From 7a7cd5c1806b0b5e640160720641afd0aa8b3602 Mon Sep 17 00:00:00 2001
From: Matthew Beaudouin-Lafon <matthew.beaudouin-lafon@students.olin.edu>
Date: Mon, 28 Mar 2016 01:22:57 -0400
Subject: [PATCH 1/2] ToolBox

---
 evolve_text.py | 327 ++++++++++++++++++++++++++++---------------------
 1 file changed, 185 insertions(+), 142 deletions(-)

diff --git a/evolve_text.py b/evolve_text.py
index e0202d2..63fde4a 100644
--- a/evolve_text.py
+++ b/evolve_text.py
@@ -5,7 +5,7 @@
 http://deap.readthedocs.org
 
 Usage:
-    python evolve_text.py [goal_message]
+	python evolve_text.py [goal_message]
 
 Full instructions are at:
 https://sites.google.com/site/sd15spring/home/project-toolbox/evolutionary-algorithms
@@ -19,6 +19,9 @@
 from deap import base
 from deap import tools
 
+# Experiment: increase the probability of substitution. This is where it seems to get stuck towards the end. It seems to help
+# If it wasnt so late, I would look into changing the probabilities dynamically.
+
 
 #-----------------------------------------------------------------------------
 # Global variables
@@ -31,105 +34,145 @@
 # Control whether all Messages are printed as they are evaluated
 VERBOSE = True
 
+def levenshtein_distance(s1,s2, memo):
+	""" Computes the Levenshtein distance between two input strings """
+	if memo.get((s1,s2), None) != None:
+		return memo[(s1,s2)]
+	if len(s1) == 0:
+		return len(s2)
+	if len(s2) == 0:
+		return len(s1)
+	value = min([int(s1[0] != s2[0]) + levenshtein_distance(s1[1:],s2[1:], memo), 1+levenshtein_distance(s1[1:],s2, memo), 1+levenshtein_distance(s1,s2[1:], memo)])
+	memo[(s1,s2)] = value
+	return value
+
+def two_pt_crossover(s1, s2):
+	""" Returns a two point crossover of s1 and s2. It assumes len(s2) >= len(s1). """
+	pt1 = random.randint(0, len(s1)-2)
+	pt2 = random.randint(pt1+1, len(s2)-1) # Garantees that 0<=pt1<pt2<=len(s) 
+
+	return (s1[:pt1] + s2[pt1:pt2] + s1[pt2:],s2[:pt1] + s1[pt1:pt2] + s2[:])
 
 #-----------------------------------------------------------------------------
 # Message object to use in evolutionary algorithm
 #-----------------------------------------------------------------------------
 
 class FitnessMinimizeSingle(base.Fitness):
-    """
-    Class representing the fitness of a given individual, with a single
-    objective that we want to minimize (weight = -1)
-    """
-    weights = (-1.0, )
+	"""
+	Class representing the fitness of a given individual, with a single
+	objective that we want to minimize (weight = -1)
+	"""
+	weights = (-1.0, )
 
