python - python：带有简单ODE的pyABC-实例str和int之间不支持回溯错误<=
问题描述
我有一个简单的 ODE，其中包含一些未知参数（r、C、mu 和 gamma），它可以预测清洁后表面上细菌的衰变和再生。我有清洗后不同时间点（0h、1h、2h、4h、8h和24h）细菌数量的实验数据。我正在尝试使用 EasyABC 包通过近似贝叶斯计算顺序蒙特卡罗模拟方法来估计参数分布 r、C、d 和 g。
ODE 定义如下：
实验数据如下所示：
＃前言
from pyabc import (ABCSMC,
RV, Distribution,
MedianEpsilon,
LocalTransition)
from pyabc.visualization import plot_kde_2d, plot_data_callback
import matplotlib.pyplot as plt
import os
import tempfile
import numpy as np
from scipy.integrate import odeint
import math
db_path = ("sqlite:///" +
os.path.join(tempfile.gettempdir(), "test.db"))
＃实验数据
initial_contamination=59 #For ODE
measurement_data = np.array([19,5,5,2,9]) #To compare simulation against
s=[26,2.3,4.67,4.33,4.27] #Standard deviation used in Distance
precision=5000
measurement_times = np.array([0,1,2,4,8,24]) #Hours after cleaning
#定义常微分方程：
def ode_model(contamination,t,r,C,mu,gamma):
Contamination = contamination;
return(Contamination*r*(1-Contamination/C)-mu*math.exp(-gamma*t)*Contamination)
def deterministic_run(parameters):#precision,initial_contamination,r,C,mu, gamma):
precision=5000
tmax = 24
time_space = np.linspace(0,tmax,precision+1)
sim=odeint(ode_model,initial_contamination,time_space,args=(parameters["r"],parameters["C"],parameters["mu"],parameters["gamma"]))
num_at_1=sim[int(precision*1/50.0)]
num_at_2=sim[int(precision*2/50.0)]
num_at_4=sim[int(precision*4/50.0)]
num_at_8=sim[int(precision*8/50.0)]
num_at_24=sim[int(precision*24/50.0)]
return([num_at_1,num_at_2,num_at_4,num_at_8,num_at_24])
#定义先验分布
parameter_prior = Distribution(r=RV("uniform", 0, 4),
C=RV("uniform", 6, 15),
mu=RV("uniform", 0, 4),
gamma=RV("uniform", 0, 4))
parameter_prior.get_parameter_names()
#定义欧几里得距离：
def Distance(x,y,s):
# computes the Euclidean distance between two lists of the same length
if len(x) == len(y):
return math.sqrt(sum([(((x[i]-y[i])/s[i])**2) for i in range(len(x))]))
else:
return 'lists not the same length'
#设置ABC-SMC配置
abc = ABCSMC(models=deterministic_run,
parameter_priors=parameter_prior,
distance_function=Distance,
population_size=50,
transitions=LocalTransition(k_fraction=.3),
eps=MedianEpsilon(500, median_multiplier=0.7))
abc.new(db_path, {"Contamination": measurement_data})
#运行ABC-SMC
h = abc.run(minimum_epsilon=0.1, max_nr_populations=5)
我得到的错误
类型错误：“str”和“int”的实例之间不支持“<=”
这指的是acceptor.py的第100行
def initialize(self, t: int, get_weighted_distances: Callable[[], pd.DataFrame], distance_function: Distance, x_0: dict): """ 初始化。该方法最初由ABCSMC框架调用，可用于校准接受器到初始统计。默认是什么都不做。
Parameters
----------
t: int
The timepoint to initialize the acceptor for.
get_weighted_distances: Callable[[], pd.DataFrame]
Returns on demand the distances for initializing the acceptor.
distance_function: Distance
Distance object. The acceptor should not modify it, but might
extract some meta information.
x_0: dict
The observed summary statistics.
"""
pass
但我无法弄清楚它有什么问题。任何想法将不胜感激。
编辑：完整追溯：
runfile('/Users/YYY/Downloads/Beth/Code/pyABC_Cleaning.py', wdir='/Users/YYY/Downloads/Beth/Code')
INFO:Sampler:Parallelizing the sampling on 8 cores.
INFO:History:Start <ABCSMC(id=1, start_time=2020-06-22 09:19:29.808488, end_time=None)>
INFO:ABC:t: 0, eps: 500.
Process Process-1:
Traceback (most recent call last):
Process Process-4:
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
Traceback (most recent call last):
Process Process-2:
Process Process-3:
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
Process Process-5:
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
Process Process-6:
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
Process Process-7:
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
TypeError: '<=' not supported between instances of 'str' and 'int'
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
TypeError: '<=' not supported between instances of 'str' and 'int'
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
Process Process-8:
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
TypeError: '<=' not supported between instances of 'str' and 'int'
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
TypeError: '<=' not supported between instances of 'str' and 'int'
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
TypeError: '<=' not supported between instances of 'str' and 'int'
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
self._target(*self._args, **self._kwargs)
TypeError: '<=' not supported between instances of 'str' and 'int'
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 37, in work
new_sim = simulate_one()
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
TypeError: '<=' not supported between instances of 'str' and 'int'
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 598, in simulate_one
weight_function)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 683, in _evaluate_proposal
x_0)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/model.py", line 213, in accept
par=pars)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 306, in __call__
distance_function, eps, x, x_0, t, par)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/acceptor/acceptor.py", line 242, in accept_use_current_time
accept = d <= eps(t)
TypeError: '<=' not supported between instances of 'str' and 'int'
Traceback (most recent call last):
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicorebase.py", line 100, in get_if_worker_healthy
item = queue.get(True, 5)
File "/Users/YYY/opt/anaconda3/lib/python3.7/multiprocessing/queues.py", line 105, in get
raise Empty
Empty
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/YYY/Downloads/Beth/Code/pyABC_Cleaning.py", line 115, in <module>
h = abc.run(minimum_epsilon=0.1, max_nr_populations=5)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/smc.py", line 890, in run
pop_size, simulate_one, max_eval)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/base.py", line 151, in sample_until_n_accepted
sample = f(self, n, simulate_one, max_eval, all_accepted)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicore_evaluation_parallel.py", line 121, in sample_until_n_accepted
val = get_if_worker_healthy(processes, queue)
File "/Users/YYY/opt/anaconda3/lib/python3.7/site-packages/pyabc/sampler/multicorebase.py", line 104, in get_if_worker_healthy
raise ProcessError("At least one worker is dead.")
ProcessError: At least one worker is dead.
解决方案
错误来自这一行，是由您的距离函数返回一个字符串引起的。您将距离定义为：
def Distance(x,y,s):
# computes the Euclidean distance between two lists of the same length
if len(x) == len(y):
return math.sqrt(sum([(((x[i]-y[i])/s[i])**2) for i in range(len(x))]))
else:
return 'lists not the same length'
所以我猜你最终会遇到这种else情况，返回字符串并用你看到的错误杀死工人。您必须检查x并y找出导致它们长度不同的原因。
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