Dr. Florian Wilhelm
March 13th 2016
PyData Amsterdam
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What‘s the best model to
describe our data?
And what does „best“ actually mean?

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Simple model
„Generality“
Complex model
„Best Fit“
Occam‘s Razor:
„It is vain to do with more
what can be done with fewer“

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Simple Model
ℋ1
Complex model
ℋ2
Space of all possible datasets 𝐷

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Simple Model
ℋ1
Complex model
ℋ2
ℋ1 fits only a small subset of 𝐷 well

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Simple Model
ℋ1
Complex model
ℋ2
ℋ2 can fit large parts of 𝐷 well

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Prefer the model with high evidence for a given dataset
Source: D. J. C. MacKay. Bayesian Interpolation. 1992

1. Model fitting: Assume ℋ𝑖 is the right model and fit its parameters 𝒘 with Bayes:
𝑃 𝒘 𝐷, ℋ𝑖 =
𝑃 𝐷 𝒘, ℋ𝑖 𝑃(𝒘|ℋ𝑖)
𝑃(𝐷|ℋ𝑖)
“Business as usual”
2. Model comparison: Compare different models with the help of their evidence
𝑃 𝐷 ℋ𝑖 and model prior 𝑃 ℋ𝑖 :
𝑃 ℋ𝑖 𝐷 ∝ 𝑃 𝐷 ℋ𝑖 𝑃 ℋ𝑖
“Occam‘s razor at work“
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Marginalize & approximate:
𝑃 𝐷 ℋ𝑖 = 𝑃 𝐷 𝒘, ℋ𝑖 𝑃 𝒘 ℋ𝑖 𝑑𝒘
𝑃 𝐷 ℋ𝑖 ≅ 𝑃 𝐷 𝒘 𝑀𝑃, ℋ𝑖 𝑃 𝒘 𝑀𝑃 ℋ𝑖 ∆𝒘
𝑒𝑣𝑖𝑑𝑒𝑛𝑐𝑒 ≅ 𝑏𝑒𝑠𝑡 𝑓𝑖𝑡 𝑙𝑖𝑘𝑒𝑙𝑖ℎ𝑜𝑜𝑑 × 𝑂𝑐𝑐𝑎𝑚 𝑓𝑎𝑐𝑡𝑜𝑟
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Occam factor:
∆𝒘
∆ 𝟎 𝒘
Source: D. J. C. MacKay. Bayesian Interpolation. 1992

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Given:
 Dataset 𝐷 = 𝑥 𝑛, 𝑡 𝑛 with 𝑛 = 1 … 𝑁
 Set of (non-linear) functions Φ = {𝜙ℎ: 𝑥 ⟼ 𝜙(𝑥)} with ℎ = 1 … 𝑀
Assumption:
𝑦 𝒙; 𝒘 =
ℎ=1
𝑀
𝑤ℎ 𝜙ℎ(𝒙) ,
𝑡 𝑛 = 𝑦 𝒙; 𝒘 + 𝜐 𝑛,
where 𝜐 𝑛 is an additive noise with 𝒩 0, 𝛼−1
Task: Find min
𝒘
‖Φ𝒘 − 𝒕‖2
(Ordinary Least Squares)
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Problem:
Having too many features leads to overfitting!
Regularization
Assumption: „Weights are small“
𝑝 𝒘; 𝜆 ~𝒩(0, 𝜆−1 𝕀)
Task: Given 𝛼, 𝜆 find
min
𝒘
𝛼 Φ𝒘 − 𝒕 2 + 𝜆 𝒘 2

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Consider each 𝛼𝑖, 𝜆𝑖 defining a model ℋ𝑖 𝛼, 𝜆 .
Yes! That means we can use
our Bayesian Interpolation to
find 𝒘, 𝜶, 𝝀 with the highest
evidence!
This is the idea behind BayesianRidge as found in sklearn.linear_model

Consider that each weight has an individual variance, so that
𝑝 𝒘 𝝀 ~𝒩 0, Λ−1 ,
where Λ = diag(𝜆1, … , 𝜆 𝐻), 𝜆ℎ ∈ ℝ+.
Now, our minimization problem is:
min
𝒘
𝛼 Φ𝒘 − 𝒕 2 + 𝒘 𝑡Λ𝒘
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Pruning: If precision 𝜆ℎ of feature ℎ is high, its weight 𝑤ℎ is very likely to
be close to zero and is therefore pruned.
This is called Sparse Bayesian Learning or Automatic Relevance
Determination. Found as ARDRegression under sklearn.linear_model.

