DNABERT
Stanza
DNABERT | Stanza | |
---|---|---|
1 | 8 | |
546 | 7,060 | |
- | 0.7% | |
3.1 | 9.8 | |
2 months ago | 5 days ago | |
Python | Python | |
Apache License 2.0 | GNU General Public License v3.0 or later |
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DNABERT
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[D] New to DNABERT
If I want to get started, they said it's optional to pre-train (so you can skip to step 3). This is where I got tripped up: "Note that the sequences are in kmer format, so you will need to convert your sequences into that." From what I understand, you need to do this so that all of the sequences are the same length? So kmer=6 means all of the sequences are length 6? Someone suggested that I take the first nucleotide in the promoter and grab 3 nucleotides before and 3 nucleotides after (+/-3 bases). I don't think that's how the kmer thing works though? I tried replicating how I think it works down below (I got confused on the last row of the 'after' df). Please correct me if I'm wrong!
Stanza
- Down and Out in the Magic Kingdom
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Parts of speech tagged for German
I use Python's spacy library: https://spacy.io/models/de or stanza: https://stanfordnlp.github.io/stanza/ each with their respective language models.
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Off the shelf sentence parsers?
stanza has a constituency parser. There's a model compatible with the dev branch with an accuracy of 95.8 on PTB, using Roberta as a bottom layer, so it's pretty decent at this point. (The currently released model is not as accurate, but it's easy to get the better model to you.) There's also Tregex as a Java addon which can very easily search for a noun phrase highest up in the tree: NP !>> NP will search for a noun phrase which is not dominated by any higher up noun phrase.
- The Spacy NER model for Spanish is terrible
- Spacy vs NLTK for Spanish Language Statistical Tasks
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Stanza not tokenising sentences as expected
I am using Stanza to tokenise the sentences:
- Stanza β A Python NLP Package for Many Human Languages
What are some alternatives?
courses - This repository is a curated collection of links to various courses and resources about Artificial Intelligence (AI)
spaCy - π« Industrial-strength Natural Language Processing (NLP) in Python
datasets - π€ The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools
NLTK - NLTK Source
stanford-tensorflow-tutorials - This repository contains code examples for the Stanford's course: TensorFlow for Deep Learning Research.
BERT-NER - Pytorch-Named-Entity-Recognition-with-BERT
Jieba - η»ε·΄δΈζεθ―
nlp-recipes - Natural Language Processing Best Practices & Examples
flair - A very simple framework for state-of-the-art Natural Language Processing (NLP)
bioconvert - Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
pytext - A natural language modeling framework based on PyTorch