 
 class Message(list):
-    """
-    Representation of an individual Message within the population to be evolved
-
-    We represent the Message as a list of characters (mutable) so it can
-    be more easily manipulated by the genetic operators.
-    """
-    def __init__(self, starting_string=None, min_length=4, max_length=30):
-        """
-        Create a new Message individual.
-
-        If starting_string is given, initialize the Message with the
-        provided string message. Otherwise, initialize to a random string
-        message with length between min_length and max_length.
-        """
-        # Want to minimize a single objective: distance from the goal message
-        self.fitness = FitnessMinimizeSingle()
-
-        # Populate Message using starting_string, if given
-        if starting_string:
-            self.extend(list(starting_string))
-
-        # Otherwise, select an initial length between min and max
-        # and populate Message with that many random characters
-        else:
-            initial_length = random.randint(min_length, max_length)
-            for i in range(initial_length):
-                self.append(random.choice(VALID_CHARS))
-
-    def __repr__(self):
-        """Return a string representation of the Message"""
-        # Note: __repr__ (if it exists) is called by __str__. It should provide
-        #       the most unambiguous representation of the object possible, and
-        #       ideally eval(repr(obj)) == obj
-        # See also: http://stackoverflow.com/questions/1436703
-        template = '{cls}({val!r})'
-        return template.format(cls=self.__class__.__name__,     # "Message"
-                               val=self.get_text())
-
-    def get_text(self):
-        """Return Message as string (rather than actual list of characters)"""
-        return "".join(self)
+	"""
+	Representation of an individual Message within the population to be evolved
+
+	We represent the Message as a list of characters (mutable) so it can
+	be more easily manipulated by the genetic operators.
+	"""
+	def __init__(self, starting_string=None, min_length=4, max_length=30):
+		"""
+		Create a new Message individual.
+
+		If starting_string is given, initialize the Message with the
+		provided string message. Otherwise, initialize to a random string
+		message with length between min_length and max_length.
+		"""
+		# Want to minimize a single objective: distance from the goal message
+		self.fitness = FitnessMinimizeSingle()
+
+		# Populate Message using starting_string, if given
+		if starting_string:
+			self.extend(list(starting_string))
+
+		# Otherwise, select an initial length between min and max
+		# and populate Message with that many random characters
+		else:
+			initial_length = random.randint(min_length, max_length)
+			for i in range(initial_length):
+				self.append(random.choice(VALID_CHARS))
+
+	def __repr__(self):
+		"""Return a string representation of the Message"""
+		# Note: __repr__ (if it exists) is called by __str__. It should provide
+		#       the most unambiguous representation of the object possible, and
+		#       ideally eval(repr(obj)) == obj
+		# See also: http://stackoverflow.com/questions/1436703
+		template = '{cls}({val!r})'
+		return template.format(cls=self.__class__.__name__,     # "Message"
+							   val=self.get_text())
+
+	def get_text(self):
+		"""Return Message as string (rather than actual list of characters)"""
+		return "".join(self)
 
 
 #-----------------------------------------------------------------------------
 # Genetic operators
 #-----------------------------------------------------------------------------
 
-# TODO: Implement levenshtein_distance function (see Day 9 in-class exercises)
-# HINT: Now would be a great time to implement memoization if you haven't
-
 def evaluate_text(message, goal_text, verbose=VERBOSE):
-    """
-    Given a Message and a goal_text string, return the Levenshtein distance
-    between the Message and the goal_text as a length 1 tuple.
-    If verbose is True, print each Message as it is evaluated.
-    """
-    distance = levenshtein_distance(message.get_text(), goal_text)
-    if verbose:
-        print "{msg:60}\t[Distance: {dst}]".format(msg=message, dst=distance)
-    return (distance, )     # Length 1 tuple, required by DEAP
-
-
-def mutate_text(message, prob_ins=0.05, prob_del=0.05, prob_sub=0.05):
-    """
-    Given a Message and independent probabilities for each mutation type,
-    return a length 1 tuple containing the mutated Message.
-
-    Possible mutations are:
-        Insertion:      Insert a random (legal) character somewhere into
-                        the Message
-        Deletion:       Delete one of the characters from the Message
-        Substitution:   Replace one character of the Message with a random
-                        (legal) character
-    """
-
-    if random.random() < prob_ins:
-        # TODO: Implement insertion-type mutation
-        pass
-
-    # TODO: Also implement deletion and substitution mutations
-    # HINT: Message objects inherit from list, so they also inherit
-    #       useful list methods
-    # HINT: You probably want to use the VALID_CHARS global variable
-
-    return (message, )   # Length 1 tuple, required by DEAP
+	"""
+	Given a Message and a goal_text string, return the Levenshtein distance
+	between the Message and the goal_text as a length 1 tuple.
+	If verbose is True, print each Message as it is evaluated.
+	"""
+	distance = levenshtein_distance(message.get_text(), goal_text, {})
+	if verbose:
+		print "{msg:60}\t[Distance: {dst}]".format(msg=message, dst=distance)
+	return (distance, )     # Length 1 tuple, required by DEAP
+
+# def mutate_text(s):
+# 	# Pick a type
+# 	choice = random.randint(0,2)
+# 	char_pos = random.randint(0, len(s)-1)
+
+# 	# Insertion
+# 	if choice == 0:
+# 		print 'Insert'
+# 		return s[:char_pos]+random.choice(VALID_CHARS)+s[char_pos:]
+
+# 	# Substitution
+# 	if choice == 1:
+# 		print "Substitute"
+# 		return s[:char_pos]+random.choice(VALID_CHARS)+s[char_pos+1:]
+
+# 	# Deletion
+# 	if choice == 2:
+# 		print "Delete"
+# 		return s[:char_pos]+s[char_pos+1:]
+
+def mutate_text(message, prob_ins=0.05, prob_del=0.05, prob_sub=0.3):
+	"""
+	Given a Message and independent probabilities for each mutation type,
+	return a length 1 tuple containing the mutated Message.
+
+	Possible mutations are:
+		Insertion:      Insert a random (legal) character somewhere into
+						the Message
+		Deletion:       Delete one of the characters from the Message
+		Substitution:   Replace one character of the Message with a random
+						(legal) character
+	"""
+
+	if random.random() < prob_ins:
+		print "Insert"
+		char_pos = random.randint(0, len(message))
+		message.insert(char_pos, random.choice(VALID_CHARS))
+
+	if random.random() < prob_del:
+		print "Delete"
+		char_pos = random.randint(0, len(message)-1)
+		del message[char_pos]
+
+	if random.random() < prob_sub:
+		print "Substitute"
+		char_pos = random.randint(0, len(message)-1)
+		message[char_pos] = random.choice(VALID_CHARS)
+
+	return (message, )   # Length 1 tuple, required by DEAP
 
