Blame for README.md

---
license: other
task_categories:
- other
pretty_name: BEND 2.0
license_name: bend2-source-specific
license_link: LICENSE.md
tags:
- biology
- genomics
- dna
- benchmark
- sequence-design
- bend2
configs:
- config_name: atlas_sequences
  default: true
  data_files:
  - split: data
    path: data/atlas-population.parquet
- config_name: atlas_source_activity
  data_files:
  - split: data
    path: data/atlas-source-activities.parquet
- config_name: atlas_candidate_activity
  data_files:
  - split: data
    path: data/atlas-candidate-activities.parquet
- config_name: sequence_prior
  data_files:
  - split: data
    path: data/prior-panel.parquet
- config_name: siraj_cell_activity
  data_files:
  - split: data
    path: data/siraj_selective.parquet
---

<picture>
  <source media="(max-width: 600px)" srcset="https://huggingface.co/datasets/yhsure/BEND2/resolve/main/media/readme-banner-narrow.svg">
  <img src="https://huggingface.co/datasets/yhsure/BEND2/resolve/main/media/readme-banner.png" alt="BEND 2.0 — Benchmarking the capabilities needed to design DNA">
</picture>

[Paper](https://arxiv.org/abs/2611.03806) · [Code](https://github.com/MachineLearningLifeScience/BEND2) · [Live leaderboard](https://machinelearninglifescience.github.io/BEND2/)

We built BEND 2.0 to test whether genomic models can guide the design of DNA. Across eight tasks, we examine how they predict sequence function, account for cell type and genetic background, and choose sequences that produce a desired response.

<picture>
  <source media="(max-width: 600px) and (prefers-color-scheme: dark)" srcset="https://huggingface.co/datasets/yhsure/BEND2/resolve/main/media/capabilities-narrow-dark.svg">
  <source media="(max-width: 600px)" srcset="https://huggingface.co/datasets/yhsure/BEND2/resolve/main/media/capabilities-narrow-light.svg">
  <source media="(prefers-color-scheme: dark)" srcset="https://huggingface.co/datasets/yhsure/BEND2/resolve/main/media/capabilities-wide-dark.svg">
  <img src="https://huggingface.co/datasets/yhsure/BEND2/resolve/main/media/capabilities-wide-light.svg" alt="Five capabilities: sequence priors, functional prediction, biological context, genetic interactions and genomic design.">
</picture>

This repository contains the data used by the benchmark: fixed sequence panels, prepared measurements and unchanged copies of the larger source files. Download only what you need, or keep the complete **1.39 GB** release locally.

[Browse files](https://huggingface.co/datasets/yhsure/BEND2/tree/main/data) · [File guide](FILES.md) · [Source terms](LICENSE.md) · [Citation](#citation)

## Start with the enhancer sequences

Atlas contains 7,657 sequences used by BEND 2.0. Models learn from 5,246 sequences, then choose among 2,411 candidates to produce a desired pattern of activity across twelve cell types.

```python
import pyarrow.compute as pc
import pyarrow.parquet as pq
from huggingface_hub import hf_hub_download

path = hf_hub_download(
    "yhsure/BEND2",
    "data/atlas-population.parquet",
    repo_type="dataset",
    revision="v1.0",
)
sequences = pq.read_table(path)
candidates = sequences.filter(
    pc.equal(sequences["split"], "candidate")
).select(["id", "sequence"])
```

The table keeps the training, validation and candidate assignments, plus 27 excluded sequences for traceability. The two [activity tables](FILES.md#atlas) contain the measured responses. The viewer above shows each table separately; its `data` label is not a training split.

<details>
<summary><strong>Download the full release or use it with BEND 2.0</strong></summary>

Install `huggingface_hub` to download files; the example above also uses `pyarrow`.

```python
from huggingface_hub import snapshot_download

snapshot_download(
    "yhsure/BEND2",
    repo_type="dataset",
    revision="v1.0",
    local_dir="bend2-data",
    allow_patterns=["data/*", "assets.json", "checksums.json", "LICENSE.md"],
)
```

If you already have the BEND 2.0 evaluation package, point it to this local copy:

```bash
export BEND2_ASSET_DIR="$PWD/bend2-data/data"
bend2 run my_model.py --tasks siraj --output results/my-model
```

The package checks the files against its existing manifest. Its small bundled datasets are unchanged. Model weights and embeddings are separate from this data release.

