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Fix dataset loading, and other minor fixes #21

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Fix dataset loading, and other minor fixes #21

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92ece3c
replace np.loads with pkl.loads
christopher-beckham Apr 14, 2024
4182bed
DiskResource is now based on HF datasets
christopher-beckham Apr 20, 2024
34eba51
Complete migration to HF-style disk resource, suppress annoying warni…
christopher-beckham Apr 21, 2024
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4 changes: 2 additions & 2 deletions design_bench/datasets/continuous/ant_morphology_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in ANT_MORPHOLOGY_FILES]

@staticmethod
Expand All @@ -213,7 +213,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in ANT_MORPHOLOGY_FILES]

def __init__(self, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/continuous/dkitty_morphology_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in DKITTY_MORPHOLOGY_FILES]

@staticmethod
Expand All @@ -213,7 +213,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in DKITTY_MORPHOLOGY_FILES]

def __init__(self, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/continuous/hopper_controller_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in HOPPER_CONTROLLER_FILES]

@staticmethod
Expand All @@ -213,7 +213,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in HOPPER_CONTROLLER_FILES]

def __init__(self, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/continuous/superconductor_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in SUPERCONDUCTOR_FILES]

@staticmethod
Expand All @@ -217,7 +217,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in SUPERCONDUCTOR_FILES]

def __init__(self, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/continuous/toy_continuous_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in TOY_CONTINUOUS_FILES]

@staticmethod
Expand All @@ -226,7 +226,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in TOY_CONTINUOUS_FILES]

def __init__(self, **kwargs):
Expand Down
1 change: 1 addition & 0 deletions design_bench/datasets/dataset_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -460,6 +460,7 @@ def __init__(self, x_shards, y_shards, internal_batch_size=32,
self.map_normalize_x()
if is_normalized_y:
self.map_normalize_y()

self.subsample(max_samples=max_samples,
distribution=distribution,
min_percentile=min_percentile,
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/chembl_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -627,7 +627,7 @@ def register_x_shards(assay_chembl_id="CHEMBL1794345",

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in CHEMBL_FILES
if f"{standard_type}-{assay_chembl_id}" in file]

Expand Down Expand Up @@ -660,7 +660,7 @@ def register_y_shards(assay_chembl_id="CHEMBL1794345",

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in CHEMBL_FILES
if f"{standard_type}-{assay_chembl_id}" in file]

Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/cifar_nas_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in NAS_FILES]

@staticmethod
Expand All @@ -238,7 +238,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in NAS_FILES]

def __init__(self, soft_interpolation=0.6, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/gfp_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,7 +229,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in GFP_FILES]

@staticmethod
Expand All @@ -249,7 +249,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in GFP_FILES]

def __init__(self, soft_interpolation=0.6, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/nas_bench_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in NAS_BENCH_FILES]

@staticmethod
Expand All @@ -263,7 +263,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in NAS_BENCH_FILES]

def __init__(self, soft_interpolation=0.6, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/tf_bind_10_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,7 @@ def register_x_shards(transcription_factor='pho4'):

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in TF_BIND_10_FILES
if transcription_factor in file]

Expand Down Expand Up @@ -253,7 +253,7 @@ def register_y_shards(transcription_factor='pho4'):

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in TF_BIND_10_FILES
if transcription_factor in file]

Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/tf_bind_8_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,7 @@ def register_x_shards(transcription_factor='SIX6_REF_R1'):

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in TF_BIND_8_FILES
if transcription_factor in file]

Expand Down Expand Up @@ -253,7 +253,7 @@ def register_y_shards(transcription_factor='SIX6_REF_R1'):

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in TF_BIND_8_FILES
if transcription_factor in file]

Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/toy_discrete_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,7 +231,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in TOY_DISCRETE_FILES]

@staticmethod
Expand All @@ -251,7 +251,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in TOY_DISCRETE_FILES]

def __init__(self, soft_interpolation=0.6, **kwargs):
Expand Down
4 changes: 2 additions & 2 deletions design_bench/datasets/discrete/utr_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,7 @@ def register_x_shards():

return [DiskResource(
file, is_absolute=False,
download_target=f"{SERVER_URL}/{file}",
download_target=file,
download_method="direct") for file in UTR_FILES]

@staticmethod
Expand All @@ -238,7 +238,7 @@ def register_y_shards():

return [DiskResource(
file.replace("-x-", "-y-"), is_absolute=False,
download_target=f"{SERVER_URL}/{file.replace('-x-', '-y-')}",
download_target=file.replace('-x-', '-y-'),
download_method="direct") for file in UTR_FILES]

def __init__(self, soft_interpolation=0.6, **kwargs):
Expand Down
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