def som(problem, iterations, learning_rate=0.8):
"""Solve the TSP using a Self-Organizing Map."""
# Obtain the normalized set of cities (w/ coord in [0,1])
cities = problem.copy()
cities[['x', 'y']] = normalize(cities[['x', 'y']]) # 归一化
# The population size is 8 times the number of cities 神经元个数
n = cities.shape[0] * 3
#n = cities.shape[0] * 3 # 测试用，by EE526
# Generate an adequate network of neurons:
network = generate_network(cities, n, c=4)
print('Network of {} neurons created. Starting the iterations:'.format(n))
for i in range(iterations):
# Check for plotting interval
if i % 100 == 0: # 每隔100次画出神经元图像
plot_network(cities,
network,
name='out_files\process\city_network%d.png' %
(i // 100))
if not i % 100: # if i%100==0
print('\t> Iteration {}/{}'.format(i, iterations), end="\r")
# Choose a random city
city = cities.sample(1)[['x', 'y']].values # 随机从cities中选取一组数，1*2数组
winner_idx = select_closest(network, city)
# Generate a filter that applies changes to the winner's gaussian
gaussian = get_neighborhood(winner_idx, n // 10,
network.shape[0]) # 高斯核函数是算法的核心
# Update the network's weights (closer to the city)
network += gaussian[:, np.newaxis] * learning_rate * (
city - network) # np.newaxis在该位置增加一维，变成神经元数*1维
# 实际上就是为了让对应的移动乘以对应的坐标
# Decay the variables
learning_rate = learning_rate * 0.99997
n = n * 0.9994
# Check if any parameter has completely decayed.
if n < 1:
print('Radius has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
if learning_rate < 0.001:
print('Learning rate has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
else:
print('Completed {} iterations.'.format(iterations))
# plot 部分
plot_network(cities, network)
route = get_route(cities, network)
cities = problem.copy()
citiesReal = cities[['x', 'y']] # 取实际坐标
plot_route(citiesReal, route)
return route
def som(problem, iterations, learning_rate=0.8):
'''
Solve the TSP using a Self-Organizing Map.
:params problem(dataframe): 城市坐标
:params iterations(int): 最大迭代次数
:learning_rate(float): 学习率
:return route
'''
cities = problem.copy()
# Obtain the normalized set of cities (w/ coord in [0,1])
cities[['x', 'y']] = normalize(cities[['x', 'y']])
# The population size is 8 times the number of cities
# <Hyperparameter:times>
n = cities.shape[0] * 8
# Generate an adequate network of neurons:
# (n,2)
network = generate_network(n)
print('Network of {} neurons created. Starting the iterations:'.format(n))
for i in range(iterations):
if not i % 100:
print('\t> Iteration {}/{}'.format(i, iterations), end="\r")
# Choose a random city
city = cities.sample(1)[['x', 'y']].values
winner_idx = select_closest(network, city)
# Generate a filter that applies changes to the winner's gaussian
# <Hyperparameter:radius>
gaussian = get_neighborhood(winner_idx, n // 10, network.shape[0])
# Update the network's weights (closer to the city)
network += gaussian[:, np.newaxis] * learning_rate * (city - network)
# Decay the variables
# <Hyperparameter:decay rate>
learning_rate = learning_rate * 0.99997
n = n * 0.9997
# Check for plotting interval
if not i % 1000:
plot_network(cities, network, name='diagrams/{:05d}.png'.format(i))
# Check if any parameter has completely decayed.
if n < 1:
print('Radius has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
if learning_rate < 0.001:
print('Learning rate has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
else:
print('Completed {} iterations.'.format(iterations))
plot_network(cities, network, name='diagrams/final.png')
route = get_route(cities, network)
plot_route(cities, route, 'diagrams/route.png')
return route
def som(problem, iterations, learning_rate=0.8):
"""Solve the TSP using a Self-Organizing Map."""
