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Health Advances LLC
BOSTON | SAN FRANCISCO | ZUG | HONG KONG
www.healthadvances.com
Artificial Intelligence in
Diagnostic Development
Kristine C. Mechem
Presented at
January 7, 2020
2
Introduction to Artificial Intelligence
Source: Health Advances analysis, Davenport 2019 Future Healthc J.
Types of AI
In Healthcare
Natural
Language
Processing
Robotic
Process
Automation
Machine
Learning
Rule-Based
Expert
Systems
Physical Robots
Focus
Not a Focus
• Learns patterns to
classify data
• Infers conclusions
about data or images
Artificial intelligence (AI) refers to a wide umbrella of techniques that employ computer
software to perform ‘human-like’ skills and can be employed for various uses in healthcare.
• Turns language into data
points
• Can create, understand, and
classify clinical documentation
or research reports
• Sets up ‘if-then’ rules
to guide prompts
• Used in electronic
medical records for
clinical decision
support
• Drives robotic surgical systems
• Used in many types of surgical procedures
• Performs structured
digital automations
• Used in routine tasks
such as hospital billing
and records
3
Machine learning (ML) is a form of artificial intelligence that generates algorithms to detect
useful patterns from large, unstructured data sets.
Overview of Machine Learning Algorithms
Unsupervised learning:
Looks for patterns to group data in the
absence of ground truth (e.g., diagnosis)
Supervised learning:
Training data teaches algorithm the
difference between groups
Machine Learning Algorithms
Data Clustering
Cluster Output:
Data points grouped
together by
similarities
Dimensionality
Reduction
Classification
Discrete Output:
Sick vs Healthy
Benign vs Malignant
Type I vs Type II
Regression
Numerical Output:
Disease risk (%)
Mortality (years)
Stage 1 vs 2 vs 3
Source: Health Advances analysis, Medium, Uddin 2019 BMC Med Inform Decis Mak.
Data Output:
Image recognition
Facial recognition
Text mining
Support Vector
Machines
Naïve Bayes
K-Nearest Neighbor
Neural Networks
Linear Regression
Logistic Regression
Decision Tree
Random Forest
K-Means
Hierarchical Clustering
Mixture of Gaussians
Neural Networks
Neural Networks
Autoencoders
Principle Component
Discriminant Analysis
Learning
Type
Algorithm
Class
Output
Type
Example
Algorithms
Dx Signature Development Automated image analysis
Relevant to:
4
Application of ML in Diagnostic Panel Development
Biological Markers
Protein markers
Metabolic analytes
Biopsy material
Clinical Covariates
Medical history
General factors
Tumor morphology
Nucleic Acid Sequencing
Genomic or cfDNA sequencing
RNA transcriptome analysis
Biomarker Signature
Source: Health Advances analysis, Uddin 2019 BMC Med Inform Decis Mak.
ML inputs large amounts of clinical and sample data to identify a biomarker signature that
is characteristic of the disease state, which can then be used as a diagnostic test.
Machine
Learning
5
To diagnose a disease for which no single
factor can provide a diagnosis
• For when no single gene mutation or antigen
characteristically defines a given disease
– Example disease: Lupus erythematosus is not
diagnosable with any single-biomarker test
Train ML on
healthy vs disease to
find biomarker
signature
To provide a more in-depth diagnosis
• For stratifying a disease into various
subgroups and stages, or potential to respond
to a therapy
– Example: OncotypeDx for predicting need for
adjuvant chemotherapy in breast cancer
Train ML on
patient sub-groups
to find differentiating
factors
To improve existing diagnostic tests
• New panels could be easier to use, faster, or
more cost-effective than existing tests, thus
driving wider adoption
– Example: Cologuard replaces invasive colonoscopy
procedure with stool test and improves specificity
over FIT
Train ML to improve
test metrics
ML can facilitate new diagnostics for diseases that were previously undiagnosable or poorly
diagnosed and improve treatment selection by bettering understanding disease progression
Drivers of ML Utilization in Diagnostic Development
Drivers of
ML Utilization
Source: Health Advances interviews and analysis.
6
ML utilization in biomarker signature discovery and diagnostic development falls into two
major use cases: panel-based tests and sequencing-based tests.