 
 #-----------------------------------------------------------------------------
@@ -137,58 +180,58 @@ def mutate_text(message, prob_ins=0.05, prob_del=0.05, prob_sub=0.05):
 #-----------------------------------------------------------------------------
 
 def get_toolbox(text):
-    """Return DEAP Toolbox configured to evolve given 'text' string"""
+	"""Return DEAP Toolbox configured to evolve given 'text' string"""
 
-    # The DEAP Toolbox allows you to register aliases for functions,
-    # which can then be called as "toolbox.function"
-    toolbox = base.Toolbox()
+	# The DEAP Toolbox allows you to register aliases for functions,
+	# which can then be called as "toolbox.function"
+	toolbox = base.Toolbox()
 
-    # Creating population to be evolved
-    toolbox.register("individual", Message)
-    toolbox.register("population", tools.initRepeat, list, toolbox.individual)
+	# Creating population to be evolved
+	toolbox.register("individual", Message)
+	toolbox.register("population", tools.initRepeat, list, toolbox.individual)
 
-    # Genetic operators
-    toolbox.register("evaluate", evaluate_text, goal_text=text)
-    toolbox.register("mate", tools.cxTwoPoint)
-    toolbox.register("mutate", mutate_text)
-    toolbox.register("select", tools.selTournament, tournsize=3)
+	# Genetic operators
+	toolbox.register("evaluate", evaluate_text, goal_text=text)
+	toolbox.register("mate",  tools.cxTwoPoint) #two_pt_crossover)
+	toolbox.register("mutate", mutate_text)
+	toolbox.register("select", tools.selTournament, tournsize=3)
 
-    # NOTE: You can also pass function arguments as you define aliases, e.g.
-    #   toolbox.register("individual", Message, max_length=200)
-    #   toolbox.register("mutate", mutate_text, prob_sub=0.18)
+	# NOTE: You can also pass function arguments as you define aliases, e.g.
+	#   toolbox.register("individual", Message, max_length=200)
+	#   toolbox.register("mutate", mutate_text, prob_sub=0.18)
 
-    return toolbox
+	return toolbox
 
 
 def evolve_string(text):
-    """Use evolutionary algorithm (EA) to evolve 'text' string"""
+	"""Use evolutionary algorithm (EA) to evolve 'text' string"""
 
-    # Set random number generator initial seed so that results are repeatable.
-    # See: https://docs.python.org/2/library/random.html#random.seed
-    #      and http://xkcd.com/221
-    random.seed(4)
+	# Set random number generator initial seed so that results are repeatable.
+	# See: https://docs.python.org/2/library/random.html#random.seed
+	#      and http://xkcd.com/221
+	random.seed(4)
 
