Alexander Lex

interactive data visualization; visual data analysis for molecular biology Last update: 2014-07-16 

Alexander Lex I am a post-doctoral visualization researcher at the Visual Computing Group led by Hanspeter Pfister at the Harvard School of Engineering and Applied Sciences. I received my PhD, Master's and Undergraduate degrees from the Institute for Computer Graphics and Vision at the Graz University of Technology where I studied under the supervision of Prof. Dieter Schmalstieg. In 2011 I was a visiting researcher at Prof. Peter Park's Computational Genomics Research Group at Harvard Medical School.

My primary research interests are interactive data visualization and analysis especially applied to molecular biology and pharmacology, and human computer interaction. My focus is my work on Caleydo, which is both, software that can be used by life science experts to visualize biomolecular data and pathways, but also a platform for implementing prototypes of radical visualization ideas.

I am particularly interested in subset visualization (think slice & dice) for heterogeneous datasets in a molecular biology context. A recent application example of this research is StratomeX, a Caleydo view for cancer subtype analysis.

My second major research topic is visualization related to biological networks (pathways). Examples are the Entourage and enRoute techniques which enable users to explore large quantities of experimental data in the context of multiple pathways.

On the more theoretic side I investigate how to visually express relationships between either visible or currently invisible items on the screen.

I am on the program committee for InfoVis and BioVis. For the latter I'm also poster co-chair. I review for a wide range of publications including IEEE TVCG, CG&A, and BMC Bioinformatics.

Current Research Projects

Check out past projects here

UpSet http://vcg.github.io/upset/about/

UpSet is a visualization technique for set-based data. It was developed out of the desire to make set visualization scalable and efficient. Sets are often visualized with Venn and Euler diagrams, which are neither scalable nor are they good at communicating the underlying data. UpSet is a new approach to set visualization that uses efficient visual encodings for set sizes, intersection sizes and element attributes.

Caleydo http://caleydo.org

Caleydo is our open-source visualization framework developed by a team of research labs. Active since 2008 Caleydo is the platform for many bio-related visualization projects.

Caleydo StratomeXhttp://stratomex.caleydo.org

StratomeX is a visual analysis technique for cancer subtype visualization. Its purpose is to enable analysts to investigate groupings of patients (stratifications) across many datasets and properties enabling them to judge and characterize potential cancer subytpes.

LineUphttp://lineup.caleydo.org

LineUp is a visualization technique for multi-attribute rankings. It enables analysts to create and explore custom rankings of datasets with more than one attribute. We also use LineUp for data assignment, querying and to find good matches or supporting evidence for stratifications in StratomeX, Entourage and enRoute.

Caleydo enRoutehttp://enroute.caleydo.org

enRoute is a technique that enables analysts to explore large and heterogeneous experimental datasets in the context of biological pathways. The central idea is to let users specify relevant paths in a pathway and present these paths in a separate view juxtaposed with experimental data.

Caleydo Entouragehttp://entourage.caleydo.org

Entourage works in concert with enRoute to manage multiple pathways, find interdependencies between pathways and discover related pathways. The core idea of Entourage is that of contextual subsets. To manage the limited display space we don't show multiple complete pathways but instead display a contextually relevant subset of nodes and edges.

Mu-8 /ˈmyuteɪt/http://mu-8.com

Mu-8 (from 'mutate') is our approach to uncover which mutation of an amino-acid sequence causes a functional breakdown in a protein. Mu-8 was conceived as a contribution to the 2013 BioVis Contest and was originally developed together with students of Harvard's CS 171 - Visualization class.

Mu-8 visualizes differences of principal components of a mutated protein relative to its protein family, in addition to the conservation of regions of the sequence, 3D structure and proximity data.

