5. Genetic Programming

The gp module provides the methods and classes to perform Genetic Programming with DEAP. It essentially contains the classes to build a Genetic Program Tree, and the functions to evaluate it.

This module support both strongly and loosely typed GP.

class deap.gp.PrimitiveTree(content)

Tree spefically formated for optimization of genetic programming operations. The tree is represented with a list where the nodes are appended in a depth-first order. The nodes appended to the tree are required to define to have an attribute arity which defines the arity of the primitive. An arity of 0 is expected from terminals nodes.

height

Return the height of the tree, or the depth of the deepest node.

root

Root of the tree, the element 0 of the list.

searchSubtree(begin)

Return a slice object that corresponds to the range of values that defines the subtree which has the element with index begin as its root.

class deap.gp.PrimitiveSet(name, arity, prefix='ARG')

Class same as PrimitiveSetTyped, except there is no definition of type.

addEphemeralConstant(ephemeral)

Add an ephemeral constant to the set.

addPrimitive(primitive, arity, symbol=None)

Add primitive primitive with arity arity to the set.

addTerminal(terminal, name=None)

Add a terminal to the set.

class deap.gp.Primitive(primitive, args, ret)

Class that encapsulates a primitive and when called with arguments it returns the Python code to call the primitive with the arguments.

>>> import operator
>>> pr = Primitive(operator.mul, (int, int), int)
>>> pr.format(1, 2)
'mul(1, 2)'

class deap.gp.Operator(operator, symbol, args, ret)

Class that encapsulates an operator and when called with arguments it returns the Python code to call the operator with the arguments. It acts as the Primitive class, but instead of returning a function and its arguments, it returns an operator and its operands.

>>> import operator
>>> op = Operator(operator.mul, '*', (int, int), int)
>>> op.format(1, 2)
'(1 * 2)'
>>> op2 = Operator(operator.neg, '-', (int,), int)
>>> op2.format(1)
'-(1)'

class deap.gp.Terminal(terminal, symbolic, ret)

Class that encapsulates terminal primitive in expression. Terminals can be values or 0-arity functions.

class deap.gp.Ephemeral(func, ret)

Class that encapsulates a terminal which value is set at run-time. The value of the Ephemeral can be regenerated by creating a new Ephemeral object with the same parameters (func and ret).

deap.gp.stringify(expr)

Evaluate the expression expr into a string.

deap.gp.evaluate(expr, pset)

Evaluate the expression expr into Python code object.

deap.gp.lambdify(expr, pset)

Return a lambda function of the expression expr.

Note

This function is a stripped version of the lambdify function of sympy0.6.6.

deap.gp.lambdifyADF(expr)

Return a lambda function created from a list of trees. The first element of the list is the main tree, and the following elements are automatically defined functions (ADF) that can be called by the first tree.

class deap.gp.PrimitiveSetTyped(name, in_types, ret_type, prefix='ARG')

Class that contains the primitives that can be used to solve a Strongly Typed GP problem. The set also defined the researched function return type, and input arguments type and number.

addADF(adfset)

Add an Automatically Defined Function (ADF) to the set.

adfset is a PrimitiveSetTyped containing the primitives with which the ADF can be built.

addEphemeralConstant(ephemeral, ret_type)

Add an ephemeral constant to the set. An ephemeral constant is a no argument function that returns a random value. The value of the constant is constant for a Tree, but may differ from one Tree to another.

ephemeral function with no arguments that returns a random value. ret_type is the type of the object returned by the function.

addPrimitive(primitive, in_types, ret_type, symbol=None)

Add a primitive to the set.

primitive is a callable object or a function. in_types is a list of argument’s types the primitive takes. ret_type is the type returned by the primitive.

addTerminal(terminal, ret_type, name=None)

Add a terminal to the set.

terminal is an object, or a function with no arguments. ret_type is the type of the terminal. name defines the name of the terminal in the expression. This should be used : to define named constant (i.e.: pi); to speed the evaluation time when the object is long to build; when the object does not have a __repr__ functions that returns the code to build the object; when the object class is not a Python built-in.

renameArguments(**kargs)

Rename function arguments with new names from kargs.

terminalRatio

Return the ratio of the number of terminals on the number of all kind of primitives.

deap.gp.graph(expr)

Construct the graph of an tree expression. The tree expression must be valid. It returns in order a node list, an edge list, and a dictionary of the per node labels. The node are represented by numbers, the edges are tuples connecting two nodes (number), and the labels are values of a dictionary for which keys are the node numbers.

Parameters:expr – A tree expression to convert into a graph. Returns:A node list, an edge list, and a dictionary of labels.

The returned objects can be used directly to populate a pygraphviz graph:

import pygraphviz as pgv

# [...] Execution of code that produce a tree expression

nodes, edges, labels = graph(expr)

g = pgv.AGraph()
g.add_nodes_from(nodes)
g.add_edges_from(edges)
g.layout(prog="dot")

for i in nodes:
    n = g.get_node(i)
    n.attr["label"] = labels[i]

g.draw("tree.pdf")

or a NetworX graph:

import matplotlib.pyplot as plt
import networkx as nx

# [...] Execution of code that produce a tree expression

nodes, edges, labels = graph(expr)

g = nx.Graph()
g.add_nodes_from(nodes)
g.add_edges_from(edges)
pos = nx.graphviz_layout(g, prog="dot")

nx.draw_networkx_nodes(g, pos)
nx.draw_networkx_edges(g, pos)
nx.draw_networkx_labels(g, pos, labels)
plt.show()

Note

We encourage you to use pygraphviz as the nodes might be plotted out of order when using NetworX.