-    # Get configured toolbox and create a population of random Messages
-    toolbox = get_toolbox(text)
-    pop = toolbox.population(n=300)
+	# Get configured toolbox and create a population of random Messages
+	toolbox = get_toolbox(text)
+	pop = toolbox.population(n=300)
 
-    # Collect statistics as the EA runs
-    stats = tools.Statistics(lambda ind: ind.fitness.values)
-    stats.register("avg", numpy.mean)
-    stats.register("std", numpy.std)
-    stats.register("min", numpy.min)
-    stats.register("max", numpy.max)
+	# Collect statistics as the EA runs
+	stats = tools.Statistics(lambda ind: ind.fitness.values)
+	stats.register("avg", numpy.mean)
+	stats.register("std", numpy.std)
+	stats.register("min", numpy.min)
+	stats.register("max", numpy.max)
 
-    # Run simple EA
-    # (See: http://deap.gel.ulaval.ca/doc/dev/api/algo.html for details)
-    pop, log = algorithms.eaSimple(pop,
-                                   toolbox,
-                                   cxpb=0.5,    # Prob. of crossover (mating)
-                                   mutpb=0.2,   # Probability of mutation
-                                   ngen=500,    # Num. of generations to run
-                                   stats=stats)
+	# Run simple EA
+	# (See: http://deap.gel.ulaval.ca/doc/dev/api/algo.html for details)
+	pop, log = algorithms.eaSimple(pop,
+								   toolbox,
+								   cxpb=0.5,    # Prob. of crossover (mating)
+								   mutpb=0.2,   # Probability of mutation
+								   ngen=500,    # Num. of generations to run
+								   stats=stats)
 
-    return pop, log
+	return pop, log
 
 
 #-----------------------------------------------------------------------------
@@ -197,22 +240,22 @@ def evolve_string(text):
 
 if __name__ == "__main__":
 
-    # Get goal message from command line (optional)
-    import sys
-    if len(sys.argv) == 1:
-        # Default goal of the evolutionary algorithm if not specified.
-        # Pretty much the opposite of http://xkcd.com/534
-        goal = "SKYNET IS NOW ONLINE"
-    else:
-        goal = " ".join(sys.argv[1:])
-
-    # Verify that specified goal contains only known valid characters
-    # (otherwise we'll never be able to evolve that string)
-    for char in goal:
-        if char not in VALID_CHARS:
-            msg = "Given text {goal!r} contains illegal character {char!r}.\n"
-            msg += "Valid set: {val!r}\n"
-            raise ValueError(msg.format(goal=goal, char=char, val=VALID_CHARS))
-
-    # Run evolutionary algorithm
-    pop, log = evolve_string(goal)
+	# Get goal message from command line (optional)
+	import sys
+	if len(sys.argv) == 1:
+		# Default goal of the evolutionary algorithm if not specified.
+		# Pretty much the opposite of http://xkcd.com/534
+		goal = "SKYNET IS NOW ONLINE"
+	else:
+		goal = " ".join(sys.argv[1:])
+
+	# Verify that specified goal contains only known valid characters
+	# (otherwise we'll never be able to evolve that string)
+	for char in goal:
+		if char not in VALID_CHARS:
+			msg = "Given text {goal!r} contains illegal character {char!r}.\n"
+			msg += "Valid set: {val!r}\n"
+			raise ValueError(msg.format(goal=goal, char=char, val=VALID_CHARS))
+
+	# Run evolutionary algorithm
+	pop, log = evolve_string(goal)

From 2055e770517c934e0dc4a6a026504514bd14ab0c Mon Sep 17 00:00:00 2001
From: Matthew Beaudouin-Lafon <matthew.beaudouin-lafon@students.olin.edu>
Date: Fri, 6 May 2016 11:22:05 -0400
Subject: [PATCH 2/2] Copied commented results in evolve_text.py into
 results.txt

---
 results.txt | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 results.txt

diff --git a/results.txt b/results.txt
new file mode 100644
index 0000000..3a6e3ac
--- /dev/null
+++ b/results.txt
@@ -0,0 +1,2 @@
+Experiment: increase the probability of substitution. This is where it seems to get stuck towards the end. It seems to help
+If it wasnt so late, I would look into changing the probabilities dynamically.
\ No newline at end of file