modify reference format

src/evox/algorithms/mo/bce_ibea.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. Bi-criterion evolution based IBEA algorithm is described in the following papers:
+#
+# Title: Pareto or Non-Pareto: Bi-Criterion Evolution in Multiobjective Optimization
+# Link: https://ieeexplore.ieee.org/abstract/document/7347391
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -162,11 +173,7 @@ def body_fun(i, vals):
 
 @jit_class
 class BCEIBEA(Algorithm):
-    """Bi-criterion evolution based IBEA
-
-    link: https://ieeexplore.ieee.org/abstract/document/7347391
-    Inspired by PlatEMO.
-
+    """
     Note: The number of outer iterations needs to be set to Maximum Generation*2+1.
 
     Args:

src/evox/algorithms/mo/bige.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. BiGE algorithm is described in the following papers:
+#
+# Title: Bi-goal evolution for many-objective optimization problems
+# Link: https://doi.org/10.1016/j.artint.2015.06.007
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 from jax import vmap
@@ -51,10 +62,6 @@ def calc_sh(fit_a, pr_a, fit_b, pr_b, r):
 
 @jit_class
 class BiGE(Algorithm):
-    """BiGE algorithm
-
-    link: https://doi.org/10.1016/j.artint.2015.06.007
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/eagmoead.py

@@ -1,3 +1,15 @@
+# --------------------------------------------------------------------------------------
+# 1. EAG-MOEA/D algorithm is described in the following papers:
+#
+# Title: An External Archive Guided Multiobjective Evolutionary Algorithm Based on Decomposition for Combinatorial
+# Optimization
+# Link: https://ieeexplore.ieee.org/abstract/document/6882229
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 from functools import partial
@@ -28,11 +40,6 @@ def environmental_selection(fitness, n):
 
 @jit_class
 class EAGMOEAD(Algorithm):
-    """EAG-MOEA/D algorithm
-
-    link: https://ieeexplore.ieee.org/abstract/document/6882229
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/gde3.py

@@ -1,7 +1,16 @@
+# --------------------------------------------------------------------------------------
+# 1. GDE3 algorithm is described in the following papers:
+#
+# Title: GDE3: the third evolution step of generalized differential evolution
+# Link: https://ieeexplore.ieee.org/document/1554717
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
-from jax import vmap
-from functools import partial
 
 from evox import Algorithm, jit_class, State
 from evox.operators import (
@@ -13,10 +22,6 @@
 
 @jit_class
 class GDE3(Algorithm):
-    """GDE3 algorithm
-
-    link: https://ieeexplore.ieee.org/document/1554717
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/hype.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. HypE algorithm is described in the following papers:
+#
+# Title: HypE: An Algorithm for Fast Hypervolume-Based Many-Objective Optimization
+# Link: https://direct.mit.edu/evco/article-abstract/19/1/45/1363/HypE-An-Algorithm-for-Fast-Hypervolume-Based-Many
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 from functools import partial

src/evox/algorithms/mo/ibea.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. IBEA algorithm is described in the following papers:
+#
+# Title: Indicator-Based Selection in Multiobjective Search
+# Link: https://link.springer.com/chapter/10.1007/978-3-540-30217-9_84
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -23,11 +34,6 @@ def cal_fitness(pop_obj, kappa):
 
 @jit_class
 class IBEA(Algorithm):
-    """IBEA algorithm
-
-    link: https://link.springer.com/chapter/10.1007/978-3-540-30217-9_84
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/knea.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. KnEA algorithm is described in the following papers:
+#
+# Title: A Knee Point-Driven Evolutionary Algorithm for Many-Objective Optimization
+# Link: https://ieeexplore.ieee.org/document/6975108
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 from functools import partial
@@ -26,10 +37,6 @@ def calc_DW(fit, k):
 
 @jit_class
 class KnEA(Algorithm):
-    """KnEA algorithm
-
-    link: https://ieeexplore.ieee.org/document/6975108
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/moead.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. MOEA/D algorithm is described in the following papers:
+#
+# Title: MOEA/D: A Multiobjective Evolutionary Algorithm Based on Decomposition
+# Link: https://ieeexplore.ieee.org/document/4358754
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -9,11 +20,6 @@
 
