Datasets:
File size: 9,404 Bytes
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license: apache-2.0
task_categories:
- text-generation
tags:
- biology
- genomics
- dna
- benchmark
configs:
- config_name: motif_human
data_files:
- split: test
path: motif_human/test-*
- config_name: syn_human
data_files:
- split: test
path: syn_human/test-*
- config_name: syn_mouse
data_files:
- split: test
path: syn_mouse/test-*
dataset_info:
- config_name: syn_human
features:
- name: benchmark_id
dtype: string
- name: script_version
dtype: string
- name: annotation_source
dtype: string
- name: genome_assembly
dtype: string
- name: codon_usage_source
dtype: string
- name: recoding_mode
dtype: string
- name: optimization_rate
dtype: float64
- name: random_seed
dtype: int64
- name: window_size_bp
dtype: int64
- name: species
dtype: string
- name: chr
dtype: string
- name: chrom_length
dtype: int64
- name: strand
dtype: string
- name: cds_genome_start
dtype: int64
- name: cds_genome_end
dtype: int64
- name: window_genome_start
dtype: int64
- name: window_genome_end
dtype: int64
- name: upstream_actual
dtype: int64
- name: downstream_actual
dtype: int64
- name: is_clamped
dtype: int64
- name: transcript_id
dtype: string
- name: gene_id
dtype: string
- name: gene_name
dtype: string
- name: exon_rank
dtype: int64
- name: is_first_exon
dtype: int64
- name: frame
dtype: int64
- name: phase_gtf
dtype: int64
- name: cds_start_in_seq
dtype: int64
- name: cds_end_in_seq
dtype: int64
- name: cds_length
dtype: int64
- name: patch_start_in_seq
dtype: int64
- name: patch_end_in_seq
dtype: int64
- name: patch_length
dtype: int64
- name: n_codons_total
dtype: int64
- name: n_codons_eligible
dtype: int64
- name: n_codons_changed
dtype: int64
- name: fraction_codons_changed
dtype: float64
- name: original_sequence
dtype: string
- name: sequence
dtype: string
splits:
- name: test
num_bytes: 335904126
num_examples: 20000
download_size: 152737063
dataset_size: 335904126
- config_name: syn_mouse
features:
- name: benchmark_id
dtype: string
- name: script_version
dtype: string
- name: annotation_source
dtype: string
- name: genome_assembly
dtype: string
- name: codon_usage_source
dtype: string
- name: recoding_mode
dtype: string
- name: optimization_rate
dtype: float64
- name: random_seed
dtype: int64
- name: window_size_bp
dtype: int64
- name: species
dtype: string
- name: chr
dtype: string
- name: chrom_length
dtype: int64
- name: strand
dtype: string
- name: cds_genome_start
dtype: int64
- name: cds_genome_end
dtype: int64
- name: window_genome_start
dtype: int64
- name: window_genome_end
dtype: int64
- name: upstream_actual
dtype: int64
- name: downstream_actual
dtype: int64
- name: is_clamped
dtype: int64
- name: transcript_id
dtype: string
- name: gene_id
dtype: string
- name: gene_name
dtype: string
- name: exon_rank
dtype: int64
- name: is_first_exon
dtype: int64
- name: frame
dtype: int64
- name: phase_gtf
dtype: int64
- name: cds_start_in_seq
dtype: int64
- name: cds_end_in_seq
dtype: int64
- name: cds_length
dtype: int64
- name: patch_start_in_seq
dtype: int64
- name: patch_end_in_seq
dtype: int64
- name: patch_length
dtype: int64
- name: n_codons_total
dtype: int64
- name: n_codons_eligible
dtype: int64
- name: n_codons_changed
dtype: int64
- name: fraction_codons_changed
dtype: float64
- name: original_sequence
dtype: string
- name: sequence
dtype: string
splits:
- name: test
num_bytes: 336064778
num_examples: 20000
download_size: 152659316
dataset_size: 336064778
- config_name: motif_human
features:
- name: benchmark_id
dtype: string
- name: script_version
dtype: string
- name: annotation_source
dtype: string
- name: genome_assembly
dtype: string
- name: upstream_flank_bp
dtype: int64
- name: motif
dtype: string
- name: actual_motif
dtype: string
- name: patch_len_bp
dtype: int64
- name: start_after_bp
dtype: int64
- name: random_seed
dtype: int64
- name: species
dtype: string
- name: chr
dtype: string
- name: chrom_length
dtype: int64
- name: strand
dtype: string
- name: cds_genome_start
dtype: int64
- name: cds_genome_end
dtype: int64
- name: window_genome_start
dtype: int64
- name: window_genome_end
dtype: int64
- name: upstream_actual
dtype: int64
- name: is_clamped
dtype: int64
- name: transcript_id
dtype: string
- name: gene_id
dtype: string
- name: gene_name
dtype: string
- name: exon_rank
dtype: int64
- name: is_first_exon
dtype: int64
- name: frame
dtype: int64
- name: phase_gtf
dtype: int64
- name: cds_start_in_seq
dtype: int64
- name: cds_end_in_seq
dtype: int64
- name: cds_length
dtype: int64
- name: patch_start_in_cds
dtype: int64
- name: patch_end_in_cds
dtype: int64
- name: patch_start_in_seq
dtype: int64
- name: patch_end_in_seq
dtype: int64
- name: original_sequence
dtype: string
- name: sequence
dtype: string
splits:
- name: test
num_bytes: 334784354
num_examples: 20000
download_size: 152132105
dataset_size: 334784354
---
# Perturbation Bench
A benchmark of **sequence-level perturbation tasks** for evaluating DNA foundation models.
