Blog
The latest news from Google AI
Making Healthcare Data Work Better with Machine Learning
Friday, March 2, 2018
Posted by Patrik Sundberg, Software Engineer and Eyal Oren, Product Manager, Google Brain Team
Over the past 10 years, healthcare data has moved from being largely on paper to being
almost completely digitized
in electronic health records. But making sense of this data involves a few key challenges. First, there is no common data representation across vendors; each uses a different way to structure their data. Second, even sites that use the same vendor may differ significantly, for example, they typically use different codes for the same medication. Third, data can be spread over many tables, some containing encounters, some containing lab results, and yet others containing vital signs.
The
Fast Healthcare Interoperability Resources
(FHIR) standard addresses most of these challenges: it has a solid yet extensible data-model, is built on established Web standards, and is rapidly becoming the
de-facto standard
for both individual records and
bulk-data access
. But to enable
large-scale machine learning
, we needed a few additions: implementations in various programming languages, an efficient way to serialize large amounts of data to disk, and a representation that allows analyses of large datasets.
Today, we are happy to
open source
a
protocol buffer
implementation of the FHIR standard, which addresses these issues. The current version supports Java, and support for C++, Go, and Python will follow soon. Support for profiles will follow shortly as well, plus tools to help convert legacy data into FHIR.
FHIR as the core data model
Over the past few years, as we’ve been
partnering
with academic medical centers to apply machine learning to de-identified medical records, it became clear that we needed to address the complexity of healthcare data head-on. Indeed, for machine learning to be effective on medical data, we need a holistic view of what happened to each patient over time. And as a bonus, we want a data representation that is directly applicable in a clinical setting.
While the FHIR standard addresses most of our needs, making healthcare data substantially easier to manage than “legacy” data structures and enabling large-scale machine-learning independent of vendors, we believe the introduction of protocol buffers can help both application developers and (machine-learning) researchers use FHIR.
Current release of protocol buffers
We’ve taken care to make our protocol buffer representation suitable for both programmatic access and database queries. One of the provided examples shows how to upload FHIR data into Google Cloud
BigQuery
and have it available for querying, and we are adding other examples that upload directly from bulk data export. Our protocol buffers adhere to the FHIR standard (they are in fact auto-generated from it) but make for more elegant queries.
The current release does not yet include support for training
TensorFlow
models, but keep an eye out for future updates. We aim to open-source as much as possible of
our recent work
, to help make our research more reproducible and applicable to real-world scenarios. Furthermore, we are working closely with our colleagues in Google Cloud on more
tools
for managing healthcare data at scale.
Acknowledgements
We enjoyed great discussions and helpful feedback from the FHIR community, including
Grahame Grieve
,
Ewout Kramer
,
Josh Mandel
and others. Thanks to our colleagues at
DeepMind
, the
Google Brain team
and our
academic collaborators
.
Labels
accessibility
ACL
ACM
Acoustic Modeling
Adaptive Data Analysis
ads
adsense
adwords
Africa
AI
Algorithms
Android
Android Wear
API
App Engine
App Inventor
April Fools
Art
Audio
Augmented Reality
Australia
Automatic Speech Recognition
Awards
Cantonese
Chemistry
China
Chrome
Cloud Computing
Collaboration
Computational Imaging
Computational Photography
Computer Science
Computer Vision
conference
conferences
Conservation
correlate
Course Builder
crowd-sourcing
CVPR
Data Center
Data Discovery
data science
datasets
Deep Learning
DeepDream
DeepMind
distributed systems
Diversity
Earth Engine
economics
Education
Electronic Commerce and Algorithms
electronics
EMEA
EMNLP
Encryption
entities
Entity Salience
Environment
Europe
Exacycle
Expander
Faculty Institute
Faculty Summit
Flu Trends
Fusion Tables
gamification
Gboard
Gmail
Google Accelerated Science
Google Books
Google Brain
Google Cloud Platform
Google Docs
Google Drive
Google Genomics
Google Maps
Google Photos
Google Play Apps
Google Science Fair
Google Sheets
Google Translate
Google Trips
Google Voice Search
Google+
Government
grants
Graph
Graph Mining
Hardware
HCI
Health
High Dynamic Range Imaging
ICLR
ICML
ICSE
Image Annotation
Image Classification
Image Processing
Inbox
India
Information Retrieval
internationalization
Internet of Things
Interspeech
IPython
Journalism
jsm
jsm2011
K-12
KDD
Keyboard Input
Klingon
Korean
Labs
Linear Optimization
localization
Low-Light Photography
Machine Hearing
Machine Intelligence
Machine Learning
Machine Perception
Machine Translation
Magenta
MapReduce
market algorithms
Market Research
Mixed Reality
ML
MOOC
Moore's Law
Multimodal Learning
NAACL
Natural Language Processing
Natural Language Understanding
Network Management
Networks
Neural Networks
Nexus
Ngram
NIPS
NLP
On-device Learning
open source
operating systems
Optical Character Recognition
optimization
osdi
osdi10
patents
Peer Review
ph.d. fellowship
PhD Fellowship
PhotoScan
Physics
PiLab
Pixel
Policy
Professional Development
Proposals
Public Data Explorer
publication
Publications
Quantum AI
Quantum Computing
renewable energy
Research
Research Awards
resource optimization
Robotics
schema.org
Search
search ads
Security and Privacy
Semantic Models
Semi-supervised Learning
SIGCOMM
SIGMOD
Site Reliability Engineering
Social Networks
Software
Speech
Speech Recognition
statistics
Structured Data
Style Transfer
Supervised Learning
Systems
TensorBoard
TensorFlow
TPU
Translate
trends
TTS
TV
UI
University Relations
UNIX
User Experience
video
Video Analysis
Virtual Reality
Vision Research
Visiting Faculty
Visualization
VLDB
Voice Search
Wiki
wikipedia
WWW
YouTube
Archive
2018
May
Apr
Mar
Feb
Jan
2017
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2016
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2015
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2014
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2013
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2012
Dec
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2011
Dec
Nov
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2010
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2009
Dec
Nov
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
2008
Dec
Nov
Oct
Sep
Jul
May
Apr
Mar
Feb
2007
Oct
Sep
Aug
Jul
Jun
Feb
2006
Dec
Nov
Sep
Aug
Jul
Jun
Apr
Mar
Feb
Feed
Google
on
Follow @googleai
Give us feedback in our
Product Forums
.
