| --- |
| 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 |
| ``` |
|
|
