使用PyMC3中的协变量建立weibullAFT模型？

Question

我正在建立带有协变量模型的Weibull AFT，以便使用PyMC3和theano.tensor进行生存分析。我一直在阅读与PyMC3中与生存分析相关的所有笔记本来建立模型。但是，出现以下错误：

*File "C:\Users\71516706\Anaconda3\lib\site- 
packages\theano\tensor\basic.py", line 200, in as_tensor_variable
raise AsTensorError("Cannot convert %s to TensorType" % str_x, type(x))

AsTensorError: ('Cannot convert 0     Elemwise{neg,no_inplace}.0\n3     
Elemwise{neg,no_inplace}.0\n4     Elemwise{neg,no_inplace}.0\n6     
Elemwise{neg,no_inplace}.0\n8     Elemwise{neg,no_inplace}.0\n9     
Elemwise{neg,no_inplace}.0\n11    Elemwise{neg,no_inplace}.0\n12    
Elemwise{neg,no_inplace}.0\n14    Elemwise{neg,no_inplace}.0\n16    
Elemwise{neg,no_inplace}.0\n17    Elemwise{neg,no_inplace}.0\n18    
Elemwise{neg,no_inplace}.0\n19    Elemwise{neg,no_inplace}.0\n20    
Elemwise{neg,no_inplace}.0\n21    Elemwise{neg,no_inplace}.0\n23    
Elemwise{neg,no_inplace}.0\n25    Elemwise{neg,no_inplace}.0\n28    
Elemwise{neg,no_inplace}.0\n29    Elemwise{neg,no_inplace}.0\nName: 
runningtime_cens, dtype: object to TensorType', <class 
'pandas.core.series.Series'>)*

我要编码的模型与生命线（https://lifelines.readthedocs.io/en/latest/lifelines.fitters.html#module-lifelines.fitters.weibull_aft_fitter）中的类weibull_aft_fitter相同

我的代码是：

import pandas as pd
import numpy as np
import pymc3 as pm
import theano.tensor as tt

# Defining Log complementary cdf of Weibull distribution
def weibull_lccdf(x, alpha, beta):
    ''' Log complementary cdf of Weibull distribution. '''
    return -(x / beta)**alpha

# Importing Weibull data
data_weibull=pd.read_csv("data_weibull.csv")

# censored list
event = data_weibull['event'].values.astype(bool)

# Specifying the model
with pm.Model() as model:

    # Priors for unknown model parameters
    rho = pm.Gamma('rho', alpha=0.001, beta=0.001, testval=2)
    beta = pm.Normal('beta', mu=0, sd=0.001, shape=2, testval=0)

    # Expected value of lambda parameter
    lambda_obs = pm.Deterministic('lambda_obs', \
         tt.exp(beta[0]+beta[1]*data_weibull['temperature'][event]))
    lambda_cens = pm.Deterministic('lambda_cens', \
         tt.exp(beta[0]+beta[1]*data_weibull['temperature'][~event]))

    # Likelihood (sampling distribution) of observations
    runningtime_obs = pm.Weibull('runningtime_obs', alpha=rho, \
         beta=lambda_obs, observed=data_weibull['runningtime'][event])
    runningtime_cens = pm.Potential('runningtime_cens', \
         weibull_lccdf(data_weibull['runningtime'][~event], rho, \ 
         lambda_cens))

nc=3
ni=10000
nb=1000
nt=5

with model:
    # draw ni posterior samples
    step = pm.NUTS(vars=[rho, beta])
    start = pm.find_MAP()
    trace = pm.sample(draws=ni, tune=nb, chains=nc, step=step, cores=1, 
        start=start)


# Posterior analysis
pm.traceplot(trace, varnames=['rho', 'beta'])
pm.summary(trace, varnames=['rho', 'beta']).round(2)
pm.plot_posterior(trace, varnames=['rho', 'beta'])

Answer 1

感谢Cam.Davidson.Pilon，我将熊猫对象转换为numpy数组，如下所示：

# Expected value of lambda parameter
lambda_obs = pm.Deterministic('lambda_obs', \
     tt.exp(beta[0]+beta[1]*data_weibull['temperature'][event].values))
lambda_cens = pm.Deterministic('lambda_cens', \
     tt.exp(beta[0]+beta[1]*data_weibull['temperature'][~event].values))

# Likelihood (sampling distribution) of observations
runningtime_obs = pm.Weibull('runningtime_obs', alpha=rho, \
     beta=lambda_obs, observed=data_weibull['runningtime'][event].values)
runningtime_cens = pm.Potential('runningtime_cens', \
     weibull_lccdf(data_weibull['runningtime'][~event].values, rho, \ 
     lambda_cens))