In this session, we show how to leverage CORD dataset, containing more than 400000 scientific papers on COVID and related topics, and recent advances in natural language processing and other AI techniques to generate new insights in support of the ongoing fight against this infectious disease. The idea explored in our talk is to apply modern NLP methods, such and named entity recognition (NER) and relation extraction to article’s abstracts (and, possibly, full text), to extract some meaningful insights from the text, and to enable semantically rich search over the paper corpus. We first investigate how to train NER model using Medical NER dataset from Kaggle, and specialized version of BERT (PubMedBERT) as a feature extractor, to allow automatic extraction of such entities as medical condition names, medicine names and pathogens. Entity extraction alone can provide us with some interesting findings, such as how approaches to COVID treatment evolved with time, in terms of mentioned medicines. We demonstrate how to use Azure Machine Learning for training the model. To take this investigation one step further, we also investigate the usage of pre-trained medical models, available as Text Analytics for Health service on the Microsoft Azure cloud. In addition to many entity types, it can also extract relations (such as the dosage of medicine provisioned), entity negation, and entity mapping to some well-known medical ontologies. We investigate the best way to use Azure ML at scale to score large paper collection, and to store the results.

1. How Machine Learning and AI
can support the fight against COVID-19
Francesca Lazzeri, PhD
Principal Cloud Advocate Manager, Microsoft
@frlazzeri
Dmitry Soshnikov, PhD
Senior Cloud Advocate, Microsoft
@shwars

2. Problem
Around 30,000 scientific papers
related to COVID appear
monthly

3. CORD Papers Dataset
Data Source
https://allenai.org/data/cord-19
https://www.kaggle.com/allen-institute-for-ai/CORD-19-
research-challenge
CORD-19 Dataset
Contains over 400,000 scholarly articles about
COVID-19 and the coronavirus family of viruses
for use by the global research community
200,000 articles with full text

4. Natural Language Processing
Common tasks for NLP:
• Intent Classification
• Named Entity Recognition (NER)
• Keyword Extraction
• Text Summarization
• Question Answering
• Open Domain Question Answering
Language Models:
• Recurrent Neural Network (LSTM, GRU)
• Transformers
• GPT-2
• BERT
• Microsoft Turing-NLG
• GPT-3
Microsoft Learn Module:
Introduction to NLP with PyTorch
aka.ms/pytorch_nlp
docs.microsoft.com/en-us/learn/paths/pytorch-fundamentals/

5. How BERT Works (Simplified)
Masked Language Model + Next Sentence Prediction
During holidays, I like to ______ with my dog. It is so cute.
0.85 Play
0.05 Sleep
0.09 Fight
0.80 YES
0.20 NO
BERT contains 345 million parameters => very difficult to train from scratch! In
most of the cases it makes sense to use pre-trained language model.

6. Main Idea
Use NLP tools to extract semi-structured data from papers, to enable
semantically rich queries over the paper corpus.
Extracted
JSON
Cosmos
DB
Database
Power BI
Dashboard
SQL Queries
Azure
Semantic
Search
NER
Relations
Text
Analytics
for Health
CORD
Corpus

7. Part 1: Extracting Entities and Relations
Base Language Model
Dataset
Kaggle Medical NER:
• ~40 papers
• ~300 entities
Generic BC5CDR Dataset
• 1500 papers
• 5000 entities
• Disease / Chemical
Generic BERT Model
Pre-training BERT on Medical
texts
PubMedBERT pre-trained
model by Microsoft Research
Huggingface Transformer Library: https://huggingface.co/

8. 6794356|t|Tricuspid valve regurgitation and lithium carbonate toxicity in a newborn
infant.
6794356|a|A newborn with massive tricuspid regurgitation, atrial flutter, congestive
heart failure, and a high serum lithium level is described. This is the first patient
to initially manifest tricuspid regurgitation and atrial flutter, and the 11th
described patient with cardiac disease among infants exposed to lithium compounds in
the first trimester of pregnancy. Sixty-three percent of these infants had tricuspid
valve involvement. Lithium carbonate may be a factor in the increasing incidence of
congenital heart disease when taken during early pregnancy. It also causes neurologic
depression, cyanosis, and cardiac arrhythmia when consumed prior to delivery.
6794356 0 29 Tricuspid valve regurgitation Disease D014262
6794356 34 51 lithium carbonate Chemical D016651
6794356 52 60 toxicity Disease D064420
6794356 105 128 tricuspid regurgitation Disease D014262
6794356 130 144 atrial flutter Disease D001282
6794356 146 170 congestive heart failure Disease D006333
6794356 189 196 lithium Chemical D008094
6794356 265 288 tricuspid regurgitation Disease D014262
6794356 293 307 atrial flutter Disease D001282
6794356 345 360 cardiac disease Disease D006331
6794356 386 393 lithium Chemical D008094
6794356 511 528 Lithium carbonate Chemical D016651
6794356 576 600 congenital heart disease Disease D006331

