Data Visualization Tools

With a sharp increase in the volume and complexity of big datasets for research and drug discovery labs, data visualization is needed to clearly express the complex patterns. It is more important than ever to develop data visualization and exploration tools alongside the rest of the analytics, as opposed to later in the game. The Data Visualization Tools track will discuss new visualization tools, dashboards, and platforms, as well as ways that these tools can help solve problems, validate, and interpret the data science and artificial intelligence insights. How can your visualization methods be validated as to their ability to provide full analytic results that may extend well beyond 2 or 3 dimensions?

Final Agenda

Monday, April 20

9:00 am - 5:00 pm Hackathon*

*Pre-registration required.

Tuesday, April 21

7:30 am Workshop Registration Open and Morning Coffee

8:30 am - 3:30 pm Hackathon*

*Pre-registration required.


8:30 - 11:30 am Recommended Morning Pre-Conference Workshops*

W3. Introduction to Data Visualization for Biomedical Applications

Nils Gehlenborg, PhD, Assistant Professor, Department of Biomedical Informatics, Harvard Medical School

Alexander Lex, PhD, Assistant Professor, SCI Institute, School of Computing, University of Utah

12:30 - 3:30 pm Recommended Afternoon Pre-Conference Workshops*

W14. Deep Learning for Image Analysis

Peter Henstock, PhD, AI & Machine Learning Lead, Pfizer

*Separate registration required.

2:00 - 6:30 Main Conference Registration Open

PLENARY KEYNOTE SESSION

4:00 Welcome Remarks

Cindy Crowninshield, RDN, LDN, Executive Event Director, Cambridge Healthtech Institute

 

 

 

4:05 Keynote Introduction

4:15 PLENARY KEYNOTE PRESENTATION: NIH’s Strategic Vision for Data Science

Susan K. Gregurick, PhD, Associate Director, Data Science (ADDS) and Director, Office of Data Science Strategy (ODSS), National Institutes of Health

 

 

 

 

Rebecca Baker, PhD, Director, HEAL (Helping to End Addiction Long-term) Initiative, Office of the Director, National Institutes of Health

 

 

 

 

Riffyn_new 5:00 - 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

 

 

Wednesday, April 22

7:30 am Registration Open and Morning Coffee

PLENARY KEYNOTE SESSION

8:00 Welcome Remarks

Allison Proffitt, Editorial Director, Bio-IT World

 

 

 

8:05 Keynote Introduction

8:15 Toward Preventive Genomics: Lessons from MedSeq and BabySeq

Robert Green, MD, MPH, Professor of Medicine (Genetics) and Director, G2P Research Program/Preventive Genomics Clinic, Brigham & Women’s Hospital, Broad Institute, and Harvard Medical School

 

 

 

8:45 PANEL DISCUSSION: Game On: How AI, Citizen Science, and Human Computation Are Facilitating the Next Leap Forward

Seth CooperSeth Cooper, PhD, Assistant Professor, Khoury College of Computer Sciences, Northeastern University

 

 

 

 

 

Lancashire_LeeLee Lancashire, PhD, Chief Information Officer, Cohen Veterans Bioscience

 

 

 

 

 

Pietro Michelucci, PhD, Director, Human Computation Institute

 

 

 

 

 

Jérôme WaldispühlJérôme Waldispühl, PhD, Associate Professor, School of Computer Science, McGill University

 

 

 

 

 

While the precision medicine movement augurs for better outcomes through targeted prevention and intervention, those ambitions entail a bold new set of data challenges. Various panomic and traditional data streams must be integrated if we are to develop a comprehensive basis for individualized care. However, deriving actionable information requires complex predictive models that depend on the acquisition and integration of patient data on a massive scale. This picture is further complicated by new data streams emerging from quantified self-tracking and health social networks, both of which are driven by experimentation-feedback loops. Tackling these issues may seem insurmountable, but recent advancements in human/AI partnerships and crowdsourcing science adds a new set of capabilities to our analytic toolkit. This talk describes recent work in online collective systems that combine human and machine-based information processing to solve biomedical data problems that have been otherwise intractable, and an information processing ecosystem emerging from this work that could transform the landscape of precision medicine for all stakeholders.

