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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.