--- 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.