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

CREATING A NARRATIVE WITH YOUR DATA

10:50 Organizer’s Welcome Remarks

Cambridge Healthtech Institute

10:55 Chairperson’s Remarks

11:00 FEATURED PRESENTATION: The State of the Art in Visualizing Multivariate Networks

Lex_AlexanderAlexander Lex, PhD, Assistant Professor, SCI Institute, School of Computing, University of Utah

Multivariate networks are made up of nodes and their relationships (links), but also data about those nodes and links as attributes. Most real-world networks are associated with several attributes, and many analysis tasks depend on analyzing both, relationships and attributes. Visualization of multivariate networks, however, is challenging, especially when both the topology of the network and the attributes need to be considered concurrently. In this state-of-the-art report, we analyze current practices and classify techniques along four axes: layouts, view operations, layout operations, and data operations. We also provide an analysis of tasks specific to multivariate networks and give recommendations for which technique to use in which scenario. Finally, we survey application areas and evaluation methodologies.

11:30 Visualizing the Clinical Research Landscape – And Why It Matters for Ethics, Efficiency, and Transparency

Hey_SpencerSpencer Hey, PhD, Faculty and Co-Director of Research Ethics, Harvard Center for Bioethics, Harvard Medical School

In this talk, I will present three different pictures of clinical research landscapes–one depicting a single drug development trajectory; one depicting a family of development trajectories from drugs in the same class; one depicting the entire research portfolio from ten pharmaceutical companies. I will argue that each of these pictures has something valuable to teach about how to make the research enterprise more efficient, transparent, and ethical.

12:00 pm Sponsored Presentation (Opportunity Available)

12:30 Session Break

12:40 Luncheon Presentation I to be Announced

Frederic Lee, Business Development – Life Sciences, Amazon Web Services

1:10 Luncheon Presentation II (Sponsorship Opportunity Available)

1:40 Session Break

PLATFORMS TO FIND ACTIONABLE INSIGHTS

1:50 Chairperson’s Remarks

Baohong Zhang, PhD, Director of Genome Informatics, Translational Biology, Biogen

1:55 Integrative Data Analysis Platform

Zhang_BaohongBaohong Zhang, PhD, Director of Genome Informatics, Translational Biology, Biogen

We will present CHOmics, a web-based tool for easy profiling of CHO cell line -omics and integrative visualization. The tool has built in a comprehensive pipeline for RNA sequencing data analysis including sequencing/sample quality control, reads alignment and gene count normalization, and statistical analysis (e.g., differential expression analysis and pathway analysis). Unlike other RNAseq tools, CHOmics is designed specifically for CHO cell lines with advanced interactive functionalities to enable users to customize their analysis plan. In addition, it advances visualization by providing powerful ways (e.g., PCA plot, interactive heatmaps, Volcano plot, Pathway visualization, etc.) for visualizing data quality and statistical analysis output.

2:25 Data-Driven Modeling Platform

Corrado_PriamiCorrado Priami, PhD, President & CEO, COSBI

A user-friendly graphical platform is presented to integrate different data types in a single framework and to abstract them into actionable models. The platform speeds up research and development process and promotes data sharing.

2:55 Sponsored Presentation (Opportunity Available)

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing

LET’S GET CLINICAL

4:00 Chairperson’s Remarks

Johan Liwing, Director Market Access RWE Partnerships, Global Commercial Strategy Organization, Janssen

4:05 Tools to Find Actionable Insights in RWE

Johan Liwing, Director Market Access RWE Partnerships, Global Commercial Strategy Organization, Janssen

4:35 Semantic Data Integration Platform Supporting Personalized Healthcare by Pooling and Integrating Diverse Types of Data

Jermakowicz_EwaEwa Jermakowicz, IT Business Partner for PD Scientific Decision Support, Roche  

Truly personalized healthcare is possible only if we have access to meaningful, diverse and integrated data at scale. We established a platform allowing to pool clinical data with molecular, genomics and digital biomarkers for diverse therapeutic areas to fully capitalize Roche scientific data. To address the diversity of the scientific data we leverage a Data Commons approach to process data from source systems and a graph database to pool and share the data.

5:05 Sponsored Presentation (Opportunity Available)

 

Stellus_Technologies

 

 

5:35 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

 

RedRiver

 

 

 


6:45 End of Day

Thursday, April 23

7:30 am Registration Open and Morning Coffee

PLENARY KEYNOTE SESSION & AWARDS PROGRAM

8:00 Organizer’s Remarks

Cindy Crowninshield, RDN, LDN, Executive Event Director, Cambridge Healthtech Institute

 

 

 

 

8:05 Awards Program Introduction

8:10 Benjamin Franklin Award and Laureate Presentation

J.W. Bizzaro, Managing Director, Bioinformatics.org

 

 

 

 

Discngine8:35 Bio-IT World Innovative Practices Awards

Allison Proffitt, Editorial Director, Bio-IT World

 

 

 

 

9:00 AI in Pharma: Where We Are Today and How We Will Succeed in the Future

Natalija Jovanovic, PhD, Chief Digital Officer, Sanofi Pasteur

 

