Published on January 29, 2016
1. 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
2. Targeted Therapy against bcr-‐abl -‐-‐ Leukemia (CML)
3. Intertumor and intratumor heterogenity Burrell et al. Nature (2013):338–345
4. Bruin et al, Swanton Science 2014 Slide – thanks to Adam Marcus
5. 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
6. From Daniel Rubin’s Website
7. 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
8. 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
10. 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
11. 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
12. 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
13. 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
14. • 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
Integrative Multi-scale Analysis in Biomedical Data Science: Tools, Methods and Challenges
At this fourth CLSAC workshop, ... Integrative Multi-scale Analysis in Biomedical Data Science: Tools, Methods and Challenges.
... Brook University Institute for Advanced Computational Science ... Integrative Multi-scale Analysis in Biomedical Data Science: Tools, Methods and ...
... Courses for Skills Development in Biomedical Big Data Science ... tools for organizing biomedical Big Data for ... tailored analysis methods ...
... specific biomedical data analysis ... methods and computational tools for ... genomics data analysis, methods for ...
... this center explores new ideas in brain tumor translational research through multi-scale, integrative ... tools, data models, user ... Biomedical Image ...
Researchers have developed image analysis methods to find ... heterogeneous data collected by multi-scale, ... analysis of biomedical data, ...
We developed an integrative data science ... methods for mining observational data are ... data used in this analysis do not ...
Data Science at NYU. Research ... Data science issues stressed are the analysis of ... skilled in developing and utilizing automated methods of analyzing data.