 @jit_class
 class MOEAD(Algorithm):
-    """MOEA/D algorithm
-
-    link: https://ieeexplore.ieee.org/document/4358754
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/moeaddra.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. MOEA/D-DRA algorithm is described in the following papers:
+#
+# Title: The performance of a new version of MOEA/D on CEC09 unconstrained MOP test instances
+# Link: https://ieeexplore.ieee.org/abstract/document/4982949
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -9,11 +20,6 @@
 
 @jit_class
 class MOEADDRA(Algorithm):
-    """MOEA/D-DRA algorithm
-
-    link: https://ieeexplore.ieee.org/abstract/document/4982949
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/moeadm2m.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. MOEA/D based on MOP to MOP algorithm is described in the following papers:
+#
+# Title: Decomposition of a Multiobjective Optimization Problem Into a Number of Simple Multiobjective Subproblems
+# Link: https://ieeexplore.ieee.org/abstract/document/6595549
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -83,11 +94,6 @@ def false_fun(c):
 
 @jit_class
 class MOEADM2M(Algorithm):
-    """MOEA/D based on MOP to MOP algorithm
-
-    link: https://ieeexplore.ieee.org/abstract/document/6595549
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/nsga2.py

@@ -1,3 +1,10 @@
+# --------------------------------------------------------------------------------------
+# 1. NSGA-II algorithm is described in the following papers:
+#
+# Title: A fast and elitist multiobjective genetic algorithm: NSGA-II
+# Link: https://ieeexplore.ieee.org/document/996017
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 

src/evox/algorithms/mo/nsga3.py

@@ -1,3 +1,15 @@
+# --------------------------------------------------------------------------------------
+# 1. NSGA-III algorithm is described in the following papers:
+#
+# Title: An Evolutionary Many-Objective Optimization Algorithm Using Reference-Point-Based Nondominated Sorting
+# Approach, Part I: Solving Problems With Box Constraints
+# Link: https://ieeexplore.ieee.org/document/6600851
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -13,10 +25,6 @@
 
 @jit_class
 class NSGA3(Algorithm):
-    """NSGA-III algorithm
-
-    link: https://ieeexplore.ieee.org/document/6600851
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/rvea.py

@@ -1,6 +1,12 @@
+# --------------------------------------------------------------------------------------
+# 1. RVEA algorithm is described in the following papers:
+#
+# Title: A Reference Vector Guided Evolutionary Algorithm for Many-Objective Optimization
+# Link: https://ieeexplore.ieee.org/document/7386636
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
-from evox.utils import cos_dist
 
 from evox.operators import mutation, crossover, selection
 from evox.operators.sampling import UniformSampling, LatinHypercubeSampling
@@ -9,10 +15,6 @@
 
 @jit_class
 class RVEA(Algorithm):
-    """RVEA algorithms
-
-    link: https://ieeexplore.ieee.org/document/7386636
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/spea2.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. SPEA2 algorithm is described in the following papers:
+#
+# Title: SPEA2: Improving the strength pareto evolutionary algorithm
+# Link: https://www.research-collection.ethz.ch/handle/20.500.11850/145755
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -58,11 +69,6 @@ def body_fun(vals):
 
 @jit_class
 class SPEA2(Algorithm):
-    """SPEA2 algorithm
-
-    link: https://www.research-collection.ethz.ch/handle/20.500.11850/145755
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,

src/evox/algorithms/mo/sra.py

@@ -1,3 +1,14 @@
+# --------------------------------------------------------------------------------------
+# 1. Stochastic ranking algorithm is described in the following papers:
+#
+# Title: Stochastic Ranking Algorithm for Many-Objective Optimization Based on Multiple Indicators
+# Link: https://ieeexplore.ieee.org/abstract/document/7445185
+#
+# 2. This code has been inspired by PlatEMO.
+# More information about PlatEMO can be found at the following URL:
+# GitHub Link: https://github.com/BIMK/PlatEMO
+# --------------------------------------------------------------------------------------
+
 import jax
 import jax.numpy as jnp
 
@@ -102,11 +113,6 @@ def in_body(j, d):
 
 @jit_class
 class SRA(Algorithm):
-    """Stochastic ranking algorithm
-
-    link: https://ieeexplore.ieee.org/abstract/document/7445185
-    Inspired by PlatEMO.
-    """
 
     def __init__(
         self,