diff --git a/README.md b/README.md index b893842..bb1d8e6 100644 --- a/README.md +++ b/README.md @@ -15,14 +15,14 @@ The goal of model-based optimization is to find an input **x** that maximizes an Design-Bench can be installed with the complete set of benchmarks via our pip package. ```bash -pip install design-bench[all]==2.0.14 +pip install design-bench[all]==2.0.15 pip install morphing-agents==1.5.1 ``` Alternatively, if you do not have MuJoCo, you may opt for a minimal install. ```bash -pip install design-bench==2.0.14 +pip install design-bench==2.0.15 ``` ## Available Tasks diff --git a/example_iteration_script.py b/example_iteration_script.py new file mode 100644 index 0000000..c6eb5fc --- /dev/null +++ b/example_iteration_script.py @@ -0,0 +1,59 @@ +import pickle as pkl +import design_bench as db +import numpy as np + + +if __name__ == "__main__": + + with open("type_assay_pairs.pkl", "wb") as f: + type_assay_pairs = pkl.load(f) + + all_rank_corr = [] + + for type_name, assay_name in type_assay_pairs: + + task = db.make( + 'ChEMBLMorganFingerprint-FullyConnected-v0', + + dataset_kwargs=dict( + max_samples=None, + distribution=None, + max_percentile=50, + min_percentile=0, + assay_chembl_id=assay_name, + standard_type=type_name), + + oracle_kwargs=dict( + noise_std=0.0, + max_samples=None, + distribution=None, + max_percentile=100, + min_percentile=0, + + feature_extractor=MorganFingerprintFeatures(dtype=np.float32), + + model_kwargs=dict( + hidden_size=512, + activation='relu', + num_layers=2, + epochs=5, + shuffle_buffer=5000, + learning_rate=0.0001), + + split_kwargs=dict( + val_fraction=0.1, + subset=None, + shard_size=50000, + to_disk=True, + disk_target=f"chembl-{type_name}-{assay_name}/split", + is_absolute=False)) + + ) + + print(type_name, assay_name, + task.oracle.params['rank_correlation']) + + all_rank_corr.append(task.oracle.params['rank_correlation']) + + best_type_name, best_assay_name = \ + type_assay_pairs[np.argmax(np.array(all_rank_corr))] diff --git a/setup.py b/setup.py index 5854ec8..21227a7 100644 --- a/setup.py +++ b/setup.py @@ -7,7 +7,7 @@ LONG_DESCRIPTION = readme.read() -setup(name='design-bench', version='2.0.14', license='MIT', +setup(name='design-bench', version='2.0.15', license='MIT', packages=find_packages(include=['design_bench', 'design_bench.*']), description='Design-Bench: Benchmarks for ' 'Data-Driven Offline Model-Based Optimization', @@ -17,7 +17,7 @@ author_email='brandon@btrabucco.com', url='https://github.com/brandontrabucco/design-bench', download_url='https://github.com/' - 'brandontrabucco/design-bench/archive/v2_0_14.tar.gz', + 'brandontrabucco/design-bench/archive/v2_0_15.tar.gz', keywords=['Deep Learning', 'Neural Networks', 'Benchmark', 'Model-Based Optimization'], extras_require={'all': ['gym[mujoco]'], 'cma': ['cma']},