VisiumSA/EditJumps

One antibody sequence in, near neighbours out: insertions, deletions and substitutions placed where related natural sequences actually differ.

• Discrete edit-flow generative model over amino-acid sequences.
• ESM-2 encoder trunk + per-position edit-rate and token heads.
• Trained on aligned antibody homolog pairs to carry one natural sequence to another.

This repo holds weights only. Please check-out the official repo to learn more about the code, docs, training pipeline and evaluation artefacts: https://github.com/VisiumCH/editjumps

🚀 Quickstart

1. Install

git clone git@github.com:VisiumCH/editjumps.git
cd editjumps
uv sync --all-groups

2. Download the weights

pip install -U "huggingface_hub[cli]"
hf download VisiumSA/EditJumps --include "model/*" --local-dir ./weights

From Python:

from huggingface_hub import snapshot_download

folder = snapshot_download("VisiumSA/EditJumps", allow_patterns="model/*")

3. Run inference

From the terminal directly

uv run --group train editjumps edit \
  --sequence QVQLVESGGGLVQPGGSLRLSCAAS \
  --model ./weights/model \
  --rate-head mlp \
  --q-head esm_lm_head \
  --edits 5

Or from Python:

from pathlib import Path

from editjumps.pipeline.train.evoflows import EvoFlowsModel

model = EvoFlowsModel.load_trained(
    Path("weights/model"),
    rate_head="mlp",
    q_head="esm_lm_head",
)

Model details

Model type	Discrete flow matching over insert / delete / substitute
Trunk	Stock facebook/esm2_t12_35M_UR50D — 12 layers, hidden 480, 20 heads, vocab 33
Heads	3 rate heads (mlp) + 2 token heads, FiLM-conditioned on a time MLP
Parameters	35,213,590
Precision	fp32
Input form	Joined VH.VL antibody chains — . is a real token in the ESM-2 vocabulary
Training data	1,660,105 unordered homolog pairs from the OAS paired corpus (2,586,927 VH.VL sequences)
Objective	Bregman rate-matching path (eq. 6), linear kappa schedule
Budget	20,000 steps × batch 16 = 320,000 pairs ≈ 19% of one epoch — not converged, and not claimed to be
Optimizer	Adam, lr 1e-4, constant; no warm-up, decay or weight decay; grad-clip 1.0, seed 0
Best val loss	130.48 at step 18,500
Training cost	3 h on one A100 (0.54 s/step); ~5.8 h on an L4

The trunk is deliberately stock ESM-2 rather than the project's OAS-adapted trunk: EvoFlows §3.4 specifies no domain adaptation, only "the encoder trunk of a pre-trained ESM-2 model".

Citation

Cite this reproduction via CITATION.cff in the source repository. The papers reproduced:

@article{editJumps2026,
  title  = {When Edit Flows are Edit Jumps: replicating Edit Flows and {EvoFlows}},
  author = {Bénédict, Gabriel and Buechler, Melanie and Riera-Solà, Gerard and
            Ancos, Chloé de and Teukam, Yves Gaetan Nana and Freidank, Moritz},
  year   = {2026},
  note   = {arXiv:2609.18745}
}

@article{evoflows2026,
  title  = {EvoFlows: Evolutionary Edit-Based Flow-Matching for Protein Engineering},
  author = {Deutschmann and Ferragu and Bixby},
  year   = {2026},
  note   = {arXiv:2603.11703. ICLR 2026 "AI for Science" workshop}
}

@article{editflows2025,
  title  = {Edit Flows: Flow Matching with Edit Operations},
  author = {Havasi and Karrer and Gat},
  year   = {2025},
  note   = {arXiv:2506.09018. NeurIPS 2025}
}

License

MIT, for both the code and these weights. See the source repository.