Integrative Multi-Scale Biomedical Informatics

Joel Saltz MD, PhD

Director Center for Comprehensive Informatics

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• Leverage exascale data and computer resources to squeeze the most out of image, sensor or simulation data

• Run lots of different algorithms to derive same features

• Run lots of algorithms to derive complementary features

• Data models and data management infrastructure to manage data products, feature sets and results from classification and machine learning algorithms

Squeezing Information from Spatial Datasets

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INTEGRATIVE BIOMEDICAL INFORMATICS ANALYSIS

Reproducible anatomic/functional characterization at gross level (Radiology) and fine level (Pathology)Integration of anatomic/functional characterization with multiple types of “omic” informationCreate categories of jointly classified data to describe pathophysiology, predict prognosis, response to treatment

In Silico Center for Brain Tumor Research

Specific Aims:

1. Influence of necrosis/hypoxia on gene expression andgenetic classification.

2. Molecular correlates of highresolution nuclear morphometry.

3. Gene expression profiles that predict glioma progression.

4. Molecular correlates of MRIenhancement patterns.

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Integration of heterogeneous multiscale information

•Coordinated initiatives Pathology, Radiology, “omics”

•Exploit synergies between all initiatives to improve ability to forecast survival & response.

Radiology

Imaging

Patient Outco

me

Pathologic Features

“Omic”

Data

Lee Cooper Carlos Moreno

Example: Pathology and Gene Expression Joint Predictors of Recurrence/Survival

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INTEGRATIVE ANALYSIS OF BRAIN TUMOR DATA

In Silico Center for Brain Tumor Research

Key Data Sets

REMBRANDT: Gene expression and genomics data set of all glioma subtypes

The Cancer Genome Atlas (TCGA): Rich “omics” set of GBM, digitized Pathology and Radiology

Pathology and Radiology Images from Henry Ford Hospital, Emory, Thomas Jefferson U, MD Anderson and others

TCGA Research Network

Digital Pathology

Neuroimaging

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** Data obtained by generosity of Lisa Scarpace/Tom Mikkelsen @ HF***Thanks to Adam Flanders/Mark Curtis @ TJU

TCGA and REMBRANDT Datasets

*Some overlap with TCGA main repository but rescanned at 40X** Data obtained by generosity of Lisa Scarpace/Tom Mikkelsen @ HF***Thanks to Adam Flanders/Mark Curtis @ TJU

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*Pending Upload to NBIA portal

** Data obtained by efforts of Lisa Scarpace/Tom Mikkelsen @ HF

Neuroimaging/MRI Data

Brain Tumor Radiology and Pathology

Anaplastic Astrocytoma(WHO grade III)

Glioblastoma(WHO grade IV)

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Morphological Tissue Classification

Nuclei Segmentation

Cellular Features

Jun Kong

Whole Slide Imaging

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Requirements for High Resolution Whole Slide Feature Characterization

• 1010 pixels for each whole slide image• 10 whole slide images per patient• 108 image features per whole slide

image• 10,000 brain tumor patients• 1015 pixels• 1013 features• Hundreds of algorithms• Annotations and markups from dozens

of humans

Distinguishing Characteristic in Gliomas

Use image analysis algorithms to segment and classify microanatomic features (Nuclei, Astrocytoma, Necrosis ...) in whole slide images

Represent the segmentation and classification in a well defined structured format that can be used to correlate the pathology with other data modalities

Oligodendroglioma Astrocytoma

Nuclear QualitiesRound shaped withsmooth regular texture

Elongated with rough, irregular texture

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Astrocytoma vs OligodendroglimaOverlap in genetics, gene expression, histology

Astrocytoma vs Oligodendroglima• Assess nuclear size (area and

perimeter), shape (eccentricity, circularity major axis, minor axis, Fourier shape descriptor and extent ratio), intensity (average, maximum, minimum, standard error) and texture (entropy, energy, skewness and kurtosis).

