graphium
¶
Usage:
$ graphium [OPTIONS] COMMAND [ARGS]...
Options:
--help
: Show this message and exit.
Commands:
data
: Graphium datasets.finetune
: Utility CLI for extra fine-tuning utilities.
graphium data
¶
Graphium datasets.
Usage:
$ graphium data [OPTIONS] COMMAND [ARGS]...
Options:
--help
: Show this message and exit.
Commands:
download
: Download a Graphium dataset.list
: List available Graphium dataset.prepare
: Prepare a Graphium dataset.
graphium data download
¶
Download a Graphium dataset.
Usage:
$ graphium data download [OPTIONS] NAME OUTPUT
Arguments:
NAME
: [required]OUTPUT
: [required]
Options:
--progress / --no-progress
: [default: progress]--help
: Show this message and exit.
graphium data list
¶
List available Graphium dataset.
Usage:
$ graphium data list [OPTIONS]
Options:
--help
: Show this message and exit.
graphium data prepare
¶
Prepare a Graphium dataset.
Usage:
$ graphium data prepare [OPTIONS] OVERRIDES...
Arguments:
OVERRIDES...
: [required]
Options:
--help
: Show this message and exit.
graphium finetune
¶
Utility CLI for extra fine-tuning utilities.
Usage:
$ graphium finetune [OPTIONS] COMMAND [ARGS]...
Options:
--help
: Show this message and exit.
Commands:
admet
: Utility CLI to easily fine-tune a model on...fingerprint
: Endpoint for getting fingerprints from a...
graphium finetune admet
¶
Utility CLI to easily fine-tune a model on (a subset of) the benchmarks in the TDC ADMET group.
A major limitation is that we cannot use all features of the Hydra CLI, such as multiruns.
Usage:
$ graphium finetune admet [OPTIONS] OVERRIDES...
Arguments:
OVERRIDES...
: [required]
Options:
--name TEXT
--inclusive-filter / --no-inclusive-filter
: [default: inclusive-filter]--help
: Show this message and exit.
graphium finetune fingerprint
¶
Endpoint for getting fingerprints from a pretrained model.
The pretrained model should be a .ckpt
path or pre-specified, named model within Graphium.
The fingerprint layer specification should be of the format module:layer
.
If specified as a list, the fingerprints from all the specified layers will be concatenated.
See the docs of the graphium.finetuning.fingerprinting.Fingerprinter
class for more info.
Usage:
$ graphium finetune fingerprint [OPTIONS] FINGERPRINT_LAYER_SPEC... PRETRAINED_MODEL SAVE_DESTINATION
Arguments:
FINGERPRINT_LAYER_SPEC...
: [required]PRETRAINED_MODEL
: [required]SAVE_DESTINATION
: [required]
Options:
--output-type TEXT
: Either numpy (.npy) or torch (.pt) output [default: torch]-o, --override TEXT
: Hydra overrides--help
: Show this message and exit.