Getting Started in Text Mining
A brief introduction to bio-text mining from Cohen and Hunter. More than ten years old but still quite relevant. See also an earlier paper by the same authors.
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Biomedical Literature Mining link.springer.com
A (non-free) volume of Methods in Molecular Biology from 2014. Chapters covers introductory principles in text mining, applications in the biological sciences, and potential for use in clinical or medical safety scenarios.
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JensenLab text mining exercises jensenlab.org
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BioC-BioGRID bioc.sourceforge.net
paper - 120 full text articles annotated for PPI and genetic interactions. Used in the BioCreative V BioC task.
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining academic.oup.com
Bioinformatics, 2020. [All Versions]. Answering medical questions, identifying relevant clinical trials, and diagnosing diseases based on symptoms, making medical information more accessible to the general public.
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This paper from Hongfang Liu's group at Mayo Clinic sciencedirect.com
demonstrates how text embeddings trained on biomedical or clinical text can, but don't always, perform better on biomedical natural language processing tasks. That being said, pre-trained embeddings may be appropriate for your needs, especially as training domain-specific…
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Coursera - Foundations of mining non-structured medical data coursera.org
About three hours worth of video lectures on working with medical data of various types and structures, including text and image data. Appears fairly high-level and intended for beginners.
Biomedical Information Extraction › Tutorials > Pre-LLM Guides, Lectures, and Courses: “A brief introduction to bio-text mining from Cohen and Hunter. More than ten years old but still quite relevant. See also an earlier paper by the same authors.”