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prettify molecular optimization section in README.md #37

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Jul 29, 2024
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prettify molecular optimization section in README.md #37

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18 changes: 9 additions & 9 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -43,12 +43,12 @@ Instructions coming soon...
### Fine-tuning
Instructions coming soon...

### Molecular optimization
In order to run the optimization algorithm, define the Oracle as a class, that is responsible for calculating the Oracle fuction for given molecules.
### Molecular Optimization 🎯
Running the Optimization Algorithm requires two steps:

```python
# Oracle implementation scheme
**Step 1.** Define the Oracle, which is responsible to evaluate the oracle score for the given molecules. Below is presented the Oracle implementation scheme.

```python
class ExampleOracle:
def __init__(self, ...):
# maximum number of oracle calls to make
Expand All @@ -75,14 +75,14 @@ class ExampleOracle:
"""
Specify the stopping condition for the optimization process.
"""
...
return stopping_condition
```

Define configuration and hyperparameters used for the optimization process in a yaml file.
**Step 2**. Define the hyperparameters for the optimization algorithm (such as the pool size, number of similar molecules to have in the prompts, sampling temperature, etc.) in a *.yaml* file.

```yaml
# yaml config scheme

# model_hparams.yaml
checkpoint_path: /path/to/model_dir
tokenizer_path: /path/to/tokenizer_dir

Expand All @@ -97,7 +97,7 @@ rej_sample_config:
... fine tuning hyperparameters ...
```

Putting everything toghether and running the optimization process.
Calling the **optimize** function.

```python
from chemlactica.mol_opt.optimization import optimize
Expand All @@ -119,7 +119,7 @@ optimize(
)
```

[example_run.py]() illustrates a full working example of an optimization run. For more complex examples refer to the [ChemlacticaTestSuit]() repository [mol_opt/run.py]() and [retmol/run_qed.py]() files.
Refer to [example_run.py](https://github.com/YerevaNN/ChemLactica/blob/main/chemlactica/mol_opt/example_run.py) for a full working example of an optimization run. For more complex examples refer to the [ChemlacticaTestSuit]() repository [mol_opt]() and [retmol]() directories.

## Tests
The test for running the a small sized model with the same
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