# Obtain the normalized set of cities (w/ coord in [0,1])
dStep = 100 # 每隔100次保存一次数据
dSave = np.zeros(iterations // dStep) # 保存数据
cities = problem.copy()
cities[['x', 'y']] = normalize(cities[['x', 'y']]) # 归一化
# The population size is 8 times the number of cities 神经元个数
n = cities.shape[0] * 4
# Generate an adequate network of neurons:
network = generate_network(cities, n, c=2)
print('Network of {} neurons created. Starting the iterations:'.format(n))
for i in range(iterations):
# Check for plotting interval
# if i % 100 == 0: # 每隔100次画出神经元图像
# plot_network(cities, network, name='out_files\process\city_network%d.png'%(i//100))
if not i % 100: # if i%100==0
print('\t> Iteration {}/{}'.format(i, iterations), end="\r")
# Choose a random city
city = cities.sample(1)[['x', 'y']].values # 随机从cities中选取一组数，1*2数组
winner_idx = select_closest(network, city)
# print(winner_idx) # DEBUG
# 改进方案, 获胜神经元距离小于阈值，则直接获胜
if np.linalg.norm(city - network[winner_idx, :], axis=1) < 0.005: # 求距离
network[winner_idx, :] = city
# print(winner_idx)
else:
# Generate a filter that applies changes to the winner's gaussian
gaussian = get_neighborhood(winner_idx, n // 10, network.shape[0]) # 高斯核函数是算法的核心
# Update the network's weights (closer to the city)
network += gaussian[:, np.newaxis] * learning_rate * (city - network) # np.newaxis在该位置增加一维，变成神经元数*1维
# 实际上就是为了让对应的移动乘以对应的坐标
# Decay the variables
learning_rate = learning_rate * 0.99999
n = n * 0.9995 # 较好的参数是0.9991-0.9997
if not i % 100: # 每隔100次， 求距离
route = get_route(cities, network)
p = problem.reindex(route)
dSave[i // dStep] = route_distance(p)
else:
print('Completed {} iterations.'.format(iterations))
# plot 部分
plot_network(cities, network)
route = get_route(cities, network)
cities = problem.copy()
citiesReal = cities[['x', 'y']] # 取实际坐标
plot_route(citiesReal, route)
return route, dSave
def som(instancia,problem, iterations, learning_rate,delta_learning_rate, delta_n,sensi_radio,sensi_learning_rate,factor_neuronas,plotear):
"""Solve the TSP using a Self-Organizing Map."""
# Obtenemos primero las ciudades normalizadas (con coordenadas en [0,1])
cities = problem.copy()
cities[['x', 'y']] = normalize(cities[['x', 'y']])
#La población de neuronas se crea con factor_neuronas veces la cantidad de ciudades
n = cities.shape[0] * factor_neuronas
# Generamos una adecuada red de neuronas de la forma
network = generate_network(n)
if plotear:
print('Red de {} neuronas creadas. Comenzando las iteraciones:'.format(n))
for i in range(iterations):
if not i % 100:
print('\t> Iteración {}/{}'.format(i, iterations), end="\r")
# Se escoge una ciudad de forma aleatoria
city = cities.sample(1)[['x', 'y']].values
#Se busca la neurona más cercana a la ciudad, la winner neuron
winner_idx = select_closest(network, city)
#Genera un filtro que aplica los cambios al winner o BMU
gaussian = get_neighborhood(winner_idx, n//10, network.shape[0])
# Actualizar los pesos de la red según una distribución gaussiana
network += gaussian[:,np.newaxis] * learning_rate * (city - network)
# actualizar las parametros
learning_rate = learning_rate * delta_learning_rate
n = n * delta_n
# Chequear para plotear cada 1000 iteraciones
if plotear:
if not i % 1000:
plot_network(cities, network, name='imagenes/'+instancia+'/{:05d}.png'.format(i))
# Chequear si algún parametro a caído por debajo de la sensibilidad
if n < sensi_radio:
print('Radio por debajo de sensibilidad, Se ha terminado la ejecución',
'a {} las iteraciones'.format(i))
break
if learning_rate < sensi_learning_rate:
print('Learning rate por debajo de sensibilidad, Se ha terminado la ejecución',
'a las {} iteraciones'.format(i))
break
else:
print('Se han completado las {} iteraciones.'.format(iterations))
if plotear:
plot_network(cities, network, name='imagenes/'+instancia+'/final.png')
route = get_route(cities, network)
if plotear:
plot_route(cities, route, 'imagenes/'+instancia+'/route.png')
return route
def som(problem, iterations, learning_rate=0.8):
"""Solve the TSP using a Self-Organizing Map."""