</details>

## Eight tasks

| Task | What is evaluated | Data |
| :--- | :--- | :--- |
| **Sequence prior** | Recovering a hidden DNA base | 512 GRCh38 windows |
| **Splicing effects** | Predicting how mutations change splicing | 590,104 variants in 466 genes · OpenSplice |
| **Cell differences** | Predicting how a mutation's effect differs between two cells | 170,292 substitutions in 128 elements · Siraj |
| **Tissue identification** | Identifying tissues from predicted expression profiles | 5,782 held-out genes, 51 tissues · GTEx |
| **Genetic interactions** | Predicting how a mutation's effect depends on the surrounding alleles | 68,026 paired mutations in 114 elements · Siraj |
| **Matching a response** | Choosing an edit with a similar effect to a reference edit | 331 targets in 110 elements · Siraj |
| **Cell-selective editing** | Increasing expression in one cell while limiting changes in another | 167,958 substitutions in 127 loci · Siraj |
| **Multi-cell design** | Choosing enhancers for a desired pattern of activity across cells | 16 patterns, 2,411 candidates · Atlas |

BEND 2.0 keeps related genes, elements or sequence families together when splitting data. Preserve these assignments when comparing models. See the [file guide](FILES.md) for the stored tables, measurements and exclusions.

## Data sources

The original studies provide the experiments; BEND 2.0 provides the benchmark selections and prepared files. Please credit both. **Each source retains its own terms**, including Siraj's noncommercial restriction.

| Source | Release | Terms |
| :--- | :--- | :--- |
| **OpenSplice** | [Experimental master table, version 5](https://doi.org/10.6084/m9.figshare.32337414.v5) | CC BY 4.0 |
| **Siraj et al.** | [Saturation mutagenesis](https://doi.org/10.5281/zenodo.15297965) | CC BY-NC 4.0 |
| **Castillo-Hair et al.** | [Atlas of AI-designed enhancers](https://doi.org/10.5281/zenodo.17410822) | CC BY 4.0 |
| **GTEx** | [v10 public expression summaries](https://gtexportal.org/home/datasets) | [GTEx data terms](https://gtexportal.org/home/license) |
| **Genome Reference Consortium / UCSC** | [GRCh38 / hg38](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/README.txt) | Reference assembly terms |

Cell-selective measurements also use ENCODE data from Ryan Tewhey's laboratory; gene coordinates use GENCODE v39. Full acknowledgements and file-specific terms are in [LICENSE.md](LICENSE.md).

The GTEx files are a frozen BEND 2.0 subset of **GTEx v10** and do not necessarily reflect the most current or accurate data available from the GTEx Portal. They contain public aggregate expression, not individual donor records or genotypes.

The original asset manifest is preserved in [assets.json](assets.json). [checksums.json](checksums.json) records the size and SHA-256 of every data file in this release.

## Citation

If you use BEND 2.0, cite the benchmark and the original datasets used in your analysis.

```bibtex
@misc{bjerregaard2026benchmarking,
  title  = {{BEND 2.0}: Benchmarking the Capabilities Needed to Design {DNA}},
  author = {Bjerregaard, Andreas and DeVries, Rachael and
            Brilli, Dionysia Danai and Antoniadis, Panagiotis and Li, Yan and
            Krogh, Anders and Boomsma, Wouter and Winther, Ole and
            Marin, Frederikke Isa},
  year   = {2026},
  eprint = {2611.03806},
  archivePrefix = {arXiv},
  primaryClass = {q-bio.GN},
  url    = {https://arxiv.org/abs/2611.03806}
}
```

[Download .bib](https://huggingface.co/datasets/yhsure/BEND2/resolve/main/BEND2.bib?download=true)