| --- |
| 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: promoter_revcomp |
| data_files: |
| - split: test |
| path: promoter_revcomp/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-* |
| - config_name: synonymous_codons |
| data_files: |
| - split: train |
| path: synonymous_codons/data.parquet |
| - config_name: tata |
| data_files: |
| - split: train |
| path: tata/data.parquet |
| dataset_info: |
| - 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 |
| - config_name: promoter_revcomp |
| features: |
| - name: benchmark_id |
| dtype: string |
| - name: species |
| dtype: string |
| - name: genome_assembly |
| dtype: string |
| - name: annotation_source |
| dtype: string |
| - name: total_window |
| dtype: int64 |
| - name: prom_up |
| dtype: int64 |
| - name: prom_down |
| dtype: int64 |
| - name: prom_len |
| dtype: int64 |
| - name: chr |
| dtype: string |
| - name: start |
| dtype: int64 |
| - name: end |
| dtype: int64 |
| - name: strand |
| dtype: string |
| - name: tss_1based |
| dtype: int64 |
| - name: epd_id |
| dtype: string |
| - name: gene_id |
| dtype: string |
| - name: tss_in_seq |
| dtype: int64 |
| - name: cds_start_in_seq |
| dtype: int64 |
| - name: cds_end_in_seq |
| dtype: int64 |
| - name: original_sequence |
| dtype: string |
| - name: sequence |
| dtype: string |
| splits: |
| - name: test |
| num_bytes: 272641634 |
| num_examples: 16451 |
| download_size: 125178388 |
| dataset_size: 272641634 |
| - 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 |
| --- |
| |
| # Carbon Perturbation Bench |
|
|
| Two **sequence-level perturbation tasks** for evaluating DNA foundation models: |
|
|
| - **`tata`** (5,000 rows): the TATA-box motif inside a real promoter is |
| disrupted with random nucleotide substitutions. Probes whether the model |
| has internalised eukaryotic promoter architecture (it should assign higher |
| log-likelihood to the intact promoter than the perturbed one). |
| - **`synonymous_codons`** (5,000 rows): codons in a real CDS are replaced |
| with synonyms encoding the same amino acid. Probes whether the model has |
| learned codon-usage bias (it should prefer native codon usage over the |
| synonymous variant). |
| |
| Both subsets share the same schema: |
| |
| | column | description | |
| |---|---| |
| | `chr`, `start`, `end`, `strand` | hg38 locus | |
| | `length` | sequence length in bp | |
| | `original_sequence` | the real (unperturbed) sequence — positive | |
| | `sequence` | the perturbed sequence — negative control | |
| |
| ## Usage |
| |
| ```python |
| from datasets import load_dataset |
| |
| tata = load_dataset("hf-carbon/carbon-perturbation-bench", "tata", split="train") |
| syn = load_dataset("hf-carbon/carbon-perturbation-bench", "synonymous_codons", split="train") |
| ``` |
| |
| ## Eval recipe |
| |
| Pairwise likelihood discrimination: score `LL(original_sequence)` vs |
| `LL(sequence)` under the model, and report `mean(LL(real) >= LL(perturbed))`. |
| A ready-to-run scorer for Carbon, GENERator, and Evo2 lives at |
| [`evaluation/perturbation_tasks.py`](https://github.com/huggingface/carbon) |
| in the Carbon release repo. |
| |
