NLP for Biomed — Lit Mining, KG Construction & NER — Hands-on

Learn how to apply natural language processing to biomedical literature, databases and clinical style text. This module walks through text preprocessing, tokenization, named entity recognition and normalization, relation extraction and knowledge graph construction for real world discovery and curation workflows.

NLP for Biomed — Lit Mining, KG Construction & NER

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Session Index

Session 1 — Biomedical Text & NLP Foundations Session 2 — NER, Entity Linking & Normalization Session 3 — Relation Extraction & Knowledge Graphs Session 4 — Literature Mining Workflows & Deliverables

Session 1

Fee: Rs 8800

Biomedical Text & NLP Foundations

Sources and types of biomedical text data

PubMed style abstracts full text articles and guidelines clinical style notes overview

NLP preprocessing for biomedical corpora

sentence splitting and tokenization lemmatization and stop word handling handling units, symbols and greek letters

Representing biomedical text numerically

bag of words and TF IDF classical word embeddings idea transformer based contextual embeddings intuition

Session 2

Fee: Rs 11800

NER, Entity Linking & Normalization

Named entity recognition for biomedical text

gene, disease and drug entities rule based vs ML and transformer NER evaluation with precision, recall and F1

Entity linking and normalization to standards

mapping to ontologies and IDs UMLS, MeSH, HGNC, DrugBank style resources disambiguation strategies and confidence scores

Preparing clean entity spans for downstream use

deduplication and canonical forms resolving overlapping entities storing entities for later graph building

Session 3

Fee: Rs 14800

Relation Extraction & Knowledge Graphs

Relation extraction concepts and patterns

co occurrence and pattern based relations supervised and distant supervision ideas simple transformer classifiers for relations

Building biomedical knowledge graphs from text

nodes as normalized entities edges as typed relations simple graph schema design

Exploring and using knowledge graphs

basic queries for neighbourhoods path based hypothesis generation exporting subgraphs for downstream ML

Session 4

Fee: Rs 18800

Literature Mining Workflows & Deliverables

End to end literature mining pipeline design

corpus selection and query strategies batch processing and incremental updates logging and error handling basics

Evaluation and quality checking of extractions

manual review samples and error types simple inter annotator agreement metrics feedback loops to improve NER and relations

Deliverables: knowledge graph and mining report pack

entity and relation tables or graph files notebooks for NER and relation extraction written summary of insights and limitations

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NLP for Biomed — Lit Mining, KG Construction & NER Training | Biostatistics & ML for Omics

NLP for Biomed — Lit Mining, KG Construction & NER — Hands-on