added the readme
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by
alan-ai
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README.md
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---
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annotations_creators:
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- no-annotation
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language_creators:
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- no-annotation
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task_categories:
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- text-classification
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tags:
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- genomics
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- dna
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- dnabert
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- bioinformatics
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- mouse-dna
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- tokenized
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source_datasets:
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- davidcechak/Mouse_DNA_v0
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language:
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- en
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license: other
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license_name: unspecified
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---
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# `Mouse_DNA_v0_DNABert6tokenized`
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## Dataset Description
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The `davidcechak/Mouse_DNA_v0_DNABert6tokenized` is a processed version of the `davidcechak/Mouse_DNA_v0` dataset. It contains mouse DNA sequences that have been tokenized using a 6-mer approach, making it directly compatible with models like DNABert for classification and other downstream tasks.
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This dataset can be used for comparative genomic analysis when used in conjunction with other tokenized datasets, such as the human DNA tokenized dataset (`simecek/Human_DNA_v0_DNABert6tokenized`). This allows for the training of classifiers that can distinguish between mouse and other species' DNA, providing a valuable resource for cross-species machine learning tasks in bioinformatics.
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## Dataset Structure
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The dataset is available in the `parquet` format and is likely split into training and testing subsets, though this needs to be confirmed.
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### Data Fields
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The dataset likely includes the following fields:
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* **tokens**: A list of integers representing the 6-mer token IDs.
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* **text**: The original DNA sequence string, consisting of the nucleotides `A`, `T`, `C`, and `G`.
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## Dataset Creation
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### Data Source
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The base `Mouse_DNA_v0` dataset likely consists of DNA sequences from the mouse reference genome (*Mus musculus*).
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### Preprocessing and Tokenization
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The raw sequences from the `Mouse_DNA_v0` dataset were processed using a 6-mer tokenization scheme:
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1. **Splitting**: Original DNA sequences were split into non-overlapping 6-mer tokens.
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2. **Mapping**: Each unique 6-mer was mapped to a unique integer ID to create a vocabulary.
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3. **Encoding**: The tokenized sequences were then represented as a list of these integer IDs.
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## Intended Uses
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The dataset can be used for:
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* **Comparative Genomics**: Comparing genomic features and training models to distinguish between species (e.g., mouse vs. human).
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* **Genomic Classification**: Training and evaluating machine learning models on tasks like species identification from DNA sequences.
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* **LLM Pre-training**: Providing a corpus for pre-training large language models on mouse DNA sequences, which can then be fine-tuned for more specific downstream tasks.
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## Limitations and Ethical Considerations
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* **Unspecified Origin**: Without an official dataset card from the author, the precise origin and collection methodology of the sequences are unknown. This may impact reproducibility and potential biases.
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* **Licensing**: The license is currently unspecified. For any public or commercial use, it is necessary to verify the terms with the author, David Cechak, on Hugging Face.
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## How to Get the Dataset
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You can easily load this dataset from the Hugging Face Hub using the `datasets` library:
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```python
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from datasets import load_dataset
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# Load the tokenized dataset
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dataset = load_dataset("davidcechak/Mouse_DNA_v0_DNABert6tokenized")
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# Access the training split
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train_dataset = dataset["train"]
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