Methods and systems for interactive evolutionary computing (IEC)

• US 7,603,326 B2
• Filed: 05/08/2006
• Issued: 10/13/2009
• Est. Priority Date: 04/04/2003
• Status: Active Grant

• Current Assignee: Telepathy Labs, Inc.
• Original Assignee: Icosystem Corp.
• Inventors: Orme, Belinda, Rothermich, Joseph, Anderson, Carl, Funes, Pablo, Malinchik, Sergey, Bonabeau, Eric, Sullivan, Mark, Bandte, Oliver
• Primary Examiner(s): Holmes; Michael B
• Application Number:
  US11/382,180
• Publication Number:
  US 20060195204A1
• Time in Patent Office: 1,254 Days
• Field of Search: 706/13
• US Class Current: 706/13
• CPC Class Codes: G06N 3/126 Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• CPC Class Codes: G16C 20/50 Molecular design, e.g. of drugs
• CPC Class Codes: G16C 20/70 Machine learning, data mining or chemometrics

Abstract

Methods and systems for interactive evolutionary computing may include generating a set of candidate molecules based on an evolutionary scheme in which an objective function is a priori mathematically unexpressed, presenting data based on the set of candidate molecules to one or more users, receiving at least one input from the user(s), the input(s) based on the user(s)'"'"'s evaluation of the presented set of candidate molecules, and, based on the input(s), using at least the evolutionary scheme and the input(s) to generate an updated set of candidate molecules, and repeating the presenting and receiving.

Claims

1. In a computer system having a processor and a user interface including a display and an input device, a method of finding a molecule with at least one desired useful characteristic, comprising:

generating in the processor a set of candidate molecules based on an evolutionary scheme in which an objective function to determine a fitness of a candidate molecule is a priori mathematically unexpressed,

presenting on the display data based on the set of candidate molecules to at least one user,

upon a stopping condition not being satisfied, receiving through the input device at least one input from the at least one user, the at least one input based on the at least one user'"'"'s evaluation of the presented set of candidate molecules,

based on the at least one input, using at least the evolutionary scheme and the at least one input to generate in the processor an updated set of candidate molecules, and

repeating the presenting, receiving and generating until a stopping condition is satisfied,

wherein the stopping condition is satisfied upon the molecule with the at least one desired useful characteristic being identified.

2. A method according to claim 1, where presenting data based on the set of candidate molecules includes selecting at least one candidate molecule from the set of candidate molecules to present.

3. A method according to claim 2, where selecting the at least one candidate molecule includes selecting based on at least one constraint.

4. A method according to claim 2, where selecting the at least one candidate molecule includes selecting based on at least one calculated property of the at least one candidate molecule.

5. A method according to claim 4, where selecting the at least one candidate molecule further includes selecting based on at least one calculated property of the at least one candidate molecule satisfying at least one condition.

6. A method according to claim 1, where presenting data based on the set of candidate molecules includes presenting a molecular structure of at least one candidate molecule of the set of candidate molecules.

7. A method according to claim 1, where presenting data based on the set of candidate molecules includes presenting at least one calculated property of at least one candidate molecule of the set of candidate molecules.

8. A method according to claim 7, where presenting data based on the set of candidate molecules further includes presenting at least one calculated value of at least one of an adsorption property, a distribution property, a metabolism property and an excretion property, of at least one candidate molecule of the set of candidate molecules.

9. A method according to claim 1, where the at least one user input includes at least one of:

a rank of a plurality of candidate molecules in the set of candidate molecules presented, a rating of a plurality of candidate molecules in the set of candidate molecules presented, a selection of at least one candidate molecule in the set of candidate molecules presented, a modification of a structure of at least one candidate molecule in the set of candidate molecules presented, a selection of at least one feature of at least one candidate molecule in the set of candidate molecules presented, an identification of at least one parent for a genetic algorithm, at least one constraint, a modification of at least one constraint, at least one condition, a modification of at least one genetic operator, and a specification of at least one genetic operator.

10. A method according to claim 1, further comprising modifying at least one candidate molecule of the set of candidate molecules presented based on at least one input from the at least one user.

11. A method according to claim 1, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules includes:

generating a population based on the evolutionary scheme and the at least one user input.

12. A method according to claim 11, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules further includes:

applying the population to at least one data set.

13. A method according to claim 11, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules further includes:

generating the updated set of candidate molecules based upon at least one calculated property of at least one member of the population.

14. A method according to claim 1, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules includes:

based on whether at least one condition is satisfied, iteratively using the evolutionary scheme and the at least one user input to generate the updated set of candidate molecules.

15. A method according to claim 14, where the at least one condition includes a specified number of generations of the evolutionary scheme having elapsed.

