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added link to preprint
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Löffler, Hannes committed Nov 7, 2023
1 parent 2c99c43 commit c2a784f
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Showing 3 changed files with 9 additions and 6 deletions.
5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -9,8 +9,9 @@ REINVENT is a molecular design tool for de novo design, scaffold hopping,
R-group replacement, linker design, molecule optimization, and other small
molecule design tasks. At its heart, REINVENT uses a Reinforcement Learning
(RL) algorithm to generate optimized molecules compliant with a user defined
property profile defined as a multi-component score. See AUTHORS.md for
paper references.
property profile defined as a multi-component score.

A preprint is available on ChemRxiv: [REINVENT4: Modern AI-Driven Generative Molecule Design](https://chemrxiv.org/engage/chemrxiv/article-details/65463cafc573f893f1cae33a). See AUTHORS.md for references to previous papers.


Requirements
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7 changes: 4 additions & 3 deletions reinvent/runmodes/TL/learning.py
Original file line number Diff line number Diff line change
Expand Up @@ -105,9 +105,10 @@ def __init__(
s = DataStructs.BulkTanimotoSimilarity(fps[n], fps[n + 1 :])
sim.extend(s)

self.tb_reporter.add_histogram(
"Tanimoto input SMILES", np.array(sim), 0
)
# FIXME: TB broken
#self.tb_reporter.add_histogram(
# "Tanimoto input SMILES", np.array(sim), 0
#)

# FIXME: this is only available for Mol2mol
if self._config.max_sequence_length:
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3 changes: 2 additions & 1 deletion reinvent/runmodes/TL/reports/tensorboard.py
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Expand Up @@ -59,7 +59,8 @@ def write_report(reporter, data, model: ModelAdapter, is_reinvent: bool, dataloa

reporter.add_scalar("KL divergence", kl_div, data.epoch)

reporter.add_histogram("Tanimoto similarity on RDKitFingerprint", similarities, data.epoch)
# FIXME: TB broken
#reporter.add_histogram("Tanimoto similarity on RDKitFingerprint", similarities, data.epoch)

# FIXME: rows and cols depend on sample_batch_size
image_tensor = make_grid_image(smilies, sample_nlls, "NLL", ROWS * COLS, ROWS)
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