Taykhoom/atg-gamba

GAMBA ATG Contexts

This dataset packages GAMBA's translation-initiation representation benchmark. It samples 2,000 complete MANE Select transcript examples from chr1–chr22, exactly balanced across strand and stratified by chromosome; each example contributes five candidate sites:

1. the true translation start;
2. a nearby noncoding ATG, 2–5 kb away;
3. a far noncoding ATG, at least 100 kb away;
4. a same-transcript in-frame methionine;
5. a same-transcript out-of-frame ATG motif.

The five rows share one pair_id, yielding 10,000 rows per configuration.

Loading

from datasets import load_dataset

bidi = load_dataset("Taykhoom/atg-gamba", "bidi", split="test")
causal = load_dataset("Taykhoom/atg-gamba", "causal", split="test")

Choosing a context

Use the context geometry appropriate for the evaluated model:

Config	Context placement	Intended models
causal	The three-base ATG is end-anchored after strand orientation.	Evo2 and other left-to-right/autoregressive models.
bidi	The three-base ATG is centered in the context.	GAMBA encoders, GPN-Star, PhyloGPN, distilled students, and other bidirectional models.

Every released sequence is exactly 2,048 bp. Using the wrong configuration changes which flanking bases the model can see and does not reproduce the paper protocol.

Evaluation protocol

The source data has five labels:

start
noncoding_near
noncoding_far
inframe_methionine
outframe_atg

For the paper leaderboard, merge:

noncoding_near -> noncoding
noncoding_far  -> noncoding

Then evaluate frozen representations with:

• cosine distance;
• leave-one-out 1-nearest-neighbor classification;
• balanced accuracy.

Exclude all other rows sharing context_group_id with the query from its leave-one-out neighbor candidates. This groups the few exact sequence duplicates without changing the five-row transcript pair_id.

GAMBA's extraction code also reports a separate five-way Euclidean diagnostic. That is not the four-class paper leaderboard.

Dataset size

Label	Rows
start	2,000
noncoding_near	2,000
noncoding_far	2,000
inframe_methionine	2,000
outframe_atg	2,000
Total	10,000

Every row has split == "test" because ATG is a representation benchmark, not a supervised train/test dataset.

Columns

Column	Description
split	Always test.
sequence	Strand-oriented causal or bidirectional context, exactly 2,048 bp.
label, label_id	Source five-way class and numeric ID.
pair_id	Shared by the five sites from one transcript example.
context_group_id	Evaluator leakage group joining transcript examples that share any exact released context.
category, scope	Constant ATG category and roi pooling scope.
context_policy	causal or symmetric.
chrom, start, end, source_strand	Valid contiguous zero-based, half-open hg38 motif interval and biological strand.
sequence_orientation	Explicit +/- orientation used for sequence geometry and reverse complementation.
context_start, context_end	Forward-genome coordinates represented by sequence.
roi_start, roi_end	Three-base site offsets in the strand-oriented sequence.
pool_start_in_window, pool_end_in_window	Exact representation-pooling span; identical to the three-base ROI.
name	Site identifier.
transcript_id, gene_id	Source MANE Select transcript and gene.
motif_genomic_positions	The three genomic base positions in transcript order.
transcript_offset	CDS offset for start/in-frame/out-of-frame motifs; null for noncoding controls.
delta_bp	Transcript offset for coding motifs; oriented first-base displacement for noncoding controls; zero for start.
phylop_*	Six float32 Zoonomia phyloP summaries over the three-base ATG.
phylop_context_*	Six float32 summaries over GAMBA's symmetric 2,048 bp phyloP context.

Strand convention

Minus-strand CDS blocks are reverse-complemented individually while retaining true transcript order. Minus-strand motif positions therefore run from higher to lower genomic coordinates, while start/end stores their enclosing contiguous interval. Noncoding controls are strand-aware (ATG on +, genomic CAT on -). Near/far controls exclude the union of every GENCODE v47 CDS, while coding anchors remain MANE Select. Motifs spanning a CDS splice junction are excluded deterministically rather than represented as a false contiguous interval. Independent verification confirms every emitted oriented ROI equals ATG.

PhyloP

PhyloP comes from the Zoonomia 241-mammalian track used by GAMBA. Uncovered bases become zero, scores are rounded to two decimals before summarization, and outputs are float32.

Processing and verification

The source TSV reconciliation, transcript sampling, context construction, phyloP calculation, output hashes, and exact reference comparison are available at the processing reference below. The corrected chromosome-by-strand cohort retains 1,208 transcript groups from the preceding release and adds 792. It contains 1,000 examples per strand. Three exact contexts shared across six rows are assigned to common leakage groups, and 2,548 detected junction-spanning source motifs are excluded:

• Processing repository
• Processing and validation documentation

Citation

Consens, M. E. et al. Predicting evolutionary rate as a pretraining task improves genome language model representations. bioRxiv (2026). https://doi.org/10.64898/2026.02.02.703275

License

The processing code derived from GAMBA is MIT licensed under the processing repository's LICENSE. This generated dataset is marked other: incorporated reference sequence, annotations, and phyloP-derived values retain their upstream terms, so no blanket MIT license is asserted for the Parquets.