16. A method according to claim 1, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules includes:

using a genetic operator to generate the updated set of candidate molecules.

17. A method according to claim 16, where the genetic operator includes at least one of:

crossover, and mutation.

18. A method according to claim 17, where the genetic operator is applied to modify a structure of at least one candidate molecule in the set of candidate molecules.

19. A method according to claim 1, where the molecule with the at least one desired useful property is identified by a user.

20. A method according to claim 1, where the molecule with the at least one desired useful property is identified based on at least one property of at least one candidate molecule in the set of candidate molecules satisfying at least one condition.

21. A method according to claim 1, where the instructions to the computer system to perform the method are communicated to a processor over a network.

22. A method according to claim 21, where the network is a local area network.

23. A method according to claim 1, where the at least one input from the at least one user is received over a network.

24. A method according to claim 23, where the network is a local area network.

25. A method according to claim 1, where the data presented on the display is transmitted over a network.

26. A method according to claim 25, where the network is a local area network.

27. A computer-readable medium having computer-readable signals stored thereon that define instructions which, as a result of being executed in a computer system having a processor and a user interface including a display and an input device, instruct the computer system to perform a method of finding a molecule with at least one desired useful characteristic, comprising:

generating in the processor a set of candidate molecules based on an evolutionary scheme in which an objective function to determine a fitness of a candidate molecule is a priori mathematically unexpressed,

presenting on the display data based on the set of candidate molecules to at least one user, upon a stopping condition not being satisfied, receiving through the input device at least one input from the at least one user, the at least one input based on the at least one user'"'"'s evaluation of the presented set of candidate molecules,

based on the at least one input, using at least the evolutionary scheme and the at least one input to generate in the processor an updated set of candidate molecules, and repeating the presenting, receiving and generating until a stopping condition is satisfied,

wherein the stopping condition is satisfied upon the molecule with the at least one desired useful characteristic being identified.

28. A computer-readable medium according to claim 27, where presenting data based on the set of candidate molecules includes selecting at least one candidate molecule from the set of candidate molecules to present.

29. A computer-readable medium according to claim 28, where selecting the at least one candidate molecule includes selecting based on at least one constraint.

30. A computer-readable medium according to claim 28, where selecting the at least one candidate molecule includes selecting based on at least one calculated property of the at least one candidate molecule.

31. A computer-readable medium according to claim 30, where selecting the at least one candidate molecule further includes selecting based on at least one calculated property of the at least one candidate molecule satisfying at least one condition.

32. A computer-readable medium according to claim 27, where presenting data based on the set of candidate molecules includes presenting a molecular structure of at least one candidate molecule of the set of candidate molecules.

33. A computer-readable medium according to claim 27, where presenting data based on the set of candidate molecules includes presenting at least one calculated property of at least one candidate molecule of the set of candidate molecules.

34. A computer-readable medium according to claim 33, where presenting data based on the set of candidate molecules further includes presenting at least one calculated value of at least one of an adsorption property, a distribution property, a metabolism property and an excretion property, of at least one candidate molecule of the set of candidate molecules.

35. A computer-readable medium according to claim 27, where the at least one user input includes at least one of:

a rank of a plurality of candidate molecules in the set of candidate molecules presented, a rating of a plurality of candidate molecules in the set of candidate molecules presented, a selection of at least one candidate molecule in the set of candidate molecules presented, a modification of a structure of at least one candidate molecule in the set of candidate molecules presented, a selection of at least one feature of at least one candidate molecule in the set of candidate molecules presented, an identification of at least one parent for a genetic algorithm, at least one constraint, a modification of at least one constraint, at least one condition, a modification of at least one genetic operator, and a specification of at least one genetic operator.

36. A computer-readable medium according to claim 27, further comprising modifying at least one candidate molecule of the set of candidate molecules presented based on at least one input from the at least one user.

37. A computer-readable medium according to claim 27, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules includes:

generating a population based on the evolutionary scheme and the at least one user input.

38. A computer-readable medium according to claim 27, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules further includes:

applying the population to at least one data set.

39. A computer-readable medium according to claim 27, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules further includes:

generating the updated set of candidate molecules based upon at least one calculated property of at least one member of the population.

40. A computer-readable medium according to claim 27, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules includes:

based on whether at least one condition is satisfied, iteratively using the evolutionary scheme and the at least one user input to generate the updated set of candidate molecules.

41. A computer-readable medium according to claim 40, where the at least one condition includes a specified number of generations of the evolutionary scheme having elapsed.

42. A computer-readable medium according to claim 27, where using at least the evolutionary scheme and the at least one input to generate the updated set of candidate molecules includes:

using a genetic operator to generate the updated set of candidate molecules.