9. NER as Token Classification
Tricuspid valve regurgitation and lithium
carbonate toxicity in a newborn infant.
Tricuspid B-DIS
valve I-DIS
regurgitation I-DIS
and O
lithium B-CHEM
carbonate I-CHEM
toxicity B-DIS
in O
a O
newborn O
infant O
. O

10. PubMedBert, Microsoft Research
from transformers import
AutoTokenizer,
BertForTokenClassification,
Trainer
mname =
“microsoft/BiomedNLP-PubMedBERT-base-
uncased-abstract”
tokenizer =
AutoTokenizer.from_pretrained(mname)
model = BertForTokenClassification
.from_pretrained(mname,
num_labels=len(unique_tags))
trainer = Trainer(
model=model,
args=training_args,
train_dataset=train_dataset,
eval_dataset=val_dataset)
trainer.train()

11. Notebooks Automated ML UX Designer
Reproducibility Automation Deployment Re-training
CPU, GPU, FPGAs IoT Edge
Azure Machine Learning
Enterprise grade service to build and deploy models at scale

12. Training NER Model Using PubMedBert on Azure ML
Describe Dataset:
name: bc5cdr
version: 1
local_path: BC5_data.txt
bc5cdr.yml
Upload to Azure ML:
$ az ml data create -f data_bc5cdr.yml
Describe Environment:
name: transformers-env
version: 1
docker:
image: mcr.microsoft.com/
azureml/openmpi3.1.2-
cuda10.1-cudnn7-ubuntu18.04
conda_file:
file: ./transformers_conda.yml
transformers-env.yml
channels:
- pytorch
dependencies:
- python=3.8
- pytorch
- pip
- pip:
- transformers
transformers_conda.yml
$ az ml environment create -f transformers-env.yml

13. Training NER Model Using PubMedBert on Azure ML
Describe Experiment:
experiment_name: nertrain
code:
local_path: .
command: >-
python
train.py --data {inputs.corpus}
environment:
azureml:transformers-env:1
compute:
target: azureml:AzMLGPUCompute
inputs:
corpus:
data: azureml:bc5cdr:1
mode: download
job.yml
Create Compute:
$ az ml compute create –n AzMLGPUCompute
--size Standard_NC6
--max-node-count 2
Submit Job:
$ az ml job create –f job.yml

14. Result
• COVID-19 not recognized,
because dataset is old
• Some other categories would
be helpful (pharmacokinetics,
biologic fluids, etc.)
• Common entities are also
needed (quantity,
temperature, etc.)
Get trained model:
$ az ml job download -n $ID
--outputs

15. Text Analytics for Health (Preview)
 Currently in Preview
 Gated service, need to apply for usage
(apply at https://aka.ms/csgate)
 Should not be implemented or deployed in any production use.
 Can be used through Web API or Container Service
 Supports:
 Named Entity Recognition (NER)
 Relation Extraction
 Entity Linking (Ontology Mapping)
 Negation Detection

16. Entity Extraction
+ Entity Linking, Negation Detection

17. Relation Extraction

18. Using Text Analytics for Health
Pip Install the Azure TextAnalytics SDK:
pip install azure.ai.textanalytics==5.1.0b5
from azure.core.credentials import AzureKeyCredential
from azure.ai.textanalytics import TextAnalyticsClient
client = TextAnalyticsClient(endpoint=endpoint,
credential=AzureKeyCredential(key), api_version="v3.1-preview.3")
Create the client:
documents = ["I have not been administered any aspirin, just 300 mg or favipiravir daily."]
poller = client.begin_analyze_healthcare_entities(documents)
result = poller.result()
Do the call:

19. Analysis Result
I have not been administered any aspirin, just 300 mg or favipiravir
daily.
HealthcareEntity(text=300 mg, category=Dosage, subcategory=None, length=6, offset=47, confidence_score=1.0,
data_sources=None, related_entities={HealthcareEntity(text=favipiravir, category=MedicationName, subcategory=None, length=11, offset=57,
confidence_score=1.0, data_sources=[HealthcareEntityDataSource(entity_id=C1138226, name=UMLS), HealthcareEntityDataSource(entity_id=J05AX27,
name=ATC), HealthcareEntityDataSource(entity_id=DB12466, name=DRUGBANK), HealthcareEntityDataSource(entity_id=398131, name=MEDCIN),
HealthcareEntityDataSource(entity_id=C462182, name=MSH), HealthcareEntityDataSource(entity_id=C81605, name=NCI),
HealthcareEntityDataSource(entity_id=EW5GL2X7E0, name=NCI_FDA)], related_entities={}): 'DosageOfMedication'})
aspirin (C0004057) [MedicationName]
300 mg [Dosage] --DosageOfMedication--> favipiravir (C1138226) [MedicationName]
favipiravir (C1138226) [MedicationName]
daily [Frequency] --FrequencyOfMedication--> favipiravir (C1138226)
[MedicationName]

