BMI Grand Rounds: Katharine Kevill: MyAsthma MyPlan

Date of Event: 
Wednesday, May 2, 2018

Speaker: Katharine Kevill, MD, MHCDS, Assistant Professor, Department of Pediatrics

Title: MyAsthma MyPlan: A Patient and Provider-Facing App

Time: Wednesday, 3pm—4pm

Location: Atkins Center – HSC Level 4 (Radiology)

AbstractMyAsthma MyPlan is the prototype of a web-based application called MyBody MyPlan which we are developing here at SBUMCthrough a collaboration between clinicians and IT experts. MyAsthma MyPlan is currently a functional application housed on aplatform within the domain. End-users include a diverse ecosystem of stakeholders: patients, parents, communitymembers and members of the health care team. This app is designed to give consistent answers to 3 questions: 1) What isthe plan? 2) How do you do it? 3) How is it going? This talk will explore the information gap in knowledge of an individual’schronic disease self-management plan that led to the development of MyAsthma MyPlan. Using MyAsthma MyPlan as a casestudy, we will consider the key features of the app architecture needed to foster efficient and effective communication of theself-management plan across the ecosystem of stakeholders. Finally, we will consider how this application fits into the transitionto value-based payment.


Educational Objectives:

  1. To appreciate the importance of chronic disease management in the U.S. healthcare system.
  2. To identify the ecosystem of stakeholders who play a role in the implementation of an individual’s chronic disease selfmanagementplan.
  3. To systematically identify barriers to communication of the self-management plan as a patient journeys across time, place andorganizations.
  4. To consider key features of an IT infrastructure needed to foster effective and efficient collaboration among stakeholders.

Andrew Post: Informatics as a Clinical Service for Quality and Research

Date of Event: 
Tuesday, May 1, 2018

Andrew PostSpeaker: Andrew Post, MD, PhD, Associate Professor of Biomedical Informatics at Emory University, Clinical Informatics Architect at Emory Healthcare, and Informatics Core Director of the Georgia Clinical and Translational Science Alliance

Title: Informatics as a Clinical Service for Quality and Research

When: Tuesday, May 1, 2018 2:00 – 3:00PM

Where: Basic Science Tower, L9 Classroom 145 (Pathology)

Abstract: The field of biomedical informatics has grown into academic departments, and recently it became possible for clinicians to gain sub-specialty certification in the field. Informatics as a clinical service contribution is a new concept at most academic centers. Potential contributions include implementation and support of methods and technologies that arose out of the informatics community; connectivity to national data networks; data standardization and integration efforts; and analytics. These contributions ideally take the form of collaborations with the IT and user communities. Methods of contributing fall into two broad categories: one-on-one consultation providing informatics expertise and methods; and provision of self-service data access systems that encode informatics expertise in how they operate. Through these contributions, informatics can close the gap between the providers of clinical data and users of clinical data.

Bio: Andrew Post, MD, PhD is Associate Professor of Biomedical Informatics at Emory University, Clinical Informatics Architect at Emory Healthcare, and Informatics Core Director of the Georgia Clinical and Translational Science Alliance. Dr. Post received his MD from the University of Pennsylvania and his PhD in Biomedical Informatics from the University of Pittsburgh. Dr. Post serves as a design lead for Emory’s clinical data warehouse. He leads Emory’s i2b2 research data warehouse. He conducts research in temporal query; extract, transform and load processes; and healthcare analytics involving clinical data. He leads a software development team in translating novel clinical research informatics methods into production-quality software for deployment at Emory and beyond. In his Georgia Clinical and Translational Science Alliance role, Dr. Post leads efforts to create coordinated access to and management of clinical data across multiple clinical sites in the Atlanta area.

BMI Grand Rounds: Giving the Power Back to Physicians – Geometry and Control in Biomedical Informatics (Part I)

Date of Event: 
Wednesday, April 25, 2018

Romeil S. SandhuSpeaker: Romeil Sandhu, PhD, Assistant Professor of Biomedical Informatics, Stony Brook University

Title: Giving the Power Back to Physicians –  Geometry and Control in Biomedical Informatics (Part I)

Time: Wednesday, 3pm—4pm

Location: Atkins Center – HSC Level 4 (Radiology)

AbstractThis talk is designed to be part one of a two-part seminar series for which we lay several foundational constructs of varying algorithmic approaches in biomedical informatics. Here, we will present basic theory and recent advances in discrete geometry and control theory as applied to network science and computational imaging. To motivate necessary mathematical ingredients, we begin by revisiting classical vision problems in segmentation, shape analysis, shape registration, and pose estimation. Concepts such as curvature and its connection to not only system robustness, but also in shape reconstruction will be introduced. From this, we then shift our attention towards how such concepts can be applied in networks to elucidate functional properties of complex systems. Lastly, we will highlight applications in biomedical informatics and set the foundation for the second part of this seminar which will focus on interactive control and incorporation of expert (physician knowledge) in a proper framework from which a host of useable clinical tools maybe deployed. This talk is designed for a graduate level audience interested recent approaches in information geometry as applied to biomedical informatics..


