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Table 1 Comparison of previous method and our method

From: Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies

Entry Formula

    

SimEnum

RepEnum

 

n

K

w

f v

time (s)

nodes

solutions

time (s)

nodes

solutions

solved

  

1

1

36

1037.04

177,074,686

414,890

163.32

44,340,488

414,890

729

  

2

1

318

2.97

392,246

44

T.O.

2,381,360,000

N.F.

65,909,572

  

3

1

334

1.22

145,213

2

T.O.

3,293,260,000

N.F.

96,860,588

C00062

26

4

1

353

0.33

34,539

1

T.O.

2,780,050,000

N.F.

81,766,176

C6H14N2O4

 

5

1

371

0.24

20,361

1

T.O.

1,561,230,000

N.F.

45,918,529

  

6

1

385

0.25

15,166

1

T.O.

569,590,000

N.F.

16,752,647

  

7

1

396

0.18

14,547

1

T.O.

79,870,000

N.F.

2,349,117

  

1

1

36

T.O.

377,260,000

N.F.

T.O.

413,000,000

N.F.

460

  

2

1

318

7.24

845,760

25

T.O.

1,442,760,000

N.F.

70,175,902

  

3

1

331

2.81

307,151

7

T.O.

3,316,970,000

N.F.

195,115,882

C03343

37

4

1

347

1.03

99,945

1

T.O.

2,494,780,000

N.F.

146,751,764

C16H22O4

 

5

1

364

0.98

87,600

1

T.O.

1,050,480,000

N.F.

61,792,941

  

6

1

382

0.76

60,194

1

T.O.

315,820,000

N.F.

18,577,647

  

7

1

399

0.57

42,538

1

T.O.

41,450,000

N.F.

2,438,235

  

1

1

38

T.O.

157,320,000

N.F.

T.O.

200,490,000

N.F.

1,388

  

2

1

326

37.59

1,940,295

238

T.O.

2,911,390,000

N.F.

66,167,954

  

3

1

348

1.71

60,792

3

T.O.

2,673,940,000

N.F.

60,771,363

C07178

46

4

1

371

0.35

14,248

1

T.O.

1,925,490,000

N.F.

43,761,136

C21H28N2O5

 

5

1

392

0.27

10,866

1

T.O.

743,940,000

N.F.

16,907,727

  

6

1

3110

0.27

10,680

1

T.O.

93,880,000

N.F.

2,133,636

  

7

1

3125

0.24

9,276

1

T.O.

19,270,000

N.F.

437,954

  

1

1

35

T.O.

382,470,000

N.F.

T.O.

552,290,000

N.F.

61

  

2

1

316

T.O.

211,800,000

N.F.

T.O.

530,930,000

N.F.

10,451,912

  

3

1

327

1395.13

144,244,042

206

T.O.

3,314,260,000

N.F.

194,956,470

C03690

61

4

1

341

121.36

11,332,363

4

T.O.

2,392,530,000

N.F.

140,737,058

C24H38O4

 

5

1

357

83.70

6,978,557

2

T.O.

958,650,000

N.F.

56,391,176

  

6

1

375

40.11

2,923,819

1

T.O.

298,600,000

N.F.

17,564,705

  

7

1

392

16.50

1,096,128

1

T.O.

38,670,000

N.F.

2,274,705

  1. Comparison of SimEnum and RepEnum for the problem ETULF.
  2. Note:
  3. (1) C00062, C03343, C07178, and C03630 are the chemical compounds in the KEGG LIGAND database, respectively;
  4. (2) n is the number of vertices in an instance preprocessed by replacing each benzene ring with a new atom having six valences;
  5. (3) K is the level of given feature vectors;
  6. (4) w is the width for constructing upper and lower feature vectors;
  7. (5) f v is the number of feature vectors in a given set;
  8. (6) “time (s)” is the CPU time in seconds;
  9. (7) T.O. means “time over” (the time limit is set to be 1,800 seconds);
  10. (8) “nodes” is (the sum of) the number of nodes of family trees that are traversed;
  11. (9) “solutions” is the number of all possible solutions;
  12. (10) “solved” is the number of feature vectors which the algorithm RepEnum solved in the time limit; and (11) N.F. means “not found.”
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BMC Bioinformatics

ISSN: 1471-2105

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