Whole slide scans from 14 TCGA GBMS (69 slides)7 purely astrocytic in morphology; 7 with 2+ oligo component399,233 nuclei analyzed for astro/oligo featuresCases were categorized based on ratio of oligo/astro cells

Machine-based Classification of TCGA GBMs (J Kong)

TCGA Gene Expression Query: c-Met overexpression

Manual: TCGA Neuropathology Attributes 120 TCGA specimens; 3 Reviewers

 Presence and Degree of:

Microvascular hyperplasia Complex/glomeruloid Endothelial hyperplasia

Necrosis Pseudopalisading pattern Zonal necrosis

Inflammation Macrophages/histiocytes Lymphocytes Neutrophils

 

Differentiation: Small cell component Gemistocytes Oligodendroglial Multi-nucleated/giant cells Epithelial metaplasia           Mesenchymal metaplasia

Other Features Perineuronal/perivascular

satellitosis Entrapped gray or white matter Micro-mineralization  

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Clustergram of selected features used in consensus clustering

Fea

ture

Ind

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Nuclear Features Used to Classify GBMs

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Consensus clustering of morphological signatures

Study includes 200 million nuclei taken from 480 slides corresponding to 167 distinct patients.

Nuclear Features Used to Classify GBMs

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Survival of morphological clusters

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Cluster 2Cluster 3

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Survival of patients by molecular tumor subtype

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Proneural

NeuralClassical

Mesenchymal

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What does this mean? Cluster 2: Gemistocytic Signature

• No association with• Transcriptional class• Age

• Molecular correlates:Wnt signaling, TP53 signaling,Oxidative phosphorylation, mRNA processing

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High Resolution Methods

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Multicore/GPU Implementation

• Nuclear/cell segmentation• Feature extraction• Generate clusters of nuclear/cell

Features• Classify nuclei/cells by feature cluster• Classify patients by populations of

classified nuclei/cells

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Multicore/GPU Feature Extraction

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Multicore/GPU Feature Extraction

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Optimizing CPU/GPU Memory Management

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Optimizing CPU/GPU Irregular Problem Performance

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Scheduling for CPU/GPU System

• PRIORITY: assigns tasks to CPUs or GPUs based on estimate of relative performance gain of each task on GPU vs on CPU and load of the CPUs and GPUs

• Sorted queue of (task, data element) tuples based on the relative speedup expected for each tuple

• As more (task, data element) tuples are created, tuples are inserted into the queue such that the queue remains sorted

• First Come First Served: simple low overhead policy

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Aggregation to reduce kernel invocation and data movement overheads

• Objects are grouped based on which image tile they are segmented from. Each tuple consists of (objects in image tile, feature computation operation)

• Perform group of tasks that are applied to the same data element (or the same chunk of data elements)

• Performance Aware Task Fusion (PATF) -- groups tasks based on GPU speedup values. Two groups of tasks: one group containing tasks with good GPU speedup values and the other group containing the remaining tasks

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Multiscale Systems BiologyEmploy multi-resolution methods to

characterize necrosis, angiogenesis and correlate these with “omics”

No enhancementNormal VesselsStable lesion

?Rim-enhancementVascular ChangesRapid progression

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Correlation of Necrosis, Angiogenesis and “omics”

• GBMs display variable and regionally heterogeneous degrees of necrosis (asterisk) and angiogenesis

• These factors may impact gene expression profiles

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Genes Correlated with Necrosis include Transcription Factors Identified as Regulators of the Mesenchymal Transition

GeneSymbol

SAM q-value(Corrected p-value)

C/EBPB < 0.000001C/EBPD < 0.000001FOSL2 < 0.000001STAT3 0.0047RUNX1 0.0082

Carro MS, et al. Nature 263: 318-25, 2010

• Frozen sections from 88 GBM samples marked to identify regions of necrosis and angiogenesis

• Extent of both necrosis and angiogenesis calculated as a percentage of total tissue area

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VASARI Feature Set

Chad HolderScott HwangAdam Flanders

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Defining Rich Set of Qualitative and Quantitative Image Biomarkers• Community-driven ontology development

project; collaboration with ASNR• Imaging features (5 categories)

– Location of lesion

– Morphology of lesion margin (definition, thickness, enhancement, diffusion)

– Morphology of lesion substance (enhancement, PS characteristics, focality/multicentricity, necrosis, cysts, midline invasion, cortical involvement, T1/FLAIR ratio)

