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mathysgrapotte committed Nov 22, 2024
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Expand Up @@ -41,9 +41,9 @@ Stimulus provides those functionalities
3. **Comprehensive Analysis**:
Generate all-against-all model report to guide data pre-processing decisions

For large scale experiments, we recommend our [nf-core](https://nf-co.re){:target="_blank"} [deepmodeloptim](https://github.com/nf-core/deepmodeloptim){:target="_blank"} pipeline which is still under development and will be released alongside stimulus v1.0.0.
For large scale experiments, we recommend our [nf-core](https://nf-co.re) [deepmodeloptim](https://github.com/nf-core/deepmodeloptim) pipeline which is still under development and will be released alongside stimulus v1.0.0.

📹 Stimulus was featured at the nextflow summit 2024 in Barcelona, which is a nice intoduction to current package capabilities, you can watch the talk [here](https://www.youtube.com/watch?v=dC5p_tXQpEs){:target="_blank"}
📹 Stimulus was featured at the nextflow summit 2024 in Barcelona, which is a nice intoduction to current package capabilities, you can watch the talk [here](https://www.youtube.com/watch?v=dC5p_tXQpEs)



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Perform comprehensive model validation including overfitting detection and out-of-distribution performance testing

6. **Informed Hyperparameter Tuning**:
Encourage tuning strategies that follow [Google's Deep Learning Tuning Playbook](https://github.com/google-research/tuning_playbook){:target="_blank"} [^1]
Encourage tuning strategies that follow [Google's Deep Learning Tuning Playbook](https://github.com/google-research/tuning_playbook) [^1]

7. **Scaling Analysis**:
Generate scaling law reports to understand prototype model behavior at different scales
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### Data encoding

Data in stimulus can take many forms (files, text, images, networks...) in order to support this diversity, stimulus relies on the [encoding module](https://mathysgrapotte.github.io/stimulus-py/reference/stimulus/data/encoding/encoders/#stimulus.data.encoding.encoders.AbstractEncoder){:target="_blank"}. List of available encoders can be found [here](https://mathysgrapotte.github.io/stimulus-py/reference/stimulus/data/encoding/encoders/#stimulus.data.encoding.encoders){:target="_blank"}.
Data in stimulus can take many forms (files, text, images, networks...) in order to support this diversity, stimulus relies on the [encoding module](https://mathysgrapotte.github.io/stimulus-py/reference/stimulus/data/encoding/encoders/#stimulus.data.encoding.encoders.AbstractEncoder). List of available encoders can be found [here](https://mathysgrapotte.github.io/stimulus-py/reference/stimulus/data/encoding/encoders/#stimulus.data.encoding.encoders).

If the provided encoders do not support the type of data you are working with, you can write your own encoder by inheriting from the `AbstractEncoder` class and implementing the `encode`, `decode` and `encode_all` methods.

- `encode` is currently optional, can return a `NotImplementedError` if the encoder does not support encoding a single data point
- `decode` is currently optional, can return a `NotImplementedError` if the encoder does not support decoding
- `encode_all` is called by other stimulus functions, and is expected to return a [`np.array`](https://numpy.org/doc/stable/reference/generated/numpy.array.html){:target="_blank"} .
- `encode_all` is called by other stimulus functions, and is expected to return a [`np.array`](https://numpy.org/doc/stable/reference/generated/numpy.array.html) .

### Expected data format

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- data_type is the column data type.

> NOTE:
> This rigid data format is expected to change once we move to release v1.0.0, data types and information will be defined in a yaml config and only column names will be required in the data, see [this github issue](https://github.com/mathysgrapotte/stimulus-py/issues/24){:target="_blank"}
> This rigid data format is expected to change once we move to release v1.0.0, data types and information will be defined in a yaml config and only column names will be required in the data, see [this github issue](https://github.com/mathysgrapotte/stimulus-py/issues/24)
### Connecting encoders and datasets

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### Loading the data

Finally, once we have defined our encoders, the experiment class and the samplesheet, stimulus will transparently load the data using the [csv.py module](https://mathysgrapotte.github.io/stimulus-py/reference/stimulus/data/csv/#stimulus.data.csv){:target="_blank"}
Finally, once we have defined our encoders, the experiment class and the samplesheet, stimulus will transparently load the data using the [csv.py module](https://mathysgrapotte.github.io/stimulus-py/reference/stimulus/data/csv/#stimulus.data.csv)

csv.py contains two important classes, `CsvLoader` and `CsvProcessing`

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