integrative multi-scale analysis in biomedical data science: tools, methods and challenges
TRANSCRIPT
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Integra(ve Mul(-‐scale Analysis in Biomedical Data Science:
Tools, Methods and Challenges
Joel Saltz Department of Biomedical Informa(cs
Stony Brook University CI4CC October 2015
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Targeted Therapy against bcr-‐abl -‐-‐ Leukemia (CML)
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Intertumor and intratumor heterogenity
Burrell et al. Nature (2013):338–345
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Bruin et al, Swanton Science 2014
Slide – thanks to Adam Marcus
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MulI-‐scale IntegraIve Analysis in Precision Medicine
• Predict treatment outcome, select, monitor treatments
• Reduce inter-‐observer variability in diagnosis
• Computer assisted exploraIon of new classificaIon schemes
• MulI-‐scale cancer simulaIons
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From Daniel Rubin’s Website
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Example: Pathology AnalyIcal Imaging
• Provide rich informaIon about morphological and funcIonal characterisIcs
• Image analysis, feature extracIon on mulIple scales • SpaIally mapped “omics” • MulIple microscopy modaliIes
Glass Slides Scanning Whole Slide Images Image Analysis
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Integra<ve Morphology/”omics”
Quantitative Feature Analysis in Pathology: Emory In Silico Center for Brain Tumor Research (PI = Dan Brat, PD= Joel Saltz) NLM/NCI: Integrative Analysis/Digital Pathology R01LM011119, R01LM009239 (Dual PIs Joel Saltz, David Foran) Marcus Foundation Grant – Ari Kaufman, Joel Saltz
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Associations
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Radiomics
Decoding tumour phenotype by noninvasive imaging using a quan<ta<ve radiomics approach
Hugo J. W. L. Aerts et. Al. Nature Communica/ons 5, ArIcle number: 4006 doi:10.1038/ncomms5006
Features
Pa<ents
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The Driving Meta Applica(on
IdenIfy and segment trillions of mulI-‐scale objects from spaIo-‐temporal datasets Extract features from objects and spaIo-‐temporal regions Support queries against ensembles of features extracted from mulIple datasets StaIsIcal analyses and machine learning to link features to physical and biological phenomena Feature driven simulaIon – use extracted features as simulaIon iniIal, boundary condiIons and to assimilate data into simulaIons
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Detect and track changes in data during production
Invert data for reservoir properties Detect and track reservoir changes
Assimilate data & reservoir properties into
the evolving reservoir model Use simulation and optimization to guide future production
Example: Oil Field Management – Joint NSF ITR with Mary Wheeler, Paul Stoffa
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Commonali(es with Physical Science and Engineering
• MulI-‐scale material/Issue structural, molecular, funcIonal characterizaIon. Design of materials with specific structural, energy storage properIes, brain, regeneraIve medicine, cancer
• IntegraIve mulI-‐scale analyses of the earth, oceans, atmosphere, ciIes, vegetaIon etc – cameras and sensors on satellites, aircra^, drones, land vehicles, staIonary cameras
• Digital astronomy • Hydrocarbon exploraIon, exploitaIon, polluIon remediaIon
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• Aerospace – wind tunnels, acquisiIon of data during flight
• Solid prinIng integraIve data analyses • Autonomous vehicles, e.g. self driving cars • Data generated by numerical simulaIon codes – PDEs, parIcle methods
• Mul$-‐scale Precision Medicine
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Thanks!