ML Use Cases in Diagnostic Panel Development
Panel-Based Tests
Patient Data
Dx Panel:
Gene A
Gene B
Gene C
ML generates a signature in the form of a
handful of biomarkers that can be
integrated into a multi-marker diagnostic
panel. The panel is locked and cannot be
evolved over time.
1 Sequencing-Based Tests
Diagnosis
Report
ML identifies a signature based on deep
sequencing data. Full or extensive
sequencing data is provided for each
new diagnosis case allowing the
algorithm ti evolve over time as it finds
new predictive genes in the dataset.
Patient Data
2
Note: Sequencing-based tests include unbiased proteomic profiling.
Source: Health Advances analysis, company websites.
7
For panel-based tests, the use of ML is limited to the biomarker discovery step. Once the
signature has been identified, the development process is similar to traditional diagnostics.
Use Case: Panel-Based Tests
Data Collection Supervised ML
Marker Validation Panel Design Final Product
All available patient
data is standardized
and inputted
ML trains on known healthy
and disease patients samples
and looks for unique features
ML identifies a biomarker signature
that is a limited number of genes or
proteins that is unique to each group
Set number of identified gene/protein
markers validated in independent
population (100s-1000s)
Markers validated as predictive
of disease incorporated into
diagnostic panel platform (e.g.,
ELISA, qPCR)
Test is a set panel;
the output is put into the
algorithm to calculate a score
Source: Health Advances analysis, company websites.
Signature Identification
Gene A
Gene
B
8
For ML-algorithms, the algorithm retains full sequencing data for each new case, can take
many data points into account, and can evolve over time as training is continuous.
Use Case: Sequencing-Based Tests
Data Collection Unsupervised ML Signature Identification
Algorithm Lockdown Final Product
All available patient data
standardized and inputted
with diagnosis groups
ML clusters data into set
number of groups without
knowing diagnosis
ML plots all available data in
thousands of dimensions and
combinations to create clusters
The clustering algorithm re-iterates
until it correctly clusters patients
by diagnosis, then it is locked
Algorithm validated for its
predictive ability on many
thousands of patients
Full sequencing data is inputted
into the algorithm; the algorithm
can continue training and evolve
Algorithm Validation


Note: Sequencing-based tests include unbiased proteomic profiling.
Source: Health Advances analysis, Decoded Science, company websites.
9
• Large number of
samples needed in
large, global clinical
trials
• Appropriately defined
controls (e.g., heavy
smokers for lung
cancer diagnosis)
• Independent training
and validation sets
• Prospective clinical
trials (retrospective or
banked samples can
be use for discovery,
training)
• Almost all ML-derived
tests will operate as
specialty labs
• VALID Act and
precedent may result
in greater FDA scrutiny
• Sequencing-based
tests can be evolved
without regulatory
input in CLIA
environment
• Physicians are not
satisfied with 80-90%
predictive sensitivity in
some ML tests
• Physicians want to
understand the
scientific logic behind
the biomarker
signatures identified
by ML
• Payers are demanding
prospective clinical
validation
• Payers want to see
that the test ultimately
changes the standard
of care and clinical
outcomes (e.g.,
reduces procedures or
improves outcomes)
• Value based pricing
possible when clinical
outcome is
significantly improved
ML-derived diagnostic tests must gain sufficient evidence in large validation studies, have clear
scientific rationale, and change the course of clinical care to successfully enter the market.
Key Barriers for Market Entry
Source: Health Advances interviews and analysis.
Validation Regulatory Adoption Reimbursement
10
While AI/ML algorithms are largely developed and ready for use, the current major
technical constraints are centered around the inputted data.
Major Technical Limitations
Patient
Data Dx
Source: Health Advances interviews and analysis.
