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pawel-czyz committed Mar 5, 2024
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Expand Up @@ -52,7 +52,7 @@ ksg = bmi.estimators.KSGEnsembleFirstEstimator(neighborhoods=(5,))
print(f"Estimate by KSG: {ksg.estimate(X, Y):.2f}")
```

### Evaluating a new estimator
## Evaluating a new estimator

The above code snippet may be convenient for estimating mutual information on a given data set or for the development of a new mutual information estimator.
However, for extensive benchmarking it may be more convenient to use one of the benchmark suites available in the `workflows/benchmark/` subdirectory.
Expand All @@ -64,9 +64,11 @@ $ snakemake -c4 -s workflows/benchmark/demo/run.smk
```

In about a minute it should generate minibenchmark results in the `generated/benchmark/demo` directory. Note that the configuration file, `workflows/benchmark/demo/config.py`, explicitly defines the estimators and tasks used, as well as the number of samples.
Hence, it is easy to benchmark a custom Python estimator by importing it and including it in the configuration dictionary.
Similarly, it is easy to change the number of samples or adjust the tasks included in the benchmark.

Hence, it is easy to benchmark a custom estimator by importing it and including it in the configuration dictionary.
More information is available [here](https://cbg-ethz.github.io/bmi/benchmarking-new-estimator/), where we cover evaluating new Python as well as non-Python estimators.

Similarly, it is easy to change the number of samples or adjust the tasks included in the benchmark.
We defined several benchmark suites with shared structure.

## List of implemented estimators
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