Pymc3 model where the results of a switch are directly observed
I have just started learning pymc3 so I might be thinking about this completely the wrong way.
Assume that we observe a vector of 10 booleans.
The process of interest generates (observed) booleans with a Bernoulli distribution with a parameter theta1. So I define a Beta prior over theta1 and define a variable with length 10 that is a sample from Bernoulli(theta1).
However, this true sample is disturbed by sometimes switching the true data to 0, with a probability theta2. So I define a switch to 0 with a probability Bernoulli(theta2).
The switched values are the observed ones. I am not sure how to tell the model that I observed the switched variables, i.e. I am not sure how to fit the model to the observed data.
This is what I have for now, and I am kind of stuck:
# observed data (already switched)
observed_data = np.random.binomial(1, 0.5, size=10)
with pm.Model() as skeptic_model:
# uniform probability of the bernoulli parameter
true_model_prior = pm.Beta("true_model_prior", 1, 1)
true_data = pm.Bernoulli("true_data", p=true_model_prior, shape=data.shape)
disturbed_data = pm.math.switch(pm.Bernoulli("disturbed", 0.1), true_data, 0)
python-3.x pymc3
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
add a comment |
I have just started learning pymc3 so I might be thinking about this completely the wrong way.
Assume that we observe a vector of 10 booleans.
The process of interest generates (observed) booleans with a Bernoulli distribution with a parameter theta1. So I define a Beta prior over theta1 and define a variable with length 10 that is a sample from Bernoulli(theta1).
However, this true sample is disturbed by sometimes switching the true data to 0, with a probability theta2. So I define a switch to 0 with a probability Bernoulli(theta2).
The switched values are the observed ones. I am not sure how to tell the model that I observed the switched variables, i.e. I am not sure how to fit the model to the observed data.
This is what I have for now, and I am kind of stuck:
# observed data (already switched)
observed_data = np.random.binomial(1, 0.5, size=10)
with pm.Model() as skeptic_model:
# uniform probability of the bernoulli parameter
true_model_prior = pm.Beta("true_model_prior", 1, 1)
true_data = pm.Bernoulli("true_data", p=true_model_prior, shape=data.shape)
disturbed_data = pm.math.switch(pm.Bernoulli("disturbed", 0.1), true_data, 0)
python-3.x pymc3
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
Before usingpymc3, you have to create that second array, the one with the switched values. How do you do it?
– David
Nov 13 '18 at 6:41
add a comment |
I have just started learning pymc3 so I might be thinking about this completely the wrong way.
Assume that we observe a vector of 10 booleans.
The process of interest generates (observed) booleans with a Bernoulli distribution with a parameter theta1. So I define a Beta prior over theta1 and define a variable with length 10 that is a sample from Bernoulli(theta1).
However, this true sample is disturbed by sometimes switching the true data to 0, with a probability theta2. So I define a switch to 0 with a probability Bernoulli(theta2).
The switched values are the observed ones. I am not sure how to tell the model that I observed the switched variables, i.e. I am not sure how to fit the model to the observed data.
This is what I have for now, and I am kind of stuck:
# observed data (already switched)
observed_data = np.random.binomial(1, 0.5, size=10)
with pm.Model() as skeptic_model:
# uniform probability of the bernoulli parameter
true_model_prior = pm.Beta("true_model_prior", 1, 1)
true_data = pm.Bernoulli("true_data", p=true_model_prior, shape=data.shape)
disturbed_data = pm.math.switch(pm.Bernoulli("disturbed", 0.1), true_data, 0)
python-3.x pymc3
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
I have just started learning pymc3 so I might be thinking about this completely the wrong way.
Assume that we observe a vector of 10 booleans.
The process of interest generates (observed) booleans with a Bernoulli distribution with a parameter theta1. So I define a Beta prior over theta1 and define a variable with length 10 that is a sample from Bernoulli(theta1).
However, this true sample is disturbed by sometimes switching the true data to 0, with a probability theta2. So I define a switch to 0 with a probability Bernoulli(theta2).
The switched values are the observed ones. I am not sure how to tell the model that I observed the switched variables, i.e. I am not sure how to fit the model to the observed data.
This is what I have for now, and I am kind of stuck:
# observed data (already switched)
observed_data = np.random.binomial(1, 0.5, size=10)
with pm.Model() as skeptic_model:
# uniform probability of the bernoulli parameter
true_model_prior = pm.Beta("true_model_prior", 1, 1)
true_data = pm.Bernoulli("true_data", p=true_model_prior, shape=data.shape)
disturbed_data = pm.math.switch(pm.Bernoulli("disturbed", 0.1), true_data, 0)
python-3.x pymc3
python-3.x pymc3
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
asked Nov 10 '18 at 17:07
whatamesswhatamess
639
639
Before usingpymc3, you have to create that second array, the one with the switched values. How do you do it?
