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Implement independent batch size for embedding fingerprints #133

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Merged
JJ-Pineda merged 2 commits into from
Jan 7, 2025
Merged

Implement independent batch size for embedding fingerprints #133

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6007969
set batch size to 100 for embedding fingerprints
JJ-Pineda Jan 7, 2025
89a9fc8
actually, compromise and set batch size to 200 as this makes things a…
JJ-Pineda Jan 7, 2025
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30 changes: 24 additions & 6 deletions src/indexing/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -138,18 +138,36 @@ pub fn batch_doc_creation(
})
.collect::<Vec<_>>();

let mut morgan_fingerprints: Vec<Fingerprint> = Vec::with_capacity(mol_attributes.len());
let mut morgan_bitvecs: Vec<BitVec<u8>> = Vec::with_capacity(mol_attributes.len());
let batch_size = 200;
let num_compounds = mol_attributes.len();
let num_batches = (num_compounds as f32 / batch_size as f32).ceil() as usize;
let mut similarity_clusters: Vec<Vec<Vec<i32>>> = Vec::with_capacity(num_batches);
let mut morgan_bitvecs: Vec<BitVec<u8>> = Vec::with_capacity(batch_size);

for attributes in &mol_attributes {
let morgan_fp = attributes.morgan_fingerprint.clone();
morgan_fingerprints.push(morgan_fp.clone());
morgan_bitvecs.push(morgan_fp.0);

if morgan_bitvecs.len() == batch_size {
let similarity_cluster_batch = encode_fingerprints(&morgan_bitvecs, true)
.map_err(|e| eyre::eyre!("Failed batched similarity cluster assignment: {e}"))?;

similarity_clusters.push(similarity_cluster_batch);
morgan_bitvecs.clear();
}
}

let similarity_clusters = encode_fingerprints(&morgan_bitvecs, true)
.map_err(|e| eyre::eyre!("Failed batched similarity cluster assignment: {e}"))?;
if !morgan_bitvecs.is_empty() {
let similarity_cluster_batch = encode_fingerprints(&morgan_bitvecs, true)
.map_err(|e| eyre::eyre!("Failed batched similarity cluster assignment: {e}"))?;

let num_compounds = mol_attributes.len();
similarity_clusters.push(similarity_cluster_batch);
}

let similarity_clusters = similarity_clusters
.into_iter()
.flatten()
.collect::<Vec<Vec<i32>>>();

let docs = (0..num_compounds)
.into_par_iter()
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