Slides -- Bioinformatics FAQ Bot

Bioinformatics FAQ Bot

San Diego Python Monthly Meetup by Hobson Lane, Travis Harper Oct 24, 2019

Thank you Travis!

  • Analyzing WikiQA
  • Architecting a Transformer

QA Bot

  • WikiQA
  • ANSQ


WikiQA state of the art

Search-based QA

Find a question-answer pair in DB Translate question to a statement, search Wikipedia

Scalable Search: O(log(N))

  • Discrete index
  • Sparse BOW vectors

Synonyms & Typos

  • Stemming
  • Lemmatizing
  • Spelling Corrector
  • BPE (bytepair encoding)


  • Full text search in Postgres
  • Trigram indexes in Databases
  • Ellastic Search


  • Page rank
  • Sparse TFIDF vectors


  • Full Text (keywords): O(log(N))
  • TFIDF (Ellastic Search): O(log(N))
  • TFIDF + Semantic Search: O(L)

Academic Search Approachs

  • Edit distance

Knowledg-based QA

  • Extract information from Wikipedia
  • Build Knowledge Graph in DB
  • Query Knowledge Graph
  • Inference on Knowledge Graph


Transformer Test Example Output


Transformer Wizard of Oz Question Answers

Written on December 19, 2019