---
license: apache-2.0
task_categories:
- text-generation
tags:
- biology
- genomics
- dna
size_categories:
- 10M<n<100M
---

# carbon-cpu-enriched-sequences

A CPU-enriched subset of the **[carbon pretraining corpus (`eukaryote_generator`)](https://huggingface.co/datasets/HuggingFaceBio/carbon-pretraining-corpus)**, combining original source fields with normalized sequences
and row-level features for quality analysis, GPU enrichment and embedding generation.

---

## Information of Features

| Feature                      | Type    | Description                                                                                                                                                                                                    |
| ---------------------------- | ------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `record_id`                  | string  | [NCBI Identifier](https://www.ncbi.nlm.nih.gov/datasets/taxonomy/) linking the row back to the source genomic record. It provides the primary record-level identity.                                           |
| `begin_of_sequence`          | string  | Beginning-of-sequence special token marking the start of a sequence record, e.g. `<s>`.                                                                                                                        |
| `end_of_sequence`            | string  | End-of-sequence special token marking the end of a sequence record, e.g. `</s>`.                                                                                                                               |
| `begin_of_gene`              | string  | Marker identifying the beginning of a gene/feature segment, e.g. `<bog>`.                                                                                                                                      |
| `end_of_gene`                | string  | Marker identifying the end of a gene/feature segment, e.g. `<eog>`.                                                                                                                                            |
| `gene_type`                  | string  | Annotation describing the type of genomic feature. In the observed data, `<cds>` represents a coding sequence and `<fng>` represents another gene-feature category.                                            |
| `species_type`               | string  | Broad biological category of the source sequence. The current data is represented as `Eukaryota`.                                                                                                              |
| `strand`                     | string  | DNA strand/orientation associated with the sequence, represented by `+` or `-`.                                                                                                                                |
| `sequence`                   | string  | The actual nucleotide sequence represented by the record. This is the primary biological sequence field.                                                                                                       |
| `molecule_type`              | string  | Molecular type of the sequence; the current data is represented as `DNA`.                                                                                                                                      |
| `topology`                   | string  | Structural topology of the molecule, such as `linear`.                                                                                                                                                         |
| `taxonomy`                   | string  | Hierarchical taxonomic lineage of the sequence, with ranks represented as a semicolon-separated lineage, e.g. `Eukaryota;Fungi;...;Agaricus`.                                                                  |
| `start`                      | int64   | Starting position of the record within the pre-trained Carbon corpus. It is a corpus coordinate, not necessarily a genomic coordinate.                                                                         |
| `end`                        | int64   | Ending position of the record within the processed/tokenized Carbon corpus.                                                                                                                                    |
| `gc_content`                 | float64 | Fraction of nucleotides that are G or C: `(G + C) / sequence_length`. It measures GC composition.                                                                                                              |
| `gc_skew`                    | float64 | Measures asymmetry between G and C: `(G - C) / (G + C)`. Positive values indicate relative G enrichment; negative values indicate relative C enrichment.                                                       |
| `sequence_length`            | int64   | Number of nucleotide bases in the sequence.                                                                                                                                                                    |
| `gene_length`                | int64   | Length of the associated gene/feature sequence. For the current records it commonly corresponds to `sequence_length`.                                                                                          |
| `shannon_entropy`            | float64 | Sequence-complexity measure based on nucleotide-frequency distribution.                                                                                                                                        |
| `kmer_frequency_vector`      | list    | A 64-element vector containing normalized frequencies of all possible DNA 3-mers (`4³ = 64`). It captures local sequence-composition patterns.                                                                 |
| `strand_normalized_sequence` | string  | Sequence transformed into a consistent orientation so that strand direction does not create artificial differences in downstream analysis.                                                                     |
| `taxonomy_domain`            | string  | Broadest taxonomic/domain-level classification extracted from the taxonomy hierarchy.                                                                                                                          |
| `taxonomy_depth`             | int64   | Number of taxonomic levels represented in the lineage. It provides a compact measure of how deeply the sequence is classified.                                                                                 |
| `is_coding_region`           | bool    | Boolean indicator of whether the record is classified as a coding sequence. The pipeline identifies `<cds>` as the coding gene type.                                                                           |
| `qc_flag`                    | string  | Quality-control status assigned to the record, indicating whether it passes the pipeline's sequence-level QC criteria.                                                                                         |

The dataset contains **both the original Carbon fields and derived enrichment features**.

---

## Dataset Summary

`carbon-cpu-enriched-sequences` provides a reusable CPU-side canonical representation of the Carbon genomic corpus before computationally expensive GPU enrichment.

The original Carbon source corpus contains approximately **46.3 million records**. This release contains **32,410,000 records**, corresponding to approximately **70% of the source row population**. The release was selected as a practical balance between corpus representation, CPU processing cost, storage requirements, and downstream GPU compute availability.

The dataset preserves the original Carbon source representation while adding CPU-derived enrichment features:

```text
Original Carbon columns
        +
CPU-derived enrichment columns
        ↓
CPU-enriched Parquet dataset
```

The current materialized release contains approximately **25 columns**, consisting of approximately **14 source/raw columns** and **11 derived enrichment columns**. The exact schema should be inspected from the Parquet files, as future enrichment revisions may add or modify derived fields.

CPU enrichment includes sequence-level and metadata-derived information such as sequence characteristics, coding status, strand/orientation information, and taxonomy depth. Coding sequences are identified using the observed Carbon representation `<cds>`.

The dataset is stored as **Apache Parquet** with **Zstandard compression**, using approximately **50,000 rows per shard**. 


## Intended Uses

This dataset is intended for research and data-engineering workflows involving genomic sequence corpora, including:

* Genomic data quality and validation analysis
* Sequence-distribution and statistical analysis
* CPU-side preprocessing research
* Dataset sampling and cohort construction
* GPU enrichment experiments
* Embedding generation
* Nearest-neighbor and clustering analysis
* Genomic foundation-model data engineering
* Benchmarking large-scale data-processing pipelines
* Construction of downstream enriched datasets

For large-scale datasets, streaming access is recommended rather than loading the entire dataset into memory.

---