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

SOA

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)

Examples

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

Prefilter

• Page rank
• Sparse TFIDF vectors

Examples

• 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

Transformer