Crossvalidation can be used for the estimation of hyperparmeters but suffers from
the curse of dimensionality (inappropriate for low-statistics).
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Source: Peter Ellerton, http://pactiss.org/2011/11/02/bayesian-inference-homo-bayesianis/

• Random 100 × 100 design matrix Φ with 100 samples and 100
features
• Weights 𝑤𝑖, 𝑖 ∈ 𝐼 = 1, … , 100 , random subset J ⊂ 𝐼 with 𝐽 = 10, and
𝑤𝑖 =
0, 𝑖 ∈ 𝐼J
𝒩(𝑤𝑖; 0, 1
4), 𝑖 ∈ 𝐽
• Target 𝒕 = Φ𝒘 + 𝝂 with random noise 𝜈𝑖 ∼ 𝒩(0, 1
50)
Task: Reconstruct the weights, especially the 10 non-zero weights!
Source: http://scikit-learn.org/stable/auto_examples/linear_model/plot_ard.html#example-linear-model-plot-ard-py
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We have to determine the parameters 𝑤, 𝜆, 𝛼 for
𝑃 𝒘, 𝝀, 𝛼 𝒕 = 𝑃 𝒘 𝒕, 𝝀, 𝛼 𝑃 𝝀, 𝛼 𝒕
1) Model fitting:
For the first factor, we have 𝑃 𝒘 𝒕, 𝝀, 𝛼 ~𝒩(𝝁, Σ) with
Σ = Λ + 𝛼Φ 𝑇
Φ −1
,
𝝁 = 𝛼ΣΦT 𝐭.
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2) Model comparison:
For the second factor, we have
𝑃 𝝀, 𝛼 𝒕 ∝ 𝑃 𝒕 𝝀, 𝛼 𝑃 𝝀 𝑃 𝛼 ,
where 𝑃 𝝀 and 𝑃(𝛼) are hyperpriors which we assume uniform.
Using marginalization, we have
𝑃 𝒕 𝝀, 𝛼 = 𝑃 𝒕 𝒘, 𝛼 𝑃 𝒘 𝝀 𝑑𝒘,
i.e. marginal likelihood or the “evidence for the hyperparameter“.
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Differentiation of the log marginal likelihood with respect to 𝜆𝑖 and 𝛼 as
well as setting these to zero, we get
𝜆𝑖 =
𝛾𝑖
𝜇𝑖
2 ,
𝛼 =
𝑁 − 𝑖 𝛾𝑖
𝒕 − Φ𝝁 2
,
with 𝛾𝑖 = 1 − 𝜆𝑖Σ𝑖𝑖.
These formulae are used to find the maximum points 𝝀 𝑀𝑃 and 𝛼 𝑀𝑃.
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1. Starting values 𝛼 = 𝜎−2(𝒕), 𝝀 = 𝟏
2. Calculate Σ = Λ + 𝛼Φ 𝑇Φ −1 and 𝒘 = 𝝁 = 𝛼ΣΦT 𝐭
3. Update 𝜆𝑖 =
𝛾 𝑖
𝜇 𝑖
2 and 𝛼 =
𝑁− 𝑖 𝛾 𝑖
𝒕−Φ𝝁 2 where 𝛾𝑖 = 1 − 𝜆𝑖Σ𝑖𝑖
4. Prune 𝜆𝑖 and 𝜙𝑖 if 𝜆𝑖 > 𝜆 𝑡ℎ𝑟𝑒𝑠ℎ𝑜𝑙𝑑
5. If not converged go to 2.
Sklearn implementation:
The parameters 𝛼1, 𝛼2 as well as 𝜆1, 𝜆2 are the hyperprior parameters
for 𝛼 and 𝝀 with
𝑃 𝛼 ∼ Γ 𝛼1, 𝛼2
−1
, 𝑃 𝜆𝑖 ∼ Γ 𝜆1, 𝜆2
−1
.
𝐸 Γ 𝛼, 𝛽 =
𝛼
𝛽
and 𝑉 Γ 𝛼, 𝛽 =
𝛼
𝛽2.
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Given a some new data 𝑥∗, a prediction for 𝑡∗ is made by
𝑃 𝑡∗ 𝒕, 𝝀 𝑀𝑃, 𝛼 𝑀𝑃 = 𝑃 𝑡∗ 𝒘, 𝛼 𝑀𝑃 𝑃 𝒘 𝒕, 𝝀 𝑀𝑃, 𝛼 𝑀𝑃 𝑑𝒘
= 𝒩 𝝁 𝑇 𝜙 𝑥∗ , 𝛼 𝑀𝑃
−1
+ 𝜙 𝑥∗
𝑡Σ𝜙 𝑥∗ .
This is a good approximation of the predictive distribution
𝑃 𝑡∗ 𝒕 = 𝑃 𝑡∗ 𝒘, 𝝀, 𝛼 𝑃 𝒘, 𝝀, 𝛼 𝒕 𝑑𝒘 𝑑𝝀 𝑑α .
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1. D. J. C. MacKay. Bayesian Interpolation. 1992
(… to understand the overall idea)
2. M. E.Tipping. Sparse Bayesian learning and the RelevanceVector
Machine. June, 2001
(… to understand the ARD algorithm)
3. T. Fletcher. RelevanceVector Machines Explained. October, 2010
(… to understand the ARD algorithm in detail)
4. D.Wipf. A NewView of Automatic Relevance Determination. 2008
(… not as good as the ones above)
Graphs from slides 7 and 9 were taken from [1] and the awesome
tutorials of Scikit-Learn were consulted many times.
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