README.md

---
pretty_name: "GAMBA Functional Region Multiclass"
license: other
tags:
- biology
- genomics
- dna
- regulatory-genomics
- genome-language-model
- multiclass-classification
- benchmark
- hg38
- parquet
configs:
- config_name: full-causal
  data_files:
  - split: all
    path: functional-multiclass-gamba-full-causal.parquet
- config_name: full-bidi
  data_files:
  - split: all
    path: functional-multiclass-gamba-full-bidi.parquet
- config_name: 100bp-causal
  data_files:
  - split: all
    path: functional-multiclass-gamba-100bp-causal.parquet
- config_name: 100bp-bidi
  data_files:
  - split: all
    path: functional-multiclass-gamba-100bp-bidi.parquet
---

# GAMBA Functional Region Multiclass

This representation benchmark asks whether frozen sequence embeddings
separate genomic functional categories. Each row is one annotated region;
`label == category`.

## Loading

```python
from datasets import load_dataset

full_bidi = load_dataset(
    "Taykhoom/functional-multiclass-gamba",
    "full-bidi",
    split="all",
)

paper_test = full_bidi.filter(
    lambda row: row["split"] == "test"
    and row["category"] != "noncoding_regions"
)
```

## Choosing a configuration

The two dimensions are independent:

| Dimension | Options | Meaning |
|---|---|---|
| Context | `causal`, `bidi` | End-anchor ROI for autoregressive models or center it for bidirectional models. |
| Pooling | `full`, `100bp` | Pool over the retained ROI or a deterministic 100 bp subspan. |

The `full` name refers to the retained ROI visible in the 2,048 bp context;
very long features may be clipped according to GAMBA's context rules. It does
not mean an unlimited genomic interval.

The 100 bp genomic target is selected once from the source interval before
either context view is constructed. Causal and bidirectional rows therefore
have identical `chrom`, `start`, and `end` targets and retain stable `pair_id`
values for unchanged source examples.

## Dataset size

| Config family | Complete rows | Held-out test | Corrected paper rows | Corrected paper test |
|---|---:|---:|---:|---:|
| `full-*` | 92,482 | 18,404 | 82,980 | 16,506 |
| `100bp-*` | 65,655 | 13,095 | 56,713 | 11,324 |

The corrected paper view excludes `category == "noncoding_regions"`.

## Labels

Full configs contain eleven labels:

| Category | Rows |
|---|---:|
| repeats | 9,987 |
| UCNE | 4,169 |
| vista_enhancer | 691 |
| promoters | 9,961 |
| UTR5 | 9,809 |
| UTR3 | 9,717 |
| coding_regions | 9,904 |
| exons | 9,926 |
| introns | 9,026 |
| upstream_TSS | 9,790 |
| noncoding_regions | 9,502 |

The 100 bp configs contain 65,655 rows, including 8,942 noncoding targets.
Promoter entries do not satisfy the 100 bp criterion and are absent;
`vista_enhancer` has 690 rows, and other categories are filtered by source
interval length. Every 100 bp sequence context is 2,048 bp. For full configs,
all 92,482 bidirectional contexts are 2,048 bp; causal has 82,502 contexts at
2,048 bp and 9,980 truncated long-feature contexts at 1,000 bp.

## Evaluation protocol

For the corrected paper evaluation:

1. filter `split == "test"`;
2. exclude `noncoding_regions`;
3. pool embeddings over the stored span;
4. perform cosine leave-one-out 1-nearest-neighbor classification;
5. report balanced accuracy.

No supervised model-fitting split is implied by Hugging Face split `all`.

## Columns

| Column group | Description |
|---|---|
| `split`, `sequence`, `label`, `pair_id` | Chromosome partition, exact input, functional class, and stable feature ID. |
| `context_group_id` | Exact model-input leakage group within this physical config. |
| `category`, `repeat_class`, `scope`, `context_policy` | Source class, nullable repeat class, `full`/`100bp` scope, and context geometry. |
| `chrom`, `start`, `end`, `source_strand` | Zero-based, half-open hg38 coordinates and biological strand; 100 bp configs store the selected target interval. |
| `sequence_orientation` | Explicit `+`/`-` orientation used for sequence geometry and reverse complementation. |
| `context_start`, `context_end` | Forward-genome context coordinates. |
| `roi_start`, `roi_end` | Retained full-feature or selected 100 bp target offsets in oriented `sequence`. |
| `pool_start_in_window`, `pool_end_in_window` | Evaluation span, identical to the stored ROI. |
| `name` | Source annotation identifier. |
| `phylop_*`, `phylop_context_*` | Pooling-span and symmetric-context phyloP summaries. |

## RepeatMasker correction

RepeatMasker genomic strand and repeat class are stored separately. This
release corrects an earlier local conversion that placed the repeat class in
the strand column, then regenerates repeat-derived contexts, pools, controls,
and phyloP features. Labels are unchanged.

Only VISTA rows with hg38 assembly and normalized positive expression are
eligible: 1,367 raw records collapse to 1,240 unique element-coordinate
records; 1,522 non-positive hg38 and 1,750 non-hg38 rows are excluded.
Inputs containing ambiguous bases are removed globally. Exact inputs with
conflicting category labels are excluded as a group; same-label duplicates
share `context_group_id`. No exact input crosses train/test.
ATG test inputs are reserved globally; the exact duplicate chr7 functional
training row is therefore excluded from full multiclass configs.

## Processing and citation

Processing and verification:

- [Processing repository](https://github.com/TaykhoomDalal/Gamba-Processing/tree/main)
- [Processing and validation documentation](https://github.com/TaykhoomDalal/Gamba-Processing/blob/main/README.md#validation)

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.