Scientific NLP From Scratch

This repository contains three compact NLP, non-Transformer projects:

• 01_pubmed_sentence_classification: PubMed RCT abstract sentence classification from Kaggle PubMed 200k RCT.
• 02_citation_intent_classification: SciCite citation intent classification from Kaggle Scicite (Classifying Citation Intents In Papers).
• 03_toxhabits_ner_bilstm: Spanish ToxHabits NER with CharCNN + BiLSTM + CRF from ToxHabits Track of BioCreative IX Challenge.

My original notebooks are kept unchanged. Each project also includes an idealistic notebook copy for quick reading and a src/ package for reusable code.

Setup

python -m venv .venv
.venv\Scripts\activate
python -m pip install --upgrade pip
python -m pip install -e .
python -m spacy download es_core_news_sm

Data

Put the files under each project's data/ directory as described in that project's data/README.md.

Projects

Each project has:

• README.md with dataset notes and run commands.
• src/<package_name>/ with data, model, training, and evaluation code.
• scripts/train.py as a simple command-line entry point.
• notebooks/*_clean.ipynb as a polished companion notebook.