# Obtain the normalized set of cities (w/ coord in [0,1])
cities = problem.copy()
cities[['x', 'y']] = normalize(cities[['x', 'y']])
# The population size is 8 times the number of cities 神经元个数
n = cities.shape[0] * 8
network = generate_network(n) # Generate an adequate network of neurons:
print('Network of {} neurons created. Starting the iterations:'.format(n))
for i in range(iterations):
if i == 0 or (not i % 1000):
plot_network(cities,
network,
name='out_files\process\city_network%d.png' %
(i // 1000 + 1))
city = cities.sample(1)[['x', 'y']].values # 随机从cities中选取一组数，1*2数组
winner_idx = select_closest(network, city)
# Generate a filter that applies changes to the winner's gaussian
gaussian = get_neighborhood(winner_idx, n // 10, network.shape[0])
# Update the network's weights (closer to the city)
network += gaussian[:, np.newaxis] * learning_rate * (
city - network) # np.newaxis在该位置增加一维，变成神经元数*1维
# 实际上就是为了让对应的移动乘以对应的坐标
# Decay the variables
learning_rate = learning_rate * 0.99997
n = n * 0.9997
# Check for plotting interval
# Check if any parameter has completely decayed.
if n < 1:
print('Radius has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
if learning_rate < 0.001:
print('Learning rate has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
# if 神经元覆盖了城市
# print('在第{}次迭代，收敛'.format(i))
else:
print('Completed {} iterations.'.format(iterations))
plot_network(cities, network)
route = get_route(cities, network)
plot_route(problem[['x', 'y']], route)
return route
def algorithm(df, params):
"""
wrapper function to put each individual algorithm inside
:param df: dataframe that contains all the input dataset
:param params: algorithm specific parameters
:return: a dictionary of { outputname: output content in memory }
"""
output = {}
# algorithm specific code
# construct network analysis
NW = Network(df, params['relations'])
output['d3js'] = NW.export_json()
output['gephi'] = NW.export_gephi()
output['pajek'] = NW.export_pajek()
output['assortativity'] = NW.assortativity()
output['node_attributes'] = NW.node_attributes()
output['edge_attributes'] = NW.edge_attributes()
output['strong_components'] = NW.strong_components()
output['weak_components'] = NW.weak_components()
output['triads'] = NW.triads()
# plot network
pruned_network = NW.prune_network()
output['div'] = plot.plot_network(
pruned_network,
params['layout'],
params['relations'],
title=params['relations'] +
' Network graph of 500 nodes with highest degree centrality')
return output
def som(problem, iterations, learning_rate=0.8):
cities = problem.copy()
cities[['x', 'y']] = normalize(cities[['x', 'y']])
n = cities.shape[0] * 8
network = generate_network(n)
print('Network of {} neurons created. Starting the iterations:'.format(n))
for i in range(iterations):
if not i % 100:
print('\t> Iteration {}/{}'.format(i, iterations), end="\r")
city = cities.sample(1)[['x', 'y']].values
winner_idx = select_closest(network, city)
gaussian = get_neighborhood(winner_idx, n // 10, network.shape[0])
network += gaussian[:, np.newaxis] * learning_rate * (city - network)
learning_rate = learning_rate * 0.99997
n = n * 0.9997
if not i % 1000:
plot_network(cities, network, name='diagrams/{:05d}.png'.format(i))
if n < 1:
print('Radius has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
if learning_rate < 0.001:
print('Learning rate has completely decayed, finishing execution',
'at {} iterations'.format(i))
break
else:
print('Completed {} iterations.'.format(iterations))