Educational Objectives:

·        Introduce the non-expert to curvature in a visual intuitive manner.

·        Introduce the non-expert to notions of network robustness.

·        Introduce the non-expert to notions of optimal mass transport.

·        Introduce the non-expert to applications related to theoretical concepts of robustness, curvature, entropy and mass transport.

·        Lay the foundation for the second part seminar series which will focus on how to effectively deploy such concepts in the clinical setting.

Pursuing the Structures of Complex Biomedical Data

Date of Event: 
Thursday, April 19, 2018

Speaker: Chen Chao, PhD, Assistant Professor, Department of Computer Science, CUNY Queens College & CUNY Graduate Center

Title: Pursuing the Structures of Complex Biomedical Data

Time: Thursday, 11:00 am- 12:00 pm

Location: Basic Science Tower, L8 Seminar Room 180

AbstractData science is reshaping biomedical research. Powerful learning methods have been developed to analyze an unprecedented quality and quantity of data. However, we observe a progressively wider gap between these methods and biomedical researchers’ quest for sensible explanations of different phenomena. This gap is largely due to the booming complexity in both the data and the methods. In this talk, I will present two projects in which we designed specialized learning and image processing methods to bring biomedical researchers closer to the truth they are after. In cardiac image analysis, we extracted and analyzed the complex and topology-rich inner surface of human ventricles. In another project, we generated multiple hypotheses from a probabilistic model for domain experts to explore. In both cases, we seek to present the data and the model in a global structural view using topological data analysis and probabilistic graphical models.

BMI Grand Rounds: Enabling Biochemical "Big-Data" With Mass Spectrometry Metabolomics

Date of Event: 
Wednesday, April 18, 2018

Adam RosebrockSpeaker: Adam Rosebrock, PhD, Assistant Professor of Pathology, Member, Stony Brook Cancer Center

Title: Enabling Biochemical "Big-Data" With Mass Spectrometry Metabolomics

Time: Wednesday, 3pm—4pm

Location: Atkins Center – HSC Level 4 (Radiology)

Bio/AbstractDr. Adam Rosebrock is an assistant professor in the Department of Pathology and a member of the Cancer Center at Stony Brook School of Medicine.  Dr. Rosebrock has a longstanding interest in leveraging big data to address fundamental biological challenges. His group is using a combination of mass spectrometry metabolomics, genetics, and big data analytical techniques to build a quantitative understanding of the biochemical wiring of cells across diverse cellular states. Dr. Rosebrock will discuss how his lab is leveraging patterns of metabolic response to identify and understand regulation of pathways and how he is linking changes in biochemical phenotype back to genetic regulators.


Educational Objectives:

  • Introduce analysis of endogenous metabolites by full-scan and targeted mass spectrometry
  • Highlight fundamental differences between metabolic, genomic, and proteomic experiments
  • Discuss current limitations of mass spectrometry metabolomics and present multiple areas where novel computational approaches may improve experimental interpretation.

BMI Grand Rounds: Computational Challenges in Developing Reliable Systems for Next Generation Sequencing

Date of Event: 
Wednesday, April 11, 2018

Chriaag PatelSpeaker: Chiraag Patel, PhD, Medical Chief of Molecular Pathology, Clinical Assistant Professor, Stony Brook University

Title: Bioinformatic Challenges Associated with Clinical Next-Generation Sequencing

Location: Atkins Center – HSC Level 4 (Radiology)

Time: Wed, April 11, 2018 3:00 - 4:00 pm

Bio/Abstract: Dr. Patel is the Medical Chief of Molecular Genetic Pathology, and is currently implementing next-generation sequencing and related technologies for the treatment of cancer at Stony Brook Medicine. He will discuss computational challenges in developing reliable systems for next generation sequencing data generation, analysis, and reporting.