Publications

Peer Reviewed Publications

UpSet screenshot
Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, and Hanspeter Pfister:
UpSet: Visualization of Intersecting Sets
IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), to appear, 2014.
ConTour screenshot
Christian Partl, Alexander Lex, Marc Streit, Hendrik Strobelt, Anne-Mai Wasserman, Hanspeter Pfister, and Dieter Schmalstieg:
ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery
IEEE Transactions on Visualization and Computer Graphics (VAST '14), to appear, 2014.
UpSet screenshot
Samuel Gratzl, Nils Gehlenborg, Alexander Lex, Hanspeter Pfister and Dieter Schmalstieg:
Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets
IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), to appear, 2014.
Hidden content visualization screenshot
Thomas Geymayer, Markus Steinberger, Alexander Lex, Marc Streit, and Dieter Schmalstieg:
Show me the Invisible: Visualizing Hidden Content - Honorable Mention award
To appear in Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI ’14), 2014.
Dual analysis method screenshot
Cagatay Turkay, Alexander Lex, Marc Streit, Hanspeter Pfister, and Helwig Hauser:
Characterizing Cancer Subtypes using the Dual Analysis Approach in Caleydo
IEEE Computer Graphics and Applications, vol. 34, no. 2, pp. 38–47, Mar. 2014.
Mu-8 Screenshot
Johnathan D Mercer, Balaji Pandian, Alexander Lex, Nicolas Bonneel, and Hanspeter Pfister :
Mu-8: Visualizing Differences between Proteins and their Families
BMC Proceedings, to appear, 2014.
Entourage screenshot
Alexander Lex, Christian Partl, Denis Kalkofen, Marc Streit, Anne Mai Wasserman, Samuel Gratzl, Dieter Schmalstieg and Hanspeter Pfister:
Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets
IEEE Transactions on Visualization and Computer Graphics (InfoVis '13), vol. 19, no. 12, pp. 2536–2545, 2013.
LineUp screenshot
Samuel Gratzl, Alexander Lex, Nils Gehlenborg, Hanspeter Pfister, and Marc Streit
LineUp: Visual Analysis of Multi-Attribute Rankings - Best paper award
IEEE Transactions on Visualization and Computer Graphics (InfoVis '13), vol. 19, no. 12, pp. 2277–2286, 2013.
enRoute screenshot
Christian Partl, Alexander Lex, Marc Streit, Denis Kalkofen, Karl Kashofer and Dieter Schmalstieg
enRoute: Dynamic Path Extraction from Biological Pathway Maps for Exploring Heterogeneous Experimental Datasets
BMC Bioinformatics, vol. 14, no. Suppl 19, p. S3, Nov. 2013
enRoute screenshot
Christian Partl, Alexander Lex, Marc Streit, Denis Kalkofen, Karl Kashofer, Dieter Schmalstieg:
enRoute: Dynamic Path Extraction from Biological Pathway Maps for In-Depth Experimental Data Analysis - Best paper award
Proceedings of the IEEE Symposium on Biological Data Visualization (BioVis ’12), 2012, pp. 107–114.
StratomeX screenshot
Alexander Lex, Marc Streit, Hans-Jörg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park and Nils Gehlenborg:
StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization - 3rd best paper award
Computer Graphics Forum (EuroVis '12), pp. 1175-1184, 31(3), June 2012
Uncertainty heatmap illustration
Clemens Holzhüter, Alexander Lex, Dieter Schmalstieg, Hans-Jörg Schulz, Heidrun Schumann and Marc Streit:
Visualizing Uncertainty in Biological Expression Data
Proceedings of the SPIE Conference on Visualization and Data Analysis (VDA '12), pp. 82940O, San Francisco, CA, USA, 2012.
Stack'n'Flip screenshot
Marc Streit, Hans-Jörg Schulz, Alexander Lex, Dieter Schmalstieg, Heidrun Schumann:
Model-Driven Design for the Visual Analysis of Heterogeneous Data
IEEE Transactions on Visualization and Computer Graphics, 18(6), pp.998-1010, 2012.
Caleydo VisBricks screenshot
Alexander Lex, Hans-Jörg Schulz, Marc Streit, Christian Partl and Dieter Schmalstieg:
VisBricks: Multiform Visualization of Large, Inhomogeneous Data
IEEE Transactions on Visualization and Computer Graphics (InfoVis'11), 17(12), pp. 2291-2300, Dec. 2011.
Visual links routing screenshot
Markus Steinberger, Manuela Waldner, Marc Streit, Alexander Lex and Dieter Schmalstieg:
Context-Preserving Visual Links - Best paper award
IEEE Transactions on Visualization and Computer Graphics (InfoVis'11), 2249-2258, 17(12), Dec. 2011.
Filter pipeline screenshot
Thomas Geymayer, Alexander Lex, Marc Streit, Dieter Schmalstieg:
Visualizing the Effects of Logically Combined Filters
Proceedings of the Conference on Information Visualisation (IV’2011), pp. 47-52, London, UK, 2011.
Caleydo Matchmaker screenshot
Alexander Lex, Marc Streit, Christian Partl, Karl Kashofer, Dieter Schmalstieg:
Comparative Analysis of Multidimensional, Quantitative Data
IEEE Transactions on Visualization and Computer Graphics (InfoVis'2010), 16(6), pp. 1027-1035, Nov.-Dec. 2010.
Visual linking screenshot
Manuela Waldner, Werner Puff, Alexander Lex, Marc Streit, Dieter Schmalstieg:
Visual Links across Applications - Best student paper award
Proceedings of the Graphics Interface (GI) 2010, Ottawa, Ontario, Canada, May 31 - June 2 2010.
Caleydo Bucket, heatmap and parallel coordinates screenshot
Alexander Lex, Marc Streit, Ernst Kruijff, Dieter Schmalstieg:
Caleydo: Design and Evaluation of a Visual Analysis Framework for Gene Expression Data in its Biological Context
Proceedings of 2010 IEEE Pacific Visualization Symposium, pp. 57-64, Taipeh, Taiwan, 2010.
Hierarchical heat map
Marc Streit, Alexander Lex, Michael Kalkusch, Kurt Zatloukal, Dieter Schmalstieg:
Caleydo: Connecting Pathways with Gene Expression
Bioinformatics, Oxford Journals, 25(20), pp. 2760-2761, 2009.
Multi-display environment mockup
Manuela Waldner, Alexander Lex, Marc Streit, Dieter Schmalstieg:
Design Considerations for Collaborative Information Workspaces in Multi-Display Environments
Proceedings of Workshop on Collaborative Visualization on Interactive Surfaces (CoVIS'09), at VisWeek, ISSN 1862-5207, pp. 5-8, Atlantic City, USA, 2009.
Parallel coordinates screenshot
Heimo Müller, Robert Reihs, Stefan Sauer, Kurt Zatloukal, Marc Streit, Alexander Lex, Bernhard Schlegl, Dieter Schmalstieg:
Connecting Genes with Diseases
Proceedings of the Symposium on Information Visualization in Biomedical Informatics, 13th International Conference on Information Visualization, Barcelona, Spain, July 2009.
Gaze-based bucket adaption illustration
Marc Streit, Alexander Lex, Heimo Müller, Dieter Schmalstieg:
Gaze-Based Focus Adaption in an Information Visualization System
IADIS Computer Graphics and Visualization and Image Processing 2009 Conference (CGVCVIP), Algarve, Portugal, June 2009.