– Alterations in vicinity of lesion (edema, edema crossing midline, hemorrhage, pial invasion, ependymal invasion, satellites, deep WM invasion, calvarial remodeling)

– Resection features (extent of nCE tissue, CE tissue, resected components)

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Emory TJU/CBIT/NCI UVA/Northwestern Henry Ford

David A Gutman1 Adam Flanders3 Max Wintermark8 Lisa Scarpace4

Lee Cooper1 Eric Huang2 Manal Jilwan8 Tom Mikkelsen4

Scott N Hwang1 Robert J Clifford2 Prashant Raghavan8

Chad A Holder1 Dina Hammoud3 Pat Mongkolwat9

Doris Gao1 John Freymann7

Carlos Moreno1 Justin Kirby7

Arun Krishnan1

Jun Kong1

Carl Jaffe6

Seena Dehkharghani1

Joel Saltz1

Dan Brat1

Imaging Predictors of survival and molecular profiles in the TCGA Glioblastoma Data set

The TCGA glioma working group

1Emory University Hospital, Atlanta, GA 2National Cancer Institute, Bethesda, MD.  3Thomas Jefferson University Hospital, Philadelphia, PA. 4Henry Ford University Hospital, Detroit, Michigan. 5National Institute of Health, Bethesda, MD.  6Boston University School of

Medicine, Boston, MA. 7SAIC-Frederick, Inc., Frederick, MD. 8University of Virginia, Charlottesville, VA. 9 Northwestern University Chicago, IL

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Correlative Imaging Results

• Minimal enhancing tumor (≤5%) strongly associated with Proneural classification (p=0.0006).

• >5% proportion of necrosis and the presence of microvascular hyperplasia in pathology slides (p=0.008).

• Greater maximum tumor dimension (T2 signal) associated with present/abundant microvascular hyperplasia (p=0.001).

< 5% Enhancement

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Correlative Imaging Results

• TP53 mutant tumors had a smaller mean tumor sizes (p=0.002) on T2-weighted or FLAIR images.

• EGFR mutant tumors were significantly larger than TP53 mutant tumors (p=0.0005).

• High level EGFR amplification was associated with >5% enhancement and >5% proportion of necrosis (p < 0.01).

> 5% Necrosis

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Automated feature extraction pipeline beingdeveloped for MRI

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Large Scale Data Management

Implemented with IBM DB2 for large scale pathology image metadata (~million markups per slide)

Represented by a complex data model capturing multi-faceted information including markups, annotations, algorithm provenance, specimen, etc.

Support for complex relationships and spatial query: multi-level granularities, relationships between markups and annotations, spatial and nested relationships

Data Models to Represent Feature Sets and Experimental Metadata

PAIS |pās| : Pathology Analytical Imaging Standards

• Provide semantically enabled data model to support pathology analytical imaging

• Data objects, comprehensive data types, and flexible relationships

• Object-oriented design, easily extensible• Reuse existing standards

– Reuse relevant classes already defined in AIM– Follow DICOM WG 26 metadata specifications on WSI

reference– Specimen information in DICOM Supplement 122 and

caTissue– Use caDSR for CDE and NCI Thesaurus for ontology

concepts

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Pathology Imaging GIS

Segmentation

Feature extraction

Image analysis

class Domain Mo...

Annotation

GeometricShape

CalculationObservation

Specimen

ImageReference

Provenance

User

PAIS

EquipmentGroup

AnatomicEntity

Subject

Field

Project

MicroscopyImageReference

DICOMImageReference

TMAImageReference

Markup

Inference

Region

WholeSlideImageReferencePatient

Surface

Collection

AnnotationReference

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Modeling and management of markup and annotation for querying and sharing through parallel RDBMS + spatial DBMS

PAIS model PAIS data management

On the fly data processing for algorithm validation/algorithm sensitivity studies, or discovery of preliminary results