– David
Nov 13 '18 at 6:41
add a comment |
Before usingpymc3, you have to create that second array, the one with the switched values. How do you do it?
– David
Nov 13 '18 at 6:41
Before using
pymc3, you have to create that second array, the one with the switched values. How do you do it?– David
Nov 13 '18 at 6:41
Before using
pymc3, you have to create that second array, the one with the switched values. How do you do it?– David
Nov 13 '18 at 6:41
add a comment |
1 Answer
1
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oldest
votes
Your model can be reframed as a product of Bernoulli random variables, and therefore as a single Bernoulli random variable with a multiplicative p. Namely, the following model is equivalent to yours:
# observed data (already considered zero-inflated)
Y = np.random.binomial(1, 0.5, size=10)
with pm.Model() as zero_inflated_beta_bernoulli:
# true_model_prior
p = pm.Beta('p', alpha=1, beta=1)
# dropout rate
d = 0.1
# disturbed_data;
y = pm.Bernoulli('y', p = (1-d)*p, observed=Y)
You could let the dropout rate also be a random variable,
# dropout rate
d = pm.Beta('d', mu=0.1, sd=0.02)
However, it should be noted that this model really can't distinguish between dropouts and original outcomes, so the posteriors are sensitive to the priors.
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
Your model can be reframed as a product of Bernoulli random variables, and therefore as a single Bernoulli random variable with a multiplicative p. Namely, the following model is equivalent to yours:
# observed data (already considered zero-inflated)
Y = np.random.binomial(1, 0.5, size=10)
with pm.Model() as zero_inflated_beta_bernoulli:
# true_model_prior
p = pm.Beta('p', alpha=1, beta=1)
# dropout rate
d = 0.1
# disturbed_data;
y = pm.Bernoulli('y', p = (1-d)*p, observed=Y)
You could let the dropout rate also be a random variable,
# dropout rate
d = pm.Beta('d', mu=0.1, sd=0.02)
However, it should be noted that this model really can't distinguish between dropouts and original outcomes, so the posteriors are sensitive to the priors.
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
add a comment |
Your model can be reframed as a product of Bernoulli random variables, and therefore as a single Bernoulli random variable with a multiplicative p. Namely, the following model is equivalent to yours:
# observed data (already considered zero-inflated)
Y = np.random.binomial(1, 0.5, size=10)
with pm.Model() as zero_inflated_beta_bernoulli:
# true_model_prior
p = pm.Beta('p', alpha=1, beta=1)
# dropout rate
d = 0.1
# disturbed_data;
y = pm.Bernoulli('y', p = (1-d)*p, observed=Y)
You could let the dropout rate also be a random variable,
# dropout rate
d = pm.Beta('d', mu=0.1, sd=0.02)
However, it should be noted that this model really can't distinguish between dropouts and original outcomes, so the posteriors are sensitive to the priors.
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
add a comment |
Your model can be reframed as a product of Bernoulli random variables, and therefore as a single Bernoulli random variable with a multiplicative p. Namely, the following model is equivalent to yours:
# observed data (already considered zero-inflated)
Y = np.random.binomial(1, 0.5, size=10)
with pm.Model() as zero_inflated_beta_bernoulli:
# true_model_prior
p = pm.Beta('p', alpha=1, beta=1)
# dropout rate
d = 0.1
# disturbed_data;
y = pm.Bernoulli('y', p = (1-d)*p, observed=Y)
You could let the dropout rate also be a random variable,
# dropout rate
d = pm.Beta('d', mu=0.1, sd=0.02)
However, it should be noted that this model really can't distinguish between dropouts and original outcomes, so the posteriors are sensitive to the priors.
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
Your model can be reframed as a product of Bernoulli random variables, and therefore as a single Bernoulli random variable with a multiplicative p. Namely, the following model is equivalent to yours:
# observed data (already considered zero-inflated)
Y = np.random.binomial(1, 0.5, size=10)
with pm.Model() as zero_inflated_beta_bernoulli:
# true_model_prior
p = pm.Beta('p', alpha=1, beta=1)
# dropout rate
d = 0.1
# disturbed_data;
y = pm.Bernoulli('y', p = (1-d)*p, observed=Y)
You could let the dropout rate also be a random variable,
# dropout rate
d = pm.Beta('d', mu=0.1, sd=0.02)
However, it should be noted that this model really can't distinguish between dropouts and original outcomes, so the posteriors are sensitive to the priors.
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
edited Nov 14 '18 at 22:59
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
answered Nov 13 '18 at 18:31
mervmerv
25.1k673109
25.1k673109
add a comment |
add a comment |
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Before using
pymc3, you have to create that second array, the one with the switched values. How do you do it?– David
Nov 13 '18 at 6:41