Thesis Papers

Doctoral Thesis
Title: Visualization of Multidimensional Data with Applications in Molecular Biology
Advisor: Prof. Dieter Schmalstieg
Co-Advisor: Dr. Nils Gehlenborg
Referee: Prof. Robert Kosara
Publication date: March 2012

Master's Thesis
Title: Exploration of Gene Expression Data in a Visually Linked Environment
Supervision: Prof. Dieter Schmalstieg
Publication date: June 2008

Bachelor's Thesis
Title: Evaluation of Medical Image Viewers and
Architectural Software Design for a Medical Image Viewer
Supervision: Prof. Horst Bischof / Dr. Martin Urschler
Publication date: June 2005

Posters and Abstracts

Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister
UpSet for Visualizing Intersecting Sets in Biology
4th Symposium on Biological Data Visualization (BioVis'14), ISMB, Boston, MA, USA, 2014.

Christian Partl, Alexander Lex, Marc Streit, Hendrik Strobelt, Anne-Mai Wassermann, Hanspeter Pfister, Dieter Schmalstieg
ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery
4th Symposium on Biological Data Visualization (BioVis'14), ISMB, Boston, MA, USA, 2014.

Marc Streit, Alexander Lex, Christian Partl, Dieter Schmalstieg, Peter J. Park and Nils Gehlenborg:
StratomeX: Guided Visual Exploration for Tumor Subtype Identification.
In The Cancer Genome Atlas' 2nd Annual Scientific Symposium, Crystal City, VA, USA, 2012.

Alexander Lex, Marc Streit, Hans-Jörg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park, Nils Gehlenborg:
StratomeX: Enabling Visualization-Driven Cancer Subtype Analysis
IEEE Symposium on Biological Data Visualization (BioVis '12), 2012.

Marc Streit, Alexander Lex, Hans-Jörg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park, Nils Gehlenborg:
Guided Visual Analysis for the Identification of Cancer Subtypes
The Cancer Genome Atlas’ Semi-Annual Steering Committee Meeting, Houston, TX, US, 25-27 April 2012.

Alexander Lex, Marc Streit, Hans-Joerg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park, Nils Gehlenborg:
StratomeX - Integrative Visualization of Tumor Subtypes in Cancer Genomics Data Sets
Visualizing Biological Data (VIZBI) 2012, Heidelberg, Germany

Alexander Lex, Peter J. Park and Nils Gehlenborg:
Supporting Subtype Characterization through Integrative Visualization of Cancer Genomics Data Sets
The Cancer Genome Atlas’ 1st Annual Scientific Symposium: Enabling Cancer Research Through TCGA, November 17-18, 2011, Washington, D.C., USA

Marc Streit, Alexander Lex, Helmut Doleisch and Dieter Schmalstieg:
Does software engineering pay off for research? Lessons learned from the Caleydo project.
Proceedings of the second Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Leipzig, Germany, July 1 - 2 2010.

