EpistasisLab / EpistasisLab/tpot

TPOT optimization gets stuck

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enhancement need contributor question
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Description

I experience that the optimization gets stuck and is not improving anymore after many hours while a new start sometimes gives a better score at the initial population already (!). The dataset is not very complex (50 variables, regression problem, 5000 rows) and i used default settings but also played around with the parameters of the genetic optimization.

What I noticed is that especially when I have poor performance, my log gets flooded with the following messages:

```
_pre_test decorator: _random_mutation_operator: num_test=0 Found array with 0 feature(s) (shape=(50, 0)) while a minimum of 1 is required by RobustScaler..
_pre_test decorator: _random_mutation_operator: num_test=1 Found array with 0 feature(s) (shape=(50, 0)) while a minimum of 1 is required by RobustScaler..
_pre_test decorator: _random_mutation_operator: num_test=2 Found array with 0 feature(s) (shape=(50, 0)) while a minimum of 1 is required by RobustScaler..
_pre_test decorator: _random_mutation_operator: num_test=3 Found array with 0 feature(s) (shape=(50, 0)) while a minimum of 1 is required by RobustScaler..
_pre_test decorator: _random_mutation_operator: num_test=0 Found array with 0 feature(s) (shape=(50, 0)) while a minimum of 1 is required by `RobustScaler.
```

Sometimes I get that warnings 80 times for a population of 100 pipelines. What exactly does the message mean and how can I improve the optimization?

Btw.: Is it possible to pass some initial pipelines to TPOT to start with a better initial population?

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