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perturbation-bench / README.md
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Regenerate with frame-mismatch exclusion and exact 8192 bp sequences
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metadata 
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 

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 in the Carbon release repo.