20. Analyzing CORD Abstracts
• All abstracts contained in CSV metadata file
• Split 400k papers into chunks of 500
• Id, Title, Journal, Authors, Publication Date
• Shuffle by date in order to get representative sample in each chunk
• Enrich each json file with text analytics data
• Entities, Relations
• Parallel processing using Azure ML

21. Parallel Sweep Job in Azure ML
CORD Dataset
(metadata.csv)
Output
storage
(Database)
Azure ML Cluster
experiment_name: cog-sweep
algorithm: grid
type: sweep_job
search_space:
number:
type: choice
values: [0, 1]
trial:
command: >-
python process.py
--number {search_space.number}
--nodes 2
--data {inputs.metacord}
inputs:
metacord:
data: azureml:metacord:1
mode: download
max_total_trials: 2
max_concurrent_trials: 2
timeout_minutes: 10000
$ az ml job create –f sweepjob.yml
…
# Parse command-line
df = pd.read_csv(args.data)
for i,(id,x) in enumerate(df.iterrows()):
if i%args.nodes == args.number:
# Process the record
# Store the result
process.py

22. Results of Text Analytics Processing
{
"gh690dai": {
"id": "gh690dai",
"title": "Beef and Pork Marketing Margins
and Price Spreads during COVID-19",
"authors": "Lusk, Jayson L.; Tonsor,
Glynn T.; Schulz, Lee L.",
"journal": "Appl Econ Perspect Policy",
"abstract": "...",
"publish_time": "2020-10-02",
"entities": [
{
"offset": 0,
"length": 16,
"text": "COVID-19-related",
"category": "Diagnosis",
"confidenceScore": 0.79,
"isNegated": false
},..]
"relations": [
{
"relationType": "TimeOfTreatment",
"bidirectional": false,
"source": {
"uri": "#/documents/0/entities/15",
"text": "previous year",
"category": "Time",
"isNegated": false,
"offset": 704
},
"target": {
"uri": "#/documents/0/entities/13",
"text": "beef",
"category": "TreatmentName",
"isNegated": false,
"offset": 642
}}]},
…

23. Storing Semi-Structured Data into Cosmos DB
Cosmos DB – NoSQL universal solution
Querying semi-structured data with SQL-like language
Paper
Paper
Entity
Entity
Relation
Collection
…
…

24. Cosmos DB & Azure Data Solutions
• Real-time access with fast read and write latencies globally, and throughput and consistency all backed by SLAs
• Multi-region writes and data distribution to any Azure region with the click of a button.
• Independently and elastically scale storage and throughput across any Azure region – even during unpredictable traffic
bursts – for unlimited scale worldwide.

25. Cosmos DB SQL Queries
Get mentioned dosages of a particular medication and papers they
are mentioned in
SELECT p.title, r.source.text
FROM papers p JOIN r IN p.relations
WHERE r.relationType='DosageOfMedication’
AND CONTAINS(r.target.text,'hydro')

26. Further Exploration: Jupyter in Cosmos DB
SQL in Cosmos DB is somehow limited
Good strategy: make query in Cosmos DB, export to Pandas
Dataframe, final exploration in Python
Jupyter support is built into Cosmos DB
Makes exporting query results to DataFrame easy!
%%sql --database CORD --container Papers --output meds
SELECT e.text, e.isNegated, p.title, p.publish_time,
ARRAY (SELECT VALUE l.id FROM l IN e.links
WHERE l.dataSource='UMLS')[0] AS umls_id
FROM papers p
JOIN e IN p.entities
WHERE e.category = 'MedicationName'

27. How Medication Strategies Change

28. Term relations

29. Term Relations

30. Terms Co-occurence
Treatment
Medicine

31. Power BI and No Code / Low Code Data Visualization
• Connect to data, including multiple data sources.
• Shape the data with queries that build insightful, compelling data
models.
• Use the data models to create visualizations and reports.
• Share your report files for others to leverage, build upon, and share.

32. Exploration: PowerBI

33. Exploration: PowerBI

34. Conclusions
Text Mining for Medical Texts can be very valuable resource
for gaining insights into large text corpus.
❶
❷ A Range of Microsoft Technologies can be used to
effectively make this a reality:
• Azure ML for Custom NER training / Parallel Sweep Jobs
• Text Analytics for Health to do NER and ontology mapping
• Cosmos DB to store and query semi-structured data
• Power BI to explore the data interactively to gain insights
• Cosmos DB Jupyter Notebooks to do deep dive into the
data w/Python

35. Resources
• Article: https://soshnikov.com/science/analyzing-medical-papers-with-azure-and-text-
analytics-for-health/
• Text Analytics for Health
• Azure Machine Learning
• Cosmos DB
• Power BI
• Jupyter Notebooks on Azure Machine Learning
• MS LEARN

36. Feedback
Your feedback is important to us.
Don’t forget to rate and review the sessions.

37. Thank You! Francesca Lazzeri, PhD
Principal Cloud Advocate Manager, Microsoft
@frlazzeri
Dmitry Soshnikov, PhD
Senior Cloud Advocate, Microsoft
@shwars