Merge pull request #9 from HaaLeo/feature/artificial-bee-colony

Feature/artificial bee colony

Author: HaaLeo

.vscode/launch.json

@@ -64,6 +64,23 @@
                 "10",
                 "14"
             ]
+        },
+        {
+            "name": "Run: Artificial Bee Colony",
+            "type": "python",
+            "request": "launch",
+            "module": "swarmlib",
+            "console": "internalConsole",
+            "args": [
+                // "--dark",
+                "--continuous",
+                "bees",
+                "-n",
+                "10",
+                "-t",
+                "5",
+                "14"
+            ]
         }
     ]
 }

.vscode/settings.json

@@ -1,36 +1,36 @@
 {
+    "cSpell.ignorePaths": [
+        "**/.git/**",
+        ".vscode",
+        ".pylintrc"
+    ],
     "cSpell.words": [
-        "networkx",
-        "pyplot",
-        "wfunc",
-        "pylint",
-        "ioff",
-        "qsize",
-        "fignum",
-        "Hanisch",
-        "pypi",
-        "isabs",
-        "getcwd",
-        "Dorigo",
         "Birattari",
+        "Dorigo",
+        "Hanisch",
         "Stuetzle",
-        "optimisation",
         "TSPLIB",
+        "ackley",
+        "fignum",
+        "functools",
+        "getcwd",
+        "ioff",
+        "isabs",
+        "michalewicz",
+        "networkx",
+        "numpy",
+        "optimisation",
         "paypal",
+        "pylint",
+        "pypi",
+        "pyplot",
+        "qsize",
         "swarmlib",
-        "numpy",
-        "michalewicz",
-        "functools",
-        "ackley"
-    ],
-    "cSpell.ignorePaths": [
-        "**/.git/**",
-        ".vscode",
-        ".pylintrc"
+        "wfunc"
     ],
+    "files.eol": "\n",
     "files.insertFinalNewline": true,
     "files.trimFinalNewlines": true,
     "python.linting.enabled": true,
-    "files.eol": "\n",
     "python.linting.pylintEnabled": true
 }

CHANGELOG.md

@@ -3,21 +3,22 @@ All notable changes to the "swarmlib" pypi package will be documented in this fi
 This project follows [semantic versioning](https://semver.org/).
 
 ## Unreleased
+* Added the _artificial bee colony_ algorithm. After each step the intermediate solution is plotted.
 
-## 2019-02-17 -v0.7.0
+## 2020-02-17 -v0.7.0
 * **Added** dark mode. It is enabled via the `--dark` flag.
 * **Changed** `--continuous` and `--interval` flags. Both are now top level flags.
 * **Changed** the API of the ant colony optimization.
 * **Changed** the `tsp_file` argument to an option. Now `--tsp-file` is optional. By default the built-in burma14 problem is used.
 
-## 2019-01-25 - v0.6.2
+## 2020-01-25 - v0.6.2
 * **Changed** cuckoo search visualization: when a nest is abandoned / newly generated color its transition differently.
 * **Fixed** cuckoo search visualization: now the abandon transition is mapped to the correct nest.
 
-## 2019-01-24 - v0.6.1
+## 2020-01-24 - v0.6.1
 * **Changed** cuckoo search: Ensure each nest is assigned a cuckoo position in the update step
 
-## 2019-01-24 - v0.6.0
+## 2020-01-24 - v0.6.0
 * **Changed** the visualization of the _firefly algorithm_ and the _cuckoo search_. Now they both include velocities.
 * **Changed** the firefly algorithm including its API. Now it replays the same problem if `--continuous` is set.
 * **Changed** the `--continuous` flag. It requires no parameter anymore.

README.md

@@ -8,19 +8,20 @@
 ## Description
 
 This repository implements several swarm optimization algorithms and visualizes their (intermediate) solutions.
-To run the algorithms one can either use the command line interface or the API.
+To run the algorithms one can either use the CLI (recommended) or the API.
 Currently, the following algorithms are implemented:
 * [Firefly Algorithm](#firefly-algorithm)
 * [Cuckoo Search](#cuckoo-search)
 * [Particle Swarm Optimization](#particle-swarm-optimization)
 * [Ant Colony Optimization](#ant-colony-optimization)
+* [Artificial Bee Colony](#artificial-bee-colony)
 
