Metadata_InChIKey stringlengths 27 27 | Metadata_SMILES stringlengths 4 225 | ecfp4_2048 listlengths 2.05k 2.05k |
|---|---|---|
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End of preview. Expand in Data Studio
CP-BG-Bench JUMP compounds
Compound fingerprints for the 1,467 unique InChIKeys present in the
cp-bg-bench-anon/jump-{c,s,cd,sd} image datasets. Used as the molecule-side
encoder cache by the CP-BG-Bench framework.
File
ecfp4_log1p_counts_2048.parquet — one row per compound, 1,467 rows.
| column | dtype | meaning |
|---|---|---|
Metadata_InChIKey |
str | join key against the image datasets' metadata.parquet |
Metadata_SMILES |
str | canonical SMILES from JUMP compound.csv.gz |
ecfp4_2048 |
list[float64] (length 2048) | fingerprint values, see below |
Join with image data on Metadata_InChIKey.
Fingerprint definition
These are not binary Morgan fingerprints. Each row is the
log1p(count) of a 2048-bit hashed Morgan fingerprint with radius 2 and
chirality, computed via RDKit:
from rdkit.Chem.rdFingerprintGenerator import GetMorganGenerator
gen = GetMorganGenerator(radius=2, fpSize=2048, includeChirality=True)
counts = gen.GetCountFingerprint(mol).ToList() # int per bit
fp = np.log1p(np.asarray(counts, dtype=np.float32))
So values are ln(count+1): 0 means no substructure hashed to that bit,
0.693 means count=1, 1.099 means count=2, and so on. Roughly 2% of bits are
non-zero per compound; mean active bits per compound is 37.
License
CC0 1.0. Underlying SMILES come from JUMP-CP compound.csv.gz (CC0 1.0).
Anonymous NeurIPS 2026 Datasets and Benchmarks submission; citation on acceptance.
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