metadata
license: mit
language:
- en
tags:
- pharmacore
- sparse
- drug-discovery
- apple-silicon
- protein-language-model
- esm2
- bioinformatics
- computational-biology
- pruning
- efficient-inference
library_name: transformers
pipeline_tag: feature-extraction
base_model: facebook/esm2_t12_35M_UR50D
model-index:
- name: esm2-35m-sparse50
results:
- task:
type: feature-extraction
name: Protein Embedding
metrics:
- type: cosine_similarity
value: 0.973
name: Quality Retention vs Dense
ESM-2 35M Sparse 50% — PharmaCore
A 50% magnitude-pruned version of facebook/esm2_t12_35M_UR50D optimized for efficient drug discovery inference on Apple Silicon.
Why This Model?
| Metric | Dense (Original) | Sparse (This) | Improvement |
|---|---|---|---|
| Parameters (active) | 33.5M | 16.7M | 50% reduction |
| Inference (M4 MPS) | 8.2ms | 7.8ms | 5% faster |
| Quality Retention | 100% | 97.3% | Minimal loss |
Use Case
Primary protein encoder in the PharmaCore drug discovery pipeline:
- Higher-capacity protein embeddings for drug-target compatibility
- De novo drug discovery and drug repurposing workflows
- Full audit trail support for regulatory transparency
- Runs entirely on consumer Apple Silicon hardware (M1/M2/M3/M4)
Usage
from transformers import AutoModel, AutoTokenizer
import torch
model = AutoModel.from_pretrained("stephenjun8192/esm2-35m-sparse50")
tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t12_35M_UR50D")
# Encode a protein target (e.g., EGFR kinase domain)
sequence = "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVL"
inputs = tokenizer(sequence, return_tensors="pt")
with torch.no_grad():
outputs = model(**inputs)
embedding = outputs.last_hidden_state.mean(dim=1) # [1, 480]
print(f"Embedding shape: {embedding.shape}")
Sparsification Method
- Technique: Global magnitude pruning (unstructured)
- Sparsity: 50% of all weight parameters set to zero
- Layers pruned: All linear layers (attention Q/K/V/O, FFN)
- Validation: Cosine similarity of embeddings vs dense model ≥ 0.973
Benchmarks (Apple M4 Mac mini, 16GB)
| Task | Time |
|---|---|
| Single protein embedding (160aa) | 7.8ms |
| Batch of 10 proteins | ~65ms |
| De novo discovery (5 molecules) | ~7s |
| Drug repurposing (12 drugs) | ~18s |
Part of PharmaCore
PharmaCore — the first AI drug discovery platform that runs entirely on a MacBook. No cloud GPUs, no API keys, no data leaves your machine.
Citation
@software{pharmacore2026,
title={PharmaCore: Apple Silicon-Native AI Drug Discovery},
author={Stephen Wu},
year={2026},
url={https://github.com/reacherwu/PharmaCore}
}