plot_network(cities, network, name='diagrams/final.png')
route = get_route(cities, network)
plot_route(cities, route, 'diagrams/route.png')
return route
def molecular_dynamics(vertices, edges, polys, parameters, T, folder): delta_t = parameters['delta_t'] lx = parameters['lx'] ly = parameters['ly'] L = np.array([lx,ly]) # time t = 0 count = 0 while t < T: # get energy for network energy = get_energy(vertices, polys, edges, parameters) # print energy # get forces for network forces = get_forces(vertices, polys, edges, parameters) print t, np.sum(forces**2)**(0.5) # move vertices vertices = move_vertices(vertices, forces, parameters) # check for T1 transitions polys, edges = T1_transition(vertices, polys, edges, parameters) # add routine to write vertices, energy, forces at every time step # can be used for plotting routines later... # write_vertices(vertices, "%s/%.2f.txt" % (folder,t)) # write edges? # write polygons? # if count % 21 == 0: plot_network(vertices, polys, L, "%s/%.2f.jpg" % (folder,t)) count += 1 t += delta_t return
correct_block = validators.check_block_time(ramificat)
validators.approve_block(correct_block, validators.all_ids)
validators.walidate_blockchain(correct_block)
validators.hide_transactions()
message = notarries.check_data_availability(
validators.shard_blockchain[-1])
verdict = notarries.walidate_challenge(
message, validators.shard_blockchain[-1])
if verdict:
validators.recognized_hider(correct_block)
communicator.comm.barrier()
if communicator.rank == 0:
beacon.burn_stake_bad_commit_availability(8)
beacon.burn_stake_notarry()
beacon.burn_stake_bad_commit_availability(10)
beacon.remove_indebted_nodes(beacon.val_acc_info,
beacon.lower_limit_vali_id,
beacon.pool_vali, 11)
beacon.remove_indebted_nodes(beacon.notary_acc_info,
beacon.lower_limit_notaries_id,
beacon.pool_notaries, 12)
communicator.comm.barrier()
if communicator.rank != 0:
validators.change_ids(communicator.comm.recv(source=0, tag=11))
notarries.change_ids(communicator.comm.recv(source=0, tag=12))
if communicator.rank == 0:
pass
plot_network(beacon.peers_in_beacon, communicator.rank)
else:
plot_network(validators.peers_in_shard, communicator.rank)
def som(problem, iterations, learning_rate=0.8):
'''
SOM解决TSP问题
'''
# 将城市数据归一化处理
cities = problem.copy()
cities[['x', 'y']] = normalize(cities[['x', 'y']])
# 神经元数量设定为城市的8倍
n = cities.shape[0] * 8
# 建立神经网络
network = generate_network(n)
print('创建{} 个神经元. 开始进行迭代:'.format(n))
for i in range(iterations):
if not i % 100:
print('\t> 迭代过程 {}/{}'.format(i, iterations), end='\r')
# 随机选择一个城市
city = cities.sample(1)[['x', 'y']].values
#优胜神经元（距离该城市最近的神经元）
winner_idx = select_closest(network, city)
# 以该神经元为中心建立高斯分布
gaussian = get_neighborhood(winner_idx, n // 10, network.shape[0])
# 更新神经元的权值，使神经元向被选中城市移动
network += gaussian[:, np.newaxis] * learning_rate * (city - network)
# 学习率衰减，方差衰减
learning_rate = learning_rate * 0.99997
n = n * 0.9997
# 每迭代1000次时作图
if not i % 1000:
plot_network(cities,
network,
name='som_diagrams/{:05d}.png'.format(i))
pass
# 判断方差和学习率是否达到阈值
if n < 1:
print('方差已经达到阈值，完成执行次数{}'.format(i))
break
if learning_rate < 0.001:
print('学习率已经达到阈值，完成执行次数{}'.format(i))
break
else:
print('完成迭代：{}次'.format(iterations))
plot_network(cities, network, name='som_diagrams/final.png')
route = get_route(cities, network)
cities = cities.reindex(route)
plot_route(cities, route, 'som_diagrams/route.png')
# 将多个png文件合成gif文件
path = os.chdir('.\som_diagrams')
pic_list = os.listdir()
create_gif(pic_list, 'result.gif', 0.3)
return route
