lighteternal/BioAssayAlign-Assay-Compound-Data

BioAssayAlign Assay-Compound Data

What this dataset is

BioAssayAlign Assay-Compound Data is a frozen assay-and-molecule dataset for assay-conditioned ranking and retrieval.

It answers questions like:

• given an assay description, which molecules in a submitted list should rank first?
• which historical assays are closest to this assay?

It is not:

• a chatbot dataset
• a generic pretraining corpus
• a clinical or patient dataset

Companion model:

• BioAssayAlign Qwen3-Embedding-0.6B Compatibility

Companion Space:

• BioAssayAlign Compatibility Explorer

What is included

This public release is focused on the prepared compatibility-ranking subset used by the published model.

Directory: prepared/compatibility-ranking/

Files:

• compat_assays.parquet
• compat_candidate_pools.parquet
• compat_train_groups.parquet
• COMPATIBILITY_PREPARED_MANIFEST.json
• SOURCE_DATASET_MANIFEST.json

This prepared subset is the one used to train the published compatibility model linked above.

For lineage and reproducibility, the release also includes:

• raw/DATASET_MANIFEST.json

That manifest records the frozen upstream sources and hashes for the full raw corpus derived from:

• PubChem BioAssay snapshot dated 2026-03-01
• ChEMBL release chembl_36

The full raw parquet pair is not included in this compact public repo. This repo is intentionally scoped to the prepared subset that reproduces the public model.

Why there are multiple parquet files

prepared/compatibility-ranking/compat_assays.parquet

Prepared assay rows used for compatibility ranking.

prepared/compatibility-ranking/compat_candidate_pools.parquet

Held-out assay candidate pools used for evaluation.

prepared/compatibility-ranking/compat_train_groups.parquet

Training groups with:

• one assay
• one positive molecule
• explicit same-assay negative molecules

Dataset scale

Source frozen corpus referenced by raw/DATASET_MANIFEST.json

Source table	Rows
assays	3,800,882
measurements	323,706,180

Prepared ranking subset used by the public model

File	Rows
compat_assays.parquet	11,195
compat_candidate_pools.parquet	1,432,532
compat_train_groups.parquet	508,216

Split counts:

Split	Assays
train	8,967
val	1,117
test	1,111

Sanitization and privacy

This public dataset does not contain patient data or direct personal identifiers.

Before release, I removed internal-only publishing clutter such as:

• shard outputs from HF CPU prep jobs
• precomputed training feature stores
• private training-only intermediate files

This public repo intentionally excludes:

• shard directories from HF CPU prep jobs
• precomputed training feature stores
• internal benchmark artifacts unrelated to the released model
• local build outputs unrelated to the public model

File schemas

prepared/compatibility-ranking/compat_train_groups.parquet

Important columns:

• assay_uid
• positive_smiles
• positive_smiles_hash
• negative_smiles
• negative_smiles_hashes
• example_weight

This is the core ranking supervision format used by the public model.

Example row

Conceptually, one training observation looks like:

{
  "assay_uid": "pubchem:720659",
  "positive_smiles": "CC1=CC(=O)N(C)C(=O)N1",
  "positive_smiles_hash": "4d6f0d...abc",
  "negative_smiles": [
    "CCOC1=CC=CC=C1",
    "CCN(CC)CCOC1=CC=CC=C1",
    "COC1=CC=CC=C1O"
  ],
  "negative_smiles_hashes": [
    "a1...",
    "b2...",
    "c3..."
  ],
  "example_weight": 1.34
}

How to load it locally

Python / pandas

import pandas as pd

train_groups = pd.read_parquet("prepared/compatibility-ranking/compat_train_groups.parquet")
compat_assays = pd.read_parquet("prepared/compatibility-ranking/compat_assays.parquet")
candidate_pools = pd.read_parquet("prepared/compatibility-ranking/compat_candidate_pools.parquet")

Python / pyarrow

import pyarrow.parquet as pq

train_groups = pq.read_table("prepared/compatibility-ranking/compat_train_groups.parquet")

How this relates to the public model

The published model was trained on:

• prepared/compatibility-ranking/compat_assays.parquet
• prepared/compatibility-ranking/compat_candidate_pools.parquet
• prepared/compatibility-ranking/compat_train_groups.parquet

Published model:

• lighteternal/BioAssayAlign-Qwen3-Embedding-0.6B-Compatibility

Upstream sources

This dataset is derived from public upstream resources including:

• PubChem BioAssay
• ChEMBL

Users are responsible for complying with the attribution and usage terms of the upstream sources.