AI Technical
Limitations
Data
Availability
Scientific
Knowledge
Data
Quality
Sample
Bias
Large sample sizes
required restrict use
to higher prevalence
disease areas
Algorithm may over-
train on sample set
and not be accurate
on other populations
Algorithm cannot
replace human
inference of scientific
and medical
knowledge
High-quality patient
sample data/clinical
history required for
analysis
11
Contact Information
Kristine Mechem, PhD
Vice President
kmechem@healthadvances.com
Health Advances LLC
9 Riverside Road
Weston, MA 02493
101 Second Street, Suite 800
San Francisco, CA 94105
781-647-3435
415.834.0800
www.healthadvances.com

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Health advances ai in diagnostic development

  • 1. Health Advances LLC BOSTON | SAN FRANCISCO | ZUG | HONG KONG www.healthadvances.com Artificial Intelligence in Diagnostic Development Kristine C. Mechem Presented at January 7, 2020
  • 2. 2 Introduction to Artificial Intelligence Source: Health Advances analysis, Davenport 2019 Future Healthc J. Types of AI In Healthcare Natural Language Processing Robotic Process Automation Machine Learning Rule-Based Expert Systems Physical Robots Focus Not a Focus • Learns patterns to classify data • Infers conclusions about data or images Artificial intelligence (AI) refers to a wide umbrella of techniques that employ computer software to perform ‘human-like’ skills and can be employed for various uses in healthcare. • Turns language into data points • Can create, understand, and classify clinical documentation or research reports • Sets up ‘if-then’ rules to guide prompts • Used in electronic medical records for clinical decision support • Drives robotic surgical systems • Used in many types of surgical procedures • Performs structured digital automations • Used in routine tasks such as hospital billing and records
  • 3. 3 Machine learning (ML) is a form of artificial intelligence that generates algorithms to detect useful patterns from large, unstructured data sets. Overview of Machine Learning Algorithms Unsupervised learning: Looks for patterns to group data in the absence of ground truth (e.g., diagnosis) Supervised learning: Training data teaches algorithm the difference between groups Machine Learning Algorithms Data Clustering Cluster Output: Data points grouped together by similarities Dimensionality Reduction Classification Discrete Output: Sick vs Healthy Benign vs Malignant Type I vs Type II Regression Numerical Output: Disease risk (%) Mortality (years) Stage 1 vs 2 vs 3 Source: Health Advances analysis, Medium, Uddin 2019 BMC Med Inform Decis Mak. Data Output: Image recognition Facial recognition Text mining Support Vector Machines Naïve Bayes K-Nearest Neighbor Neural Networks Linear Regression Logistic Regression Decision Tree Random Forest K-Means Hierarchical Clustering Mixture of Gaussians Neural Networks Neural Networks Autoencoders Principle Component Discriminant Analysis Learning Type Algorithm Class Output Type Example Algorithms Dx Signature Development Automated image analysis Relevant to:
  • 4. 4 Application of ML in Diagnostic Panel Development Biological Markers Protein markers Metabolic analytes Biopsy material Clinical Covariates Medical history General factors Tumor morphology Nucleic Acid Sequencing Genomic or cfDNA sequencing RNA transcriptome analysis Biomarker Signature Source: Health Advances analysis, Uddin 2019 BMC Med Inform Decis Mak. ML inputs large amounts of clinical and sample data to identify a biomarker signature that is characteristic of the disease state, which can then be used as a diagnostic test. Machine Learning
  • 5. 5 To diagnose a disease for which no single factor can provide a diagnosis • For when no single gene mutation or antigen characteristically defines a given disease – Example disease: Lupus erythematosus is not diagnosable with any single-biomarker test Train ML on healthy vs disease to find biomarker signature To provide a more in-depth diagnosis • For stratifying a disease into various subgroups and stages, or potential to respond to a therapy – Example: OncotypeDx for predicting need for adjuvant chemotherapy in breast cancer Train ML on patient sub-groups to find differentiating factors To improve existing diagnostic tests • New panels could be easier to use, faster, or more cost-effective than existing tests, thus driving wider adoption – Example: Cologuard replaces invasive colonoscopy procedure with stool test and improves specificity over FIT Train ML to improve test metrics ML can facilitate new diagnostics for diseases that were previously undiagnosable or poorly diagnosed and improve treatment selection by bettering understanding disease progression Drivers of ML Utilization in Diagnostic Development Drivers of ML Utilization Source: Health Advances interviews and analysis.
