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README.md

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@@ -46,6 +46,7 @@ python -m chebifier predict --smiles-file smiles.txt
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# Make predictions using a configuration file
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python -m chebifier predict --ensemble-config configs/my_config.yml --smiles-file smiles.txt
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# Get all available options
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python -m chebifier predict --help
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```
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@@ -99,6 +100,7 @@ chebi_lookup:
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to your configuration file.
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### The ensemble
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<img width="700" alt="ensemble_architecture" src="https://github.com/user-attachments/assets/9275d3cd-ac88-466f-a1e9-27d20d67543b" />
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Given a sample (i.e., a SMILES string) and models $m_1, m_2, \ldots, m_n$, the ensemble works as follows:
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1. Get predictions from each model $m_i$ for the sample.
@@ -134,7 +136,7 @@ Trust is based on the model's performance on a validation set. After training, w
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on a validation set for each class. If the `ensemble_type` is set to `wmv-f1`, the trust is calculated as 1 + the F1 score.
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If the `ensemble_type` is set to `mv` (the default), the trust is set to 1 for all models.
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### Inconsistency correction
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### Inconsistency resolution
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After a decision has been made for each class independently, the consistency of the predictions with regard to the ChEBI hierarchy
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and disjointness axioms is checked. This is
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done in 3 steps:

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