Update dataset card: describe syn_human, syn_mouse, motif_human tasks

README.md

@@ -12,10 +12,6 @@ configs:
   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
@@ -24,352 +20,104 @@ configs:
   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:
+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 (`recoding_mode = "optimize"`, `optimization_rate = 1.0`), 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)
 
-- **`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).
+A 30 bp region within a real human CDS — starting 60 bp downstream of the CDS start —
+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-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.
 
-Both subsets share the same schema:
+- Annotations: GENCODE v45 / GRCh38; 9,705 unique genes.
+- Window layout: ~8,100 bp upstream flank, CDS near the right edge.
 
-| column | description |
+---
+
+## Schema
+
+All configs share the key columns:
+
+| 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 |
+| `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 `dataset_info` above.
+
+---
 
 ## 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")
+# Synonymous codon substitution — human
+syn_human = load_dataset(
+    "HuggingFaceBio/carbon-perturbation-bench", "syn_human", split="test"
+)
+
+# Synonymous codon substitution — mouse
+syn_mouse = load_dataset(
+    "HuggingFaceBio/carbon-perturbation-bench", "syn_mouse", split="test"
+)
+
+# CAG motif insertion
+motif = load_dataset(
+    "HuggingFaceBio/carbon-perturbation-bench", "motif_human", split="test"
+)
 ```
 
-## Eval recipe
+---
+
+## Evaluation
 
-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
+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 repo.
+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
+```