Educational Objectives:

  • Define Bioinformatics Workflow for Clinical NGS
  • Understand Challenges in Data Management
  • Understand Challenges in Relevant and Reproducible Clinical Bioinformatics Analysis

Margaret Schedel: The Sounds of Science

Date of Event: 
Wednesday, April 4, 2018

Margaret SchedelSpeakerMargaret Schedel, PhD, Associate Professor, Composition and Computer Music, Director of cDACT, Director of Undergraduate Studies, Music, Stony Brook University

Title: The Sounds of Science

Location: Atkins Center – HSC Level 4 (Radiology)

Time: Wed, April 4, 2018 3:00 - 4:00 pm

AbstractIn this talk I will cover several case studies of sonification at Stony Brook University, from x-ray scattering of nano-structures, to FMRI’s of the brain, to the gait of patients with Parkinson’s. Sonification can be used for purely scientific purposes,or as the basis for musical composition. There is a continuum between auditorydisplay, which attempts to faithfully reproduce data in audio, and composition inwhich creativity can be king. In each case, aesthetic decisions must be made inorder to translate data into the auditory domain—either to bring out or hide aquality in the data or to massage the sound of the data in order to fit musicalgoals.

 Bio: Margaret Anne Schedel is a composer and cellist specializing in the creation and performance of ferociously interactive media whose works have been performedthroughout the United States and abroad. As an Associate Professor of Music atStony Brook University, she serves as Co-Director of Computer Music and is theDirector of cDACT, the consortium for digital arts, culture and technology. Herresearch focuses on gesture in music, the sustainability of technology in art,and sonification of data. In her spare time she curates exhibitions focusing on theintersection of art, science, new media, and sound.


Aristeidis Sotiras: Advancing Big Neuroimaging Data Analysis for Precision Diagnostics

Date of Event: 
Monday, April 9, 2018

Aristeidis SotirasSpeaker: Aristeidis Sotiras, Ph.D., Center for Biomedical Image Computing and Analytics University of Pennsylvania

Time: Monday, April 9th, 2018  1:30pm—2:30pm

Location: Basic Science Tower, L9 Classroom 145 (Pathology)

Abstract:  Neuroimaging has entered the “big data” era with technologies that produce massive, complex imaging data from multiple modalities that reflect brain structure and function in disease and health. Big neuroimaging data provides unprecedented opportunities to develop computational approaches that can deliver personalized, quantitative disease indexes of diagnostic and prognostic value, and have the potential to quantify the risk of developing a disease, track disease progression or the effect of pharmacological interventions in clinical trials, and deliver patient specific diagnosis before measurable clinical effects occur. I) the high dimensionality of the data may hinder the extraction of interpretable and reproducible information; II) heterogeneity, which is increasingly recognized as a key feature of brain diseases, limits the use of current analytical tools. In this talk, Dr. Sotiras will discuss novel computational approaches that leverage advanced machine learning techniques to address these challenges of I and II. First, he will describe an unsupervised multivariate analysis technique based on non-negative matrix factorization that optimally summarizes high dimensional neuroimaging data through a set of highly interpretable and reproducible imaging patterns. Second, he will discuss a semi-supervised multivariate machine learning technique that aims to reveal disease heterogeneity by jointly performing disease classification and clustering of disease sub-groups. Applications of these approaches in diverse settings highlight their broad impact as well as their role in future directions toward precision medicine.

Serverless OpenHealth at Data Commons Scale - Traversing the 20 Million Patient Records of New York's SPARCS dataset in real-time

Date of Event: 
Wednesday, March 28, 2018

BMI Grand Rounds March 28, 2018Speaker: Jonas Almeida, PhD Professor and Chief Technology Officer, Graduate Program Director, Department of Biomedical Informatics

Title: Serverless OpenHealth at Data Commons Scale - Traversing the 20 Million Patient Records of New York's SPARCS dataset in real-time

Time: Wednesday, March 28, 2018 3:00 pm- 4:00 pm

Location: Health Science Center – Level 3 Classroom 152

Abstract: The serverless OpenHealth approach to the Web as a Global Compute space brings data-intensive computation to consumer-facing platforms with no need for download or installation. This solution is validated with an accompanying interactive web application ( capable of real-time traversal of New York’s 20 million patient records of the Statewide Planning and Research Cooperative System (SPARCS). This application brings the data into the hands of those who use it, in an interactive, graphic display which includes mapping tools, the ability to export the results to Plotly for hands on data visualization and to the Google cloud where artificial intelligence can be applied for immediate data analysis, all on a cell phone That approach relies on the modern browser full stack, and, in particular, its configuration for application assembly by code injection. The opportunity, and need, to expand this approach has since increased markedly, reflecting a wider adoption of Open Data policies by Public Health Agencies. Here, we describe how the serverless scaling challenge can be achieved by the isomorphic mapping between the remote data layer API and a local (client-side, in-browser) operator. This strengthens the argument that the FAIR reproducibility needed for Population Science applications in the age of P4 Medicine is particularly well served by the Web platform.


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