 ## Installation
 
 You can install the package with `pip` from [pypi](https://pypi.org/project/swarmlib):
 
 ```
-pip3 install swarmlib
+pip install swarmlib
 
 swarm --version
 ```
@@ -72,7 +73,7 @@ In addition to the cli you can also use the API:
 ```python
 from swarmlib import FireflyProblem, FUNCTIONS
 
-problem = FireflyProblem(FUNCTIONS['michalewicz'], 14)
+problem = FireflyProblem(function=FUNCTIONS['michalewicz'], firefly_number=14)
 best_firefly = problem.solve()
 problem.replay()
 ```
@@ -116,7 +117,7 @@ This repository also implements modified _particle swarm optimization_ that was
 
 #### Features
 
-Enables to particle swarm optimization to one of the provided 2D functions. The algorithm tries to find the global minimum of the selected function.  
+Enables particle swarm optimization to one of the provided 2D functions. The algorithm tries to find the global minimum of the selected function.  
 
 Currently two functions can be selected:
 * [ackley](https://www.sfu.ca/~ssurjano/ackley.html)
@@ -175,3 +176,41 @@ problem = ACOProblem(ant_number=10)
 path, distance = problem.solve()
 problem.replay()
 ```
+
+### Artificial Bee Colony
+
+The Artificial Bee Colony (ABC) algorithm was initially proposed 2005 by Dervis Karaboga in his paper [An Idea Based on Honey Bee Swarm For Numerical Optimization](https://pdfs.semanticscholar.org/015d/f4d97ed1f541752842c49d12e429a785460b.pdf).
+In his paper Karaboga did not specify _how exactly_ new solutions shall be discovered. 
+
+Research has shown that the flight behavior of birds, fruit flies and other insects model properties of Levy flights ([Brown, Liebovitch & Glendon, 2007](https://link.springer.com/article/10.1007/s10745-006-9083-4); [Pavlyukevich, 2007](https://arxiv.org/pdf/cond-mat/0701653.pdf)). Therefore, this library's ABC implementation leverages levy flights to generate new solutions.
+
+#### Features
+
+Enables the ABC algorithm to one of the provided 2D functions. The algorithm tries to find the global minimum of the selected function.
+
+Currently two functions can be selected:
+* [ackley](https://www.sfu.ca/~ssurjano/ackley.html)
+* [michalewicz](https://www.sfu.ca/~ssurjano/michal.html)
+
+![ABC Sample](https://raw.githubusercontent.com/HaaLeo/swarmlib/master/doc/bees.gif)
+
+The plot shows all _employee bees_ as _red_ markers, the _onlooker bees_ are visualized as _blue_ markers. The best bees of all (previous) iterations are indicated by _yellow_ markers. When an employee bee exceeded its maximum _trials_ the bee is assigned a new random position. This is visualized by a _dark grey_ transition.
+Since the onlooker bees pick up an employee bee's position randomly visualizing their transitions confuses rather than it helps understanding the algorithm and therefore is omitted.
+
+To print all available options execute:
+
+```
+swarm bees -h
+```
+
+#### API
+
+In addition to the cli you can also use the API:
+
+```python
+from swarmlib import ABCProblem, FUNCTIONS
+
+problem = ABCProblem(bees=10, function=FUNCTIONS['michalewicz'])
+best_bee = problem.solve()
+problem.replay()
+```

doc/bees.gif

@@ -41,6 +41,8 @@
     keywords=[
         'swarm',
         'swarmlib',
+        'lib',
+        'library',
         'ant',
         'colony',
         'optimization',
@@ -68,7 +70,14 @@
         'particle',
         'particles',
         'pso',
-        'PSO'
+        'PSO',
+        'artificial',
+        'bee',
+        'bees',
+        'colony',
+        'ABC',
+        'abc',
+        'heuristic'
     ],
     classifiers=[
         'Development Status :: 5 - Production/Stable',

setup.py

@@ -7,4 +7,5 @@
 from .fireflyalgorithm.firefly_problem import FireflyProblem
 from .cuckoosearch.cuckoo_problem import CuckooProblem
 from .pso.pso_problem import PSOProblem
+from .abc.abc_problem import ABCProblem
 from .util.functions import FUNCTIONS

swarmlib/__init__.py

@@ -7,13 +7,13 @@
 import sys
 import argparse
 
-# pylint: disable=import-error
-# to do remove import-error
 
 from .aco4tsp.main import configure_parser as aco_parser
 from .fireflyalgorithm.main import configure_parser as firefly_parser
 from .cuckoosearch.main import configure_parser as cuckoo_parser
 from .pso.main import configure_parser as pso_parser
+from .abc.main import configure_parser as abc_parser
+
 from ._version import __version__
 
