DNABERT
spaCy
DNABERT | spaCy | |
---|---|---|
1 | 107 | |
546 | 28,849 | |
- | 1.0% | |
3.1 | 9.2 | |
2 months ago | 12 days ago | |
Python | Python | |
Apache License 2.0 | MIT License |
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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!
spaCy
- How I discovered Named Entity Recognition while trying to remove gibberish from a string.
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Step by step guide to create customized chatbot by using spaCy (Python NLP library)
Hi Community, In this article, I will demonstrate below steps to create your own chatbot by using spaCy (spaCy is an open-source software library for advanced natural language processing, written in the programming languages Python and Cython):
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Best AI SEO Tools for NLP Content Optimization
SpaCy: An open-source library providing tools for advanced NLP tasks like tokenization, entity recognition, and part-of-speech tagging.
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Who has the best documentation you’ve seen or like in 2023
spaCy https://spacy.io/
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A beginner’s guide to sentiment analysis using OceanBase and spaCy
In this article, I'm going to walk through a sentiment analysis project from start to finish, using open-source Amazon product reviews. However, using the same approach, you can easily implement mass sentiment analysis on your own products. We'll explore an approach to sentiment analysis with one of the most popular Python NLP packages: spaCy.
- Retrieval Augmented Generation (RAG): How To Get AI Models Learn Your Data & Give You Answers
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Against LLM Maximalism
Spacy [0] is a state-of-art / easy-to-use NLP library from the pre-LLM era. This post is the Spacy founder's thoughts on how to integrate LLMs with the kind of problems that "traditional" NLP is used for right now. It's an advertisement for Prodigy [1], their paid tool for using LLMs to assist data labeling. That said, I think I largely agree with the premise, and it's worth reading the entire post.
The steps described in "LLM pragmatism" are basically what I see my data science friends doing — it's hard to justify the cost (money and latency) in using LLMs directly for all tasks, and even if you want to you'll need a baseline model to compare against, so why not use LLMs for dataset creation or augmentation in order to train a classic supervised model?
[0] https://spacy.io/
[1] https://prodi.gy/
- Swirl: An open-source search engine with LLMs and ChatGPT to provide all the answers you need 🌌
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How to predict this sequence?
spaCy
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What do you all think about (setq sentence-end-double-space nil)?
I chose spacy. Although it's not state of the art, it's very well established and stable.
What are some alternatives?
courses - This repository is a curated collection of links to various courses and resources about Artificial Intelligence (AI)
TextBlob - Simple, Pythonic, text processing--Sentiment analysis, part-of-speech tagging, noun phrase extraction, translation, and more.
Stanza - Stanford NLP Python library for tokenization, sentence segmentation, NER, and parsing of many human languages
datasets - 🤗 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
nlp-recipes - Natural Language Processing Best Practices & Examples
polyglot - Multilingual text (NLP) processing toolkit
bioconvert - Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
textacy - NLP, before and after spaCy