Sunbelt Computer Software

PL/B Language Development and Support

add pretraining by sfluegel05 · Pull Request #1 · ChEB-AI/python-chebai-graph · GitHub

add pretraining#1

Merged

sfluegel05 merged 22 commits into

devfrom

feature-pretraining

Nov 29, 2024

Commits on Aug 13, 2024

add pubchem data, transformation for data masking, split resgated net into pretraining and prediction models (untested, incomplete)
sfluegel
committed

Commits on Aug 14, 2024

add pretraining config
sfluegel
committed

Commits on Aug 15, 2024

bug fixes for pretraining
sfluegel
committed

Commits on Aug 16, 2024

add masking loss (actual loss implementation missing)
sfluegel
committed

Commits on Oct 1, 2024

implement loss for masking-task, adapt preprocessing and model
sfluegel
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Commits on Oct 2, 2024

add indices
sfluegel
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fix mask_edge_label placeholder size (needs to be aligned with batch)
sfluegel
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fix mask_edge_label placeholder size (needs to be aligned with batch)
sfluegel
committed

Commits on Oct 29, 2024

add config for pretraining loss, change lr 1e-4 -> 1e-3
sfluegel
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use bce with logits for pretraining loss
sfluegel
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Commits on Nov 4, 2024

fix label post-processing
sfluegel
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Commits on Nov 5, 2024

add checks to model that allow only-atom masking without bond masking, mask atom properties partially
sfluegel
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modify mask loss for atom-only masking
sfluegel
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fix prediction filtering
sfluegel
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split model into atom- and atom-bond-pretraining models
sfluegel
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Commits on Nov 6, 2024

fix postprocessing, make transform reproducible
sfluegel
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add pretrained checkpoint option for resgated, fix config
sfluegel
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add pretrained checkpoint option for resgated
sfluegel
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fix pretrained checkpoint option for resgated
sfluegel
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use chebi file names in new format if available
sfluegel
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fix label processing
sfluegel
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add tokens files
Simon Fluegel
committed