	58.2	82.3	85.4	85.2	52.9	60.6	88.6	95.7
Ours	61.8	65.4	78.6	90.1	57.4	85.2	69.4	91.4	75.7	90.2	99.1	98.8	99.3	99.0	99.5	99.2

Table 4

Open in new tab

Macro F1 (⁠|$\% \uparrow $|⁠) and Weighted F1 (⁠|$\% \uparrow $|⁠) on eight downstream tasks. This includes gene operon prediction on E-K12, ARG prediction on three CARD categories, virulence factors classification on VFDB, enzyme function annotation on ENZYME, microbial pathogens detection on PATRIC, Nitrogen Cycle processes prediction on NCycDB. RF denotes Random Forest, and VT represents Vanilla Transformer. The highest results are highlighted with boldface. The second highest results are highlighted with underline

Method	Operons		ARG prediction						Virus		Enzyme		Pathogen		N-Cycle
	E-K12		CARD-A		CARD-D		CARD-R		VFDB		ENZYME		PATRIC		NCycDB
	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1
RF	20.2	34.8	22.4	35.3	36.1	49.0	47.8	57.6	22.4	38.5	33.6	41.2	25.3	29.8	67.0	71.7
SVM	38.6	45.2	27.6	40.5	33.6	47.2	43.3	66.2	28.0	41.4	31.3	43.6	26.6	31.2	66.9	70.3
KNN	39.9	41.0	36.9	54.4	36.4	51.3	36.2	63.5	27.3	47.1	31.4	42.9	11.0	27.4	68.8	73.2
LSTM	40.4	42.5	47.1	60.3	39.1	62.3	47.5	84.2	36.7	66.3	42.8	51.0	41.3	49.7	71.9	81.2
BiLSTM	38.2	43.8	47.4	61.9	43.5	58.1	58.9	80.3	46.1	72.1	38.7	50.2	43.3	48.5	82.0	88.4
VT	43.3	47.8	57.1	70.0	49.8	68.1	55.7	86.4	58.0	81.0	68.2	75.8	49.8	57.3	84.5	90.7
HyenaDNA	42.4	47.1	50.9	68.2	53.6	78.1	66.2	88.1	61.0	70.4	79.6	83.6	51.1	57.6	92.4	96.0
ESM-2	38.2	42.5	57.2	71.4	56.0	82.1	68.2	90.0	60.7	84.4	92.5	96.7	56.0	67.5	95.8	96.1
NT	45.1	44.8	58.5	72.0	56.2	80.2	68.0	90.3	58.3	71.6	74.1	76.7	46.1	61.9	75.1	86.5
DNABERT2	51.7	52.4	65.2	79.8	51.5	78.7	61.2	88.6	58.2	82.3	85.4	85.2	52.9	60.6	88.6	95.7
Ours	61.8	65.4	78.6	90.1	57.4	85.2	69.4	91.4	75.7	90.2	99.1	98.8	99.3	99.0	99.5	99.2

Method	Operons		ARG prediction						Virus		Enzyme		Pathogen		N-Cycle
	E-K12		CARD-A		CARD-D		CARD-R		VFDB		ENZYME		PATRIC		NCycDB
	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1	M.F1	W.F1
RF	20.2	34.8	22.4	35.3	36.1	49.0	47.8	57.6	22.4	38.5	33.6	41.2	25.3	29.8	67.0	71.7
SVM	38.6	45.2	27.6	40.5	33.6	47.2	43.3	66.2	28.0	41.4	31.3	43.6	26.6	31.2	66.9	70.3
KNN	39.9	41.0	36.9	54.4	36.4	51.3	36.2	63.5	27.3	47.1	31.4	42.9	11.0	27.4	68.8	73.2
LSTM	40.4	42.5	47.1	60.3	39.1	62.3	47.5	84.2	36.7	66.3	42.8	51.0	41.3	49.7	71.9	81.2
BiLSTM	38.2	43.8	47.4	61.9	43.5	58.1	58.9	80.3	46.1	72.1	38.7	50.2	43.3	48.5	82.0	88.4
VT	43.3	47.8	57.1	70.0	49.8	68.1	55.7	86.4	58.0	81.0	68.2	75.8	49.8	57.3	84.5	90.7
HyenaDNA	42.4	47.1	50.9	68.2	53.6	78.1	66.2	88.1	61.0	70.4	79.6	83.6	51.1	57.6	92.4	96.0
ESM-2	38.2	42.5	57.2	71.4	56.0	82.1	68.2	90.0	60.7	84.4	92.5	96.7	56.0	67.5	95.8	96.1
NT	45.1	44.8	58.5	72.0	56.2	80.2	68.0	90.3	58.3	71.6	74.1	76.7	46.1	61.9	75.1	86.5
DNABERT2	51.7	52.4	65.2	79.8	51.5	78.7	61.2	88.6	58.2	82.3	85.4	85.2	52.9	60.6	88.6	95.7
Ours	61.8	65.4	78.6	90.1	57.4	85.2	69.4	91.4	75.7	90.2	99.1	98.8	99.3	99.0	99.5	99.2

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