HDFS data staging MapReduce based queries

Workflow, Adaptivity and Quality of Service

• In-transit data processing using filter/stream systems

• Semantic Workflows• Hierarchical pipeline design with coarse

and fine grained components• Adaptivity and Quality of Service

Computerized Classification System for Grading Neuroblastoma

• Background Identification• Image Decomposition (Multi-

resolution levels)• Image Segmentation

(EMLDA)• Feature Construction (2nd

order statistics, Tonal Features)

• Feature Extraction (LDA) + Classification (Bayesian)

• Multi-resolution Layer Controller (Confidence Region)

No

YesImage Tile

InitializationI = L

Background? Label

Create Image I(L)

Segmentation

Feature Construction

Feature Extraction

Classification

Segmentation

Feature Construction

Feature Extraction

Classifier Training

Down-sampling

Training Tiles

Within ConfidenceRegion ?

I = I -1

I > 1?

Yes

Yes

No

No

TRAINING

TESTING

Slides’ Preparation

• 64990 x 59412 pixels in full resolution• Original Size: 10.8 Gb; Compressed Sized: ≈

833Mb

8x

40x

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Semantic Workflows (Wings)Collaborative Work with Yolanda Gil, Mary Hall

• A systematic strategy for composing application components into workflows

• Search for the most appropriate implementation of both components and workflows

• Component optimization– Select among implementation variants of the same

computation– Derive integer values of optimization parameters– Only search promising code variants and a restricted

parameter space

• Workflow optimization– Knowledge-rich representation of workflow properties

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Adaptivity

Framework

• Description Module (Wings): Describe application workflow using semantics of workflow components

• Execution module (Pegasus, DataCutter, Condor): Maps to resources, generates and places fine grained filter/stream pipelines

• Tradeoff Module: Schedules execution based on application level QOS

DataCutter Filter Stream Workflow

Impact

Conclusions

• Increasingly common task: Integrative analysis of complementary multi-resolution and “omic” data sources

• Elucidation of mechanisms, identify medically important disease sub-classes

• Cell level whole slide analysis of whole slide images requires innovations in parallelization, data management

• Integration of Radiology and Pathology has promise but pose additional challenges

• Role of quality of service/on demand computing

Thanks to:• In silico center team: Dan Brat (Science PI), Tahsin Kurc, Ashish Sharma, Tony Pan, David

Gutman, Jun Kong, Sharath Cholleti, Carlos Moreno, Chad Holder, Erwin Van Meir, Daniel Rubin, Tom Mikkelsen, Adam Flanders, Joel Saltz (Director)

• caGrid Knowledge Center: Joel Saltz, Mike Caliguiri, Steve Langella co-Directors; Tahsin Kurc, Himanshu Rathod Emory leads

• caBIG In vivo imaging team: Eliot Siegel, Paul Mulhern, Adam Flanders, David Channon, Daniel Rubin, Fred Prior, Larry Tarbox and many others

• In vivo imaging Emory team: Tony Pan, Ashish Sharma, Joel Saltz• Emory ATC Supplement team: Tim Fox, Ashish Sharma, Tony Pan, Edi Schreibmann, Paul

Pantalone• Digital Pathology R01: Foran and Saltz; Jun Kong, Sharath Cholleti, Fusheng Wang, Tony

Pan, Tahsin Kurc, Ashish Sharma, David Gutman (Emory), Wenjin Chen, Vicky Chu, Jun Hu, Lin Yang, David J. Foran (Rutgers)

• NIH/in silico TCGA Imaging Group: Scott Hwang, Bob Clifford, Erich Huang, Dima Hammoud, Manal Jilwan, Prashant Raghavan, Max Wintermark, David Gutman, Carlos Moreno, Lee Cooper, John Freymann, Justin Kirby, Arun Krishnan, Seena Dehkharghani, Carl Jaffe

• ACTSI Biomedical Informatics Program: Marc Overcash, Tim Morris, Tahsin Kurc, Alexander Quarshie, Circe Tsui, Adam Davis, Sharon Mason, Andrew Post, Alfredo Tirado-Ramos

• NSF Scientific Workflow Collaboration: Vijay Kumar, Yolanda Gil, Mary Hall, Ewa Deelman, Tahsin Kurc, P. Sadayappan, Gaurang Mehta, Karan Vahi

Thanks!