ChemSage 7B — Round 1 fused model

ChemSage is a QLoRA-tuned chemistry assistant for drug discovery, fine-tuned on Apple Silicon with MLX-LM.

This is the Round 1 fused model — the initial proof-of-concept on a 7B base; superseded by the 32B rounds.

Model details

Base model mlx-community/Qwen2.5-7B-Instruct-4bit
Fine-tune method QLoRA (RSLoRA, rank 32, scale 64.0)
Adapted layers 16 of 28 transformer layers
Trainable parameters ~26M (0.34% of 7.6B)
Training examples 1,200 (from 1,500 total; 80/10/10 split)
Behaviour classes 8
Training iters 750
Best val loss 0.389 (at iter 675)
Peak memory ~12 GB
Fused model size ~4.2 GB

Evaluation (5-round comparative, 2026-06-29)

Evaluated on 100 shared R5 test examples (seed=42) via eval/compare/eval_compare.py. Scores = examples where all instances correct / 100 examples (per-example pass/fail). Full report: eval/compare/results/compare_20260629_1928.html.

Metric R1 (this) R2 R3 R4 R5
SMILES validity 100% 100% 100% 100% 100%
SMARTS validity N/A 0% 100% 55% 100%
Tool executability 0% 28% 79% 71% 95%
Code attempted 14% 41% 100% 97% 100%
Python extended 36% 34% 78% 69% 99%
Code-then-quote N/A 0% 47% 19% 61%
Numerical fidelity N/A 18% 57% 47% 89%
Rounding precision 100% 100% 98% 98% 99%
Refusal accuracy 98% 98% 97% 98% 100%
QED range 100% 100% 100% 100% 100%
PDB ID validity 100% 100% 100% 100% 100%
PyMOL syntax 77% 97% 89% 89% 90%
Degeneration-free 93% 96% 91% 98% 100%
Overall 72% 63% 87% 80% 95%

Usage

# Download from HuggingFace
huggingface-cli download Dellboy/chem_sage_7b_v1 --local-dir models/chem_sage_7b_v1

mlx_lm.server --model models/chem_sage_7b_v1 --port 8081
.venv/bin/python scripts/chat.py --model models/chem_sage_7b_v1

Training history

Round Val loss Improvement
Round 1 (7B, this model) 0.389
Round 2 (32B) 0.347 10.8% over R1
Round 3 (32B) 0.054 6.4x over R2
Round 4 (32B) 0.041 24% over R3
Round 5 (32B) 0.055 early stop; rank=64, 20k examples

Built by

Marc C. Deller, D.Phil. · marcdeller.com · marc@marcdeller.com

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