 

 

 

Penguin_Computing_Tagline 9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced at 10:00

 

 

MISSED CONNECTIONS: PHARMA R&D

10:30 Organizer’s Remarks

Cambridge Healthtech Institute

10:35 Chairperson’s Remarks

10:40 Powering Question-Driven Problem Solving to Improve the Chances of Finding New Medicines

Hasan_SamiulSamiul Hasan, PhD, Scientific Analytics and Visualization Director, Data and Computational Sciences, GlaxoSmithKline

Making true “molecule”-“mechanism”-“observation” relationship connections is a time consuming, iterative and laborious process. In addition, it is very easy to miss critical information that affects key decisions or helps make plausible scientific connections. The current practice for deciphering such relationships frequently involves subject matter experts (SMEs) requesting resource from resource-constrained data science departments to refine and redo highly similar ad hoc searches. The result of this is impairment of both the pace and quality of scientific reviews. In this presentation, I show how semantic integration can be made to ultimately become part of an integrated learning framework for more informed scientific decision-making. I will take the audience through our pilot journey and highlight practical learnings that should inform subsequent endeavors.

11:10 Computational Efforts on Drug Repurposing for Rare Diseases

Li_BinBin Li, PhD, Director, Computational Biology, Takeda Pharmaceutics

We conducted in silico screens trying to repurpose >100 compounds for ~4000 rare disease indications. Various data types were utilized (protein-protein interaction network, pathways, disease driven genes, competitive intelligence, etc.), and different computational methods were implemented and evaluated. Some biologically interesting drug/disease pairs were observed.

11:40 Presentation to be Announced

 

12:10 pm Session Break

Deloitte_ConvergeHealthastrqqdqbzzwcrefyudayzaebcbewyxxfzea12:20 Luncheon Presentation I to be Announced


Schrodinger12:50 Luncheon Presentation II

 

1:20 Dessert Refreshment Break in the Exhibit Hall with Last Chance Poster Viewing

VISUALIZING AND EXPLORING SINGLE-CELL DATA

1:55 Chairperson’s Remarks

Lijian Yu, PhD, Senior Bioinformatics Specialist, AbbVie

2:00 Pediatric Cell Atlas: Using Single-Cell Technology to Understand Childhood Health and Disease

Deanne Taylor, PhD, Director of Bioinformatics, DBH, Children’s Hospital of Philadelphia

2:30 Scaling scRNASeq Visualization to Unlimited Datasets with Cellxgene Gateway

Saldanha_ALokAlok Saldanha, PhD, Technical Associate Director, NIBR Informatics, Novartis Institutes for Biomedical Research

Cellxgene Gateway is an open source tool (https://github.com/Novartis/cellxgene-gateway) which allows you to use the Cellxgene Server provided by the Chan Zuckerberg with multiple datasets. I will introduce this tool in the context of a typical single-cell RNA-Seq analysis workflow, and touch on deployment issues in an enterprise cloud with a budget.

3:00 A Software Platform to Spot Single Cells in Drug Discovery

Yu_LijianLijian Yu, PhD, Senior Bioinformatics Specialist, AbbVie

As single-cell RNA (scRNA) sequencing is increasingly used as a powerful tool to investigate human diseases and assist drug discovery process by enabling scientists to comprehend the transcriptomes of tens of thousands of individual cells, the volume and complexity of data become a huge challenge. At AbbVie we have teamed with many scientists across the globe to develop a uniform data storage and visualization platform based on Spotifire, robust data storage strategy, and web technologies to develop front end UI. Scientists can now freely explore the data and gain important insights into the cells by utilizing the data across several cells and indications. Authors: Lijian Yu, Anne-Sophie Barthelet, Rishi R. Gupta.

3:30 Embedding Single-Cell RNA-Seq Profiles in Non-Euclidean Spaces

Ding_JiaruiJiarui Ding, PhD, Postdoctoral Researcher, Aviv Regev’s Lab, Broad Institute of MIT and Harvard

Single-cell RNA-Seq has become an invaluable tool for studying biological systems in health and diseases. We introduced scPhere, a scalable deep generative model to embed cells into low-dimensional hyperspherical or hyperbolic spaces, as a more accurate representation of the data. scPhere resolves cell crowding, corrects multiple, complex batch factors, facilitates interactive visualization of large datasets, and gracefully uncovers pseudotemporal trajectories.

4:00 Close of Conference



Platinum Sponsors

accenture

BenchlingNEW

Elsevier-square

L7-informatics

linguamatics

Nutanix

PerkinElmer

Weka