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Harnessing the Power of NLP and Knowledge
Graphs for Opioid Research
Gursev Pirge, PhD
Data Scientist
John Snow Labs
Healthcare NLP
Spark NLP for Healthcare provides
- accurate,
- scalable,
- private,
- tuneable,
- modular
software library that helps healthcare
& pharma organizations build
longitudinal patient records and
knowledge graphs on real-world EHR
data.
Data Origination and Exchange
Harnessing the Power of NLP and Knowledge Graphs for Opioid Research
Spark NLP for Healthcare
Named Entity
Recognition
ICD10 Resolver
Snomed
Resolver
UMLS Resolver
Risk Adj. Module RxNorm Resolver
Assertion Status
Detection
Sentence Splitter
Tokenizer
Bert Embeddings
Relationship
Extraction
sBert
Embeddings
Spark NLP for Healthcare
CT ABDOMEN:
There is no evidence
for a retroperitoneal
hematoma. Within the
superior pole of the
left kidney, there is
a 3.9 cm cystic
lesion. A 3.3 cm
cystic lesion is also
seen within the
inferior pole of the
left kidney. No
calcifications are
noted.
Medical Question Answering
7
Harnessing the Power of NLP and Knowledge Graphs for Opioid Research
Harnessing the Power of NLP and Knowledge Graphs for Opioid Research
Opioids
- A class of drugs that include both natural and synthetic substances derived from or related to
the opium poppy plant.
- Act on opioid receptors in the brain and nervous system to provide pain relief, sedation, and
euphoria.
- Natural opiates (morphine, codeine), semi-synthetic opioids (hydrocodone, oxycodone, heroin),
and synthetic opioids (fentanyl, methadone, tramadol).
- Have high potential for misuse, addiction, and overdose, contributing to the ongoing opioid
epidemic.
10
Opioids
11
https://nida.nih.gov/research-
topics/trends-statistics/overdose-
death-rates
Opioids - NER
Opioids - NER
13
Opioids – Assertion Status Detection
14
Opioids – Assertion Status Detection
15
Opioids – RE
16
17
18
Harnessing the Power of NLP and Knowledge Graphs for Opioid Research
20
21
22
23
Neo4J – Demo App
- Collect data from PubMed - a free database including primarily the MEDLINE database of
references and abstracts on life sciences and biomedical topics.
- Use pretrained model (ner_opioid) from Spark NLP Healthcare to extract NERs from text and
filter them based on assertions and relations.
- Use the NERs to create a KG.
- Using RE models, NERs can be linked to each other.
- Example – which opioid caused which condition (even if there are multiple opioids in the same article).
24
25
26
Thank you!
27
Gursev Pirge
gursev@johnsnowlabs.com
https://www.johnsnowlabs.com/

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Harnessing the Power of NLP and Knowledge Graphs for Opioid Research

  • 1. Harnessing the Power of NLP and Knowledge Graphs for Opioid Research Gursev Pirge, PhD Data Scientist John Snow Labs
  • 2. Healthcare NLP Spark NLP for Healthcare provides - accurate, - scalable, - private, - tuneable, - modular software library that helps healthcare & pharma organizations build longitudinal patient records and knowledge graphs on real-world EHR data.
  • 5. Spark NLP for Healthcare Named Entity Recognition ICD10 Resolver Snomed Resolver UMLS Resolver Risk Adj. Module RxNorm Resolver Assertion Status Detection Sentence Splitter Tokenizer Bert Embeddings Relationship Extraction sBert Embeddings
  • 6. Spark NLP for Healthcare CT ABDOMEN: There is no evidence for a retroperitoneal hematoma. Within the superior pole of the left kidney, there is a 3.9 cm cystic lesion. A 3.3 cm cystic lesion is also seen within the inferior pole of the left kidney. No calcifications are noted.
  • 10. Opioids - A class of drugs that include both natural and synthetic substances derived from or related to the opium poppy plant. - Act on opioid receptors in the brain and nervous system to provide pain relief, sedation, and euphoria. - Natural opiates (morphine, codeine), semi-synthetic opioids (hydrocodone, oxycodone, heroin), and synthetic opioids (fentanyl, methadone, tramadol). - Have high potential for misuse, addiction, and overdose, contributing to the ongoing opioid epidemic. 10
  • 14. Opioids – Assertion Status Detection 14
  • 15. Opioids – Assertion Status Detection 15
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  • 24. Neo4J – Demo App - Collect data from PubMed - a free database including primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. - Use pretrained model (ner_opioid) from Spark NLP Healthcare to extract NERs from text and filter them based on assertions and relations. - Use the NERs to create a KG. - Using RE models, NERs can be linked to each other. - Example – which opioid caused which condition (even if there are multiple opioids in the same article). 24
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