 logging.basicConfig(
@@ -61,6 +61,7 @@ def run_swarm():
     firefly_parser(sub_parsers)
     cuckoo_parser(sub_parsers)
     pso_parser(sub_parsers)
+    abc_parser(sub_parsers)
 
     args = vars(parser.parse_args())
     if args:

swarmlib/__main__.py

@@ -0,0 +1,4 @@
+# ------------------------------------------------------------------------------------------------------
+#  Copyright (c) Leo Hanisch. All rights reserved.
+#  Licensed under the BSD 3-Clause License. See LICENSE.txt in the project root for license information.
+# ------------------------------------------------------------------------------------------------------

swarmlib/abc/__init__.py

@@ -0,0 +1,82 @@
+# ------------------------------------------------------------------------------------------------------
+#  Copyright (c) Leo Hanisch. All rights reserved.
+#  Licensed under the BSD 3-Clause License. See LICENSE.txt in the project root for license information.
+# ------------------------------------------------------------------------------------------------------
+
+from copy import deepcopy
+from functools import reduce
+import logging
+
+import numpy as np
+
+from .bees.employee_bee import EmployeeBee
+from .bees.onlooker_bee import OnlookerBee
+from .visualizer import Visualizer
+
+LOGGER = logging.getLogger(__name__)
+
+class ABCProblem():
+    """Artificial Bee Colony Problem"""
+
+    def __init__(self, **kwargs):
+        """
+        Initializes a new instance of the ABCProblem class.
+        """
+
+        self.__iteration_number = kwargs['iteration_number']
+        self.__employee_bees = [
+            EmployeeBee(**kwargs)
+            for _ in range(kwargs['bees'])
+        ]
+
+        self.__onlooker_bees = [
+            OnlookerBee(**kwargs)
+            for _ in range(kwargs['bees'])
+        ]
+
+        self.__visualizer = Visualizer(**kwargs)
+
+    def solve(self):
+        """
+        Solve the ABC problem
+        """
+        best = min(self.__employee_bees + self.__onlooker_bees, key=lambda bee: bee.value)
+        self.__visualizer.add_data(employee_bees=self.__employee_bees, onlooker_bees=self.__onlooker_bees, best_position=best.position)
+
+        for iteration in range(self.__iteration_number):
+            # Employee bee phase
+            for bee in self.__employee_bees:
+                bee.explore()
+
+            # Calculate the employee bees fitness values and probabilities
+            overall_fitness = reduce(lambda acc, curr: acc + curr.fitness, self.__employee_bees, 0)
+            employee_bees_fitness_probs = [bee.fitness/overall_fitness for bee in self.__employee_bees]
+
+            # Choose the employee bees positions proportional to their fitness
+            choices = np.random.choice(self.__employee_bees, size=len(self.__employee_bees), p=employee_bees_fitness_probs)
+
+            # Onlooker phase
+            # Explore new food sources based on the chosen employees' food sources
+            for bee, choice in zip(self.__onlooker_bees, choices):
+                bee.explore(choice.position, choice.value)
+
+            # Scout phase
+            for bee in self.__employee_bees + self.__onlooker_bees:
+                bee.reset()
+
+             # Update best food source
+            current_best = min(self.__employee_bees + self.__onlooker_bees, key=lambda bee: bee.value)
+            if current_best.value < best.value:
+                best = deepcopy(current_best)
+                LOGGER.info('Iteration %i Found new best solution="%s" at position="%s"', iteration+1, best.value, best.position)
+
+            # Add data for plotting
+            self.__visualizer.add_data(employee_bees=self.__employee_bees, onlooker_bees=self.__onlooker_bees, best_position=best.position)
+
+        return best
+
+    def replay(self):
+        """
+        Start the problems visualization.
+        """
+        self.__visualizer.replay()

swarmlib/abc/abc_problem.py

@@ -0,0 +1,4 @@
+# ------------------------------------------------------------------------------------------------------
+#  Copyright (c) Leo Hanisch. All rights reserved.
+#  Licensed under the BSD 3-Clause License. See LICENSE.txt in the project root for license information.
+# ------------------------------------------------------------------------------------------------------