Each task presents pairs of genomic sequences — one real (unperturbed) and one structurally
altered — and asks whether the model assigns higher log-likelihood to the original.
**Metric**: pairwise discrimination accuracy = `mean(LL(original) > LL(perturbed))`
---
## Tasks
### `syn_human` · `syn_mouse` — Synonymous codon substitution (20,000 pairs each)
Codons within a real CDS are replaced with the highest-frequency synonym for the target
species, while the upstream and
downstream flanking sequence is left unchanged. Amino acid identity is preserved by
construction. The model should prefer the natural codon usage over the artificially
optimised variant.
- **Human** (`syn_human`): GENCODE v45 annotations on GRCh38/hg38; codon frequencies from
CoCoPUTs (*H. sapiens* RefSeq CDS); 9,616 unique genes.
- **Mouse** (`syn_mouse`): GENCODE vM34 annotations on GRCm39/mm39; codon frequencies from
CoCoPUTs (*M. musculus* RefSeq CDS); 10,253 unique genes.
- Window size: 8,192 bp centred on the CDS (`cds_start_in_seq` / `cds_end_in_seq`).
- Mean fraction of codons changed: ~55% (range 10–95%).
### `motif_human` — CAG repeat insertion (20,000 pairs) / Triplet Expansion
A 30 bp codon-aligned region beginning 60 bp downstream of the first complete codon of the
CDS exon is replaced with 10 consecutive CAG triplets
(`CAGCAGCAGCAGCAGCAGCAGCAGCAGCAG`), mimicking the pathological trinucleotide repeat
expansions underlying polyglutamine disorders (Huntington's disease, SCAs, DRPLA).
The substitution is length- and reading-frame-preserving (30 bp in, 30 bp out), so the
total window remains 8,192 bp. All sequence outside the patch is identical between
original and perturbed.
- Annotations: GENCODE v45 / GRCh38; all CDS exons (all ranks); 9,705 unique genes.
- Window layout: first complete CDS codon always at position 8,102;
patch always at positions 8,162–8,192 (`patch_start_in_seq`–`patch_end_in_seq`).
For exons with phase 1 or 2, the 1–2 split-codon bases from the preceding exon are
placed immediately before position 8,102, so the upstream genomic context is
8,102 bp (phase 0), 8,101 bp (phase 1), or 8,100 bp (phase 2).
---
## Schema
All configs share the key columns:
| Column | Description |
|---|---|
| `original_sequence` | Real, unperturbed genomic sequence — **positive** |
| `sequence` | Structurally altered sequence — **negative** |
| `cds_start_in_seq` / `cds_end_in_seq` | CDS boundaries within the window (bp offset) |
| `chr`, `strand` | Genomic locus |
| `gene_name`, `transcript_id` | GENCODE annotation |
| `benchmark_id` | Unique row identifier |
Config-specific columns (e.g. `patch_start_in_seq`, `n_codons_changed`,
`fraction_codons_changed`, `codon_usage_source`) are described in the dataset info above.
---
## Usage
```python
from datasets import load_dataset
# Synonymous codon substitution — human
syn_human = load_dataset(
"HuggingFaceBio/perturbation-bench", "syn_human", split="test"
)
# Synonymous codon substitution — mouse
syn_mouse = load_dataset(
"HuggingFaceBio/perturbation-bench", "syn_mouse", split="test"
)
# CAG motif insertion
motif = load_dataset(
"HuggingFaceBio/perturbation-bench", "motif_human", split="test"
)
```
---
## Evaluation
A ready-to-run scorer for Carbon, GENERator, and Evo2 is available at
[`evaluation/perturbation_tasks.py`](https://github.com/huggingface/carbon)
in the Carbon release repository.
```bash
python evaluation/perturbation_tasks.py \
--task syn_human \
--model HuggingFaceBio/Carbon-3B \
--bf16
python evaluation/perturbation_tasks.py \
--task motif_human \
--model arcinstitute/evo2_7b --backend evo2 \
--bf16
```
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