| --- |
| pretty_name: "GAMBA ATG Contexts" |
| license: other |
| tags: |
| - biology |
| - genomics |
| - dna |
| - genome-language-model |
| - benchmark |
| - translation-initiation |
| - hg38 |
| - parquet |
| configs: |
| - config_name: causal |
| data_files: |
| - split: test |
| path: atg-gamba-causal.parquet |
| - config_name: bidi |
| data_files: |
| - split: test |
| path: atg-gamba-bidi.parquet |
| --- |
| |
| # GAMBA ATG Contexts |
|
|
| This dataset packages GAMBA's translation-initiation representation |
| benchmark. GAMBA samples 2,000 complete MANE Select transcript examples from |
| `chr1`–`chr22`; 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 |
|
|
| ```python |
| 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. | |
|
|
| Both sequences are at most 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: |
|
|
| ```text |
| start |
| noncoding_near |
| noncoding_far |
| inframe_methionine |
| outframe_atg |
| ``` |
|
|
| For the paper leaderboard, merge: |
|
|
| ```text |
| noncoding_near -> noncoding |
| noncoding_far -> noncoding |
| ``` |
|
|
| Then evaluate frozen representations with: |
|
|
| - cosine distance; |
| - leave-one-out 1-nearest-neighbor classification; |
| - balanced accuracy. |
|
|
| 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, at most 2,048 bp. | |
| | `label`, `label_id` | Source five-way class and numeric ID. | |
| | `pair_id` | Shared by the five sites from one transcript example. | |
| | `category`, `scope` | Constant `ATG` category and `roi` pooling scope. | |
| | `context_policy` | `causal` or `symmetric`. | |
| | `chrom`, `start`, `end`, `source_strand` | Zero-based, half-open hg38 site coordinates 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. | |
| | `delta_bp` | Signed distance from the true start; 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 |
|
|
| Only minus-strand rows are reverse-complemented. This release preserves the |
| GAMBA source convention for minus-strand three-base ATG intervals: |
| `[position, position + 3)` is extracted and then oriented. |
|
|
| ## 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: |
|
|
| https://github.com/TaykhoomDalal/Gamba-Processing/commit/549985683a1c52014a64c5781937dd25360f1553 |
|
|
| ## 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. |
|
|