43. A computer-readable medium according to claim 42, where the genetic operator includes at least one of:

crossover, and mutation.

44. A computer-readable medium according to claim 43, where the genetic operator is applied to modify a structure of at least one candidate molecule in the set of candidate molecules.

45. A computer-readable medium according to claim 27, where the molecule with the at least one desired useful property is identified by a user.

46. A computer-readable medium according to claim 27, where the molecule with the at least one desired useful property is identified based on at least one property of at least one candidate molecule in the set of candidate molecules satisfying at least one condition.

47. A system of finding a molecule with at least one desired useful characteristic, comprising:

at least one processor in communications with at least one display, the at least one processor having instructions for causing the at least one processor to;

present on the at least one display, data based on a set of candidate molecules to at least one user, the set of candidate molecules based on an evolutionary scheme in which an objective function is a priori mathematically unexpressed, receive at least one input from the at least one user, the at least one input based on the at least one user'"'"'s evaluation of the presented set of candidate molecules, and, based on the at least one user input, use at least the evolutionary scheme and the at least one input to generate an updated set of candidate molecules, and iteratively repeat the present, receive and generate instructions until a stopping condition is satisfied,

wherein the stopping condition is satisfied upon the molecule with the at least one desired useful characteristic being identified.

48. A method of finding a molecule with at least one desired useful characteristic, comprising:

at least one user viewing on a computer system display, data based on a set of candidate molecules, the set of candidate molecules having been generated in the computer system based on an evolutionary scheme in which an objective function to determine a fitness of a candidate molecule is a priori mathematically unexpressed,

the said at least one user providing through a computer system input device, at least one input, the at least one input based on the said at least one user'"'"'s evaluation of the viewed data based on the set of candidate molecules, and

repeating the generating, viewing and providing until a stopping condition is satisfied.

wherein the stopping condition is satisfied upon the molecule with the at least one desired useful characteristic being identified.

49. A method according to claim 48, where the data viewed relates to at least one candidate molecule which has been selected in the computer system based on at least one constraint.

50. A method according to claim 48, where the data viewed relates to at least one candidate molecule which has been selected in the computer system based on at least one calculated property of the at least one candidate molecule.

51. A method according to claim 50, where the data viewed relates to at least one candidate molecule which has been selected in the computer system based on at least one calculated property of the at least one candidate molecule satisfying at least one condition.

52. A method according to claim 48, where the data viewed includes a molecular structure of at least one candidate molecule of the set of candidate molecules.

53. A method according to claim 48, where the data viewed includes at least one property determined in the computer system of at least one candidate molecule of the set of candidate molecules.

54. A method according to claim 53, where the data viewed includes at least one value determined in the computer system of at least one of an adsorption property, a distribution property, a metabolism property and an excretion property, of at least one candidate molecule of the set of candidate molecules.

55. A method according to claim 48, where the at least one user input includes at least one of:

a rank of a plurality of candidate molecules in the set of candidate molecules presented, a rating of a plurality of candidate molecules in the set of candidate molecules presented, a selection of at least one candidate molecule in the set of candidate molecules presented, a modification of a structure of at least one candidate molecule in the set of candidate molecules presented, a selection of at least one feature of at least one candidate molecule in the set of candidate molecules presented, an identification of at least one parent for a genetic algorithm, at least one constraint, a modification of at least one constraint, at least one condition, a modification of at least one genetic operator, and a specification of at least one genetic operator.

56. A method according to claim 48, where in at least one iteration of the viewing step an updated set of candidate molecules is generated in the computer system by generating a population based on the evolutionary scheme and at least one user input.

57. A method according to claim 56, where generating the updated set of candidate molecules in the computer system further includes applying the population to at least one data set.

58. A method according to claim 57, where generating the updated set of candidate molecules in the computer system further includes utilizing at least one calculated property of at least one member of the population.

59. A method according to claim 48, where generating the updated set of candidate molecules in the computer system includes, based on whether at least one condition is satisfied, iteratively using the evolutionary scheme and at least one user input to generate the updated set of candidate molecules.

60. A method according to claim 59, where the at least one condition includes a specified number of generations of the evolutionary scheme having elapsed.

61. A method according to claim 48, where generating the updated set of candidate molecules in the computer system includes using a genetic operator to generate the updated set of candidate molecules.

62. A method according to claim 61, where the genetic operator includes at least one of:

crossover, and mutation.

63. A method according to claim 62, where the genetic operator is applied in the computer system to modify a structure of at least one candidate molecule in the set of candidate molecules.

64. A method according to claim 48, where the molecule with the at least one desired useful property is identified by a user.

65. A method according to claim 48, where the molecule with the at least one desired useful property is identified based on at least one property of at least one candidate molecule in the set of candidate molecules satisfying at least one condition.