  • 6. 6 ML utilization in biomarker signature discovery and diagnostic development falls into two major use cases: panel-based tests and sequencing-based tests. ML Use Cases in Diagnostic Panel Development Panel-Based Tests Patient Data Dx Panel: Gene A Gene B Gene C ML generates a signature in the form of a handful of biomarkers that can be integrated into a multi-marker diagnostic panel. The panel is locked and cannot be evolved over time. 1 Sequencing-Based Tests Diagnosis Report ML identifies a signature based on deep sequencing data. Full or extensive sequencing data is provided for each new diagnosis case allowing the algorithm ti evolve over time as it finds new predictive genes in the dataset. Patient Data 2 Note: Sequencing-based tests include unbiased proteomic profiling. Source: Health Advances analysis, company websites.
  • 7. 7 For panel-based tests, the use of ML is limited to the biomarker discovery step. Once the signature has been identified, the development process is similar to traditional diagnostics. Use Case: Panel-Based Tests Data Collection Supervised ML Marker Validation Panel Design Final Product All available patient data is standardized and inputted ML trains on known healthy and disease patients samples and looks for unique features ML identifies a biomarker signature that is a limited number of genes or proteins that is unique to each group Set number of identified gene/protein markers validated in independent population (100s-1000s) Markers validated as predictive of disease incorporated into diagnostic panel platform (e.g., ELISA, qPCR) Test is a set panel; the output is put into the algorithm to calculate a score Source: Health Advances analysis, company websites. Signature Identification Gene A Gene B
  • 8. 8 For ML-algorithms, the algorithm retains full sequencing data for each new case, can take many data points into account, and can evolve over time as training is continuous. Use Case: Sequencing-Based Tests Data Collection Unsupervised ML Signature Identification Algorithm Lockdown Final Product All available patient data standardized and inputted with diagnosis groups ML clusters data into set number of groups without knowing diagnosis ML plots all available data in thousands of dimensions and combinations to create clusters The clustering algorithm re-iterates until it correctly clusters patients by diagnosis, then it is locked Algorithm validated for its predictive ability on many thousands of patients Full sequencing data is inputted into the algorithm; the algorithm can continue training and evolve Algorithm Validation   Note: Sequencing-based tests include unbiased proteomic profiling. Source: Health Advances analysis, Decoded Science, company websites.
  • 9. 9 • Large number of samples needed in large, global clinical trials • Appropriately defined controls (e.g., heavy smokers for lung cancer diagnosis) • Independent training and validation sets • Prospective clinical trials (retrospective or banked samples can be use for discovery, training) • Almost all ML-derived tests will operate as specialty labs • VALID Act and precedent may result in greater FDA scrutiny • Sequencing-based tests can be evolved without regulatory input in CLIA environment • Physicians are not satisfied with 80-90% predictive sensitivity in some ML tests • Physicians want to understand the scientific logic behind the biomarker signatures identified by ML • Payers are demanding prospective clinical validation • Payers want to see that the test ultimately changes the standard of care and clinical outcomes (e.g., reduces procedures or improves outcomes) • Value based pricing possible when clinical outcome is significantly improved ML-derived diagnostic tests must gain sufficient evidence in large validation studies, have clear scientific rationale, and change the course of clinical care to successfully enter the market. Key Barriers for Market Entry Source: Health Advances interviews and analysis. Validation Regulatory Adoption Reimbursement
  • 10. 10 While AI/ML algorithms are largely developed and ready for use, the current major technical constraints are centered around the inputted data. Major Technical Limitations Patient Data Dx Source: Health Advances interviews and analysis. AI Technical Limitations Data Availability Scientific Knowledge Data Quality Sample Bias Large sample sizes required restrict use to higher prevalence disease areas Algorithm may over- train on sample set and not be accurate on other populations Algorithm cannot replace human inference of scientific and medical knowledge High-quality patient sample data/clinical history required for analysis
  • 11. 11 Contact Information Kristine Mechem, PhD Vice President kmechem@healthadvances.com Health Advances LLC 9 Riverside Road Weston, MA 02493 101 Second Street, Suite 800 San Francisco, CA 94105 781-647-3435 415.834.0800 www.healthadvances.com