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README.md
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# segment-nt
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elements in a sequence at a single nucleotide resolution. It was trained on 14 different classes of human genomics elements in input sequences up to 30kb. These
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include gene (protein-coding genes, lncRNAs, 5’UTR, 3’UTR, exon, intron, splice acceptor and donor sites) and regulatory (polyA signal, tissue-invariant and
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tissue-specific promoters and enhancers, and CTCF-bound sites) elements.
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A small snippet of code is given here in order to retrieve both logits and embeddings from a dummy DNA sequence.
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⚠️ The maximum sequence length is set by default at the training length of 30,000 nucleotides, or 5001 tokens (accounting for the CLS token). However,
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the `rescaling_factor` of the Rotary Embedding layer in the esm model `num_dna_tokens_inference / max_num_tokens_nt` where `num_dna_tokens_inference` is the number of tokens at inference
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(i.e 6669 for a sequence of 40008 base pairs) and `max_num_tokens_nt` is the max number of tokens on which the backbone nucleotide-transformer was trained on, i.e `2048`.
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---
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# segment-nt
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SegmentNT is a segmentation model leveraging the [Nucleotide Transformer](https://huggingface.co/InstaDeepAI/nucleotide-transformer-v2-500m-multi-species) (NT) DNA foundation model to predict the location of several types of genomics
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elements in a sequence at a single nucleotide resolution. It was trained on 14 different classes of human genomics elements in input sequences up to 30kb. These
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include gene (protein-coding genes, lncRNAs, 5’UTR, 3’UTR, exon, intron, splice acceptor and donor sites) and regulatory (polyA signal, tissue-invariant and
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tissue-specific promoters and enhancers, and CTCF-bound sites) elements.
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A small snippet of code is given here in order to retrieve both logits and embeddings from a dummy DNA sequence.
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⚠️ The maximum sequence length is set by default at the training length of 30,000 nucleotides, or 5001 tokens (accounting for the CLS token). However,
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SegmentNT-multi-species has been shown to generalize up to sequences of 50,000 bp. In case you need to infer on sequences between 30kbp and 50kbp, make sure to change
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the `rescaling_factor` of the Rotary Embedding layer in the esm model `num_dna_tokens_inference / max_num_tokens_nt` where `num_dna_tokens_inference` is the number of tokens at inference
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(i.e 6669 for a sequence of 40008 base pairs) and `max_num_tokens_nt` is the max number of tokens on which the backbone nucleotide-transformer was trained on, i.e `2048`.
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