Gudrun Schmidt-Gann, Katharina Schmid, Monika Uehlein, Joachim Struck, Andreas Bergmann, Dieter Schmalstieg, Marc Streit, Alexander Lex, Douw G. van der Nest, Martijn van Griensven and Heinz Redl:
Gene- and Protein Expression Profiling in Liver in a Sepsis-Baboon Model
32nd Annual Meeting on Shock, San Antonio, Texas, 2009.

CALEYDO
Marc Streit, Alexander Lex, Dieter Schmalstieg, Heimo Mueller, Stefan Sauer, Wilhelm Steiner, Kurt Zatloukal
ZMF.Day (Center for Medical Research), Graz, Austria, 2008.

Tutorials & Guest Lectures

Fundamentals of Visual Data Encoding

Guest lecture for CS 179: Design of Usable Interactive Systems, Prof. Krzysztof Gajos
Harvard University, Cambridge, MA, USA, 2014-02-26.

StratomeX & enRoute: Integrative Visualization with Caleydo

Nils Gehlenborg and Alexander Lex
Visualizing Biological Data (VIZBI) 2013, Cambridge, MA, USA, 2013-03.

Cancer Data Analysis with Caleydo StratomeX and enRoute

Alexander Lex and Marc Streit
Symposium on Understanding Cancer Genomics through Information Visualization
Tokyo University, Tokyo, Japan, 2013-02.

Connecting the Dots – Showing Relationships in Data and Beyond

Marc Streit, Hans-Jörg Schulz and Alexander Lex
VisWeek’12, Seattle, WA, USA, 2012-10.

Talks

Visual Data Analysis for Biology and Pharmacology

Novartis Institutes for BioMedical Research, Cambridge, MA, USA, 2014-07-09.

Visualizing Relationships between Biological Pathways

CBMI, Harvard Medical School, Boston, MA, USA, 2014-04-17.
BioIT World Conference & Expo, Boston, MA, USA, 2014-05-01.

Visualizing Multi-Attribute Rankings & A Very Short Visualization Introduction

Harvard Graduate School of Education, Strategic Data Project, Cambridge, MA, USA, 2014-03-07.

Visualization Approaches for Biomolecular Data

Georgia Tech, School of Interactive Computing, Atlanta, GA, USA, 2014-04-08
University of Calgary, Department of Computer Science, Calgary, AB, Canada, 2014-02-13.
MIT CSAIL, Cambridge, MA, USA. 2013-04-12.
UMass Lowell, Lowell, MA, USA, 2013-11-06.

Data Visualization in Molecular Biology.

Novartis Institutes for BioMedical Research, Cambridge, MA, USA, 2013-07-29.

enRoute: Dynamic Path Extraction from Biological Pathway Maps for Exploring Heterogeneous Experimental Datasets

BioIT World Conference & Expo, Boston, MA, USA, 2013-04-10.
Visualizing Biological Data (VIZBI) 2013, Cambridge, MA, USA, 2013-03-20
Symposium on Understanding Cancer Genomics through Information Visualization at Tokyo University, Tokyo, Japan. 2013-02-22.

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization

IEEE BioVis 2012, Seattle, Washington, USA. 14.10.2012
EuroVis 2012, paper presentation, Vienna, Austria, 2012-06-07.

VisBricks: Multiform Visualization of Large, Inhomogeneous Data

IEEE InfoVis 2011, Providence, Rhode Island, USA. Paper presentation, 2011-10-26.

Visualizing Biomolecular Data with the Caleydo Framework

CBMI, Harvard Medical School, Boston, MA, USA, 2011-08-12.
MRC Laboratory of Molecular Biology (LMB), Cambridge, UK, 2010-09-21.
European BioInformatics Institute (EBI), Cambridge, UK, 2010-09-20.

Visualizing the Effects of Logically Combined Filters

Information Visualization 2011, London, UK. Paper presentation, 2011-07-14.

Comparative Analysis of Multidimensional, Quantitative Data

IEEE InfoVis 2010, Salt Lake City, Utah, USA. Paper presentation, 2010-10-28.

Caleydo: Visual Analysis of Biomolecular Data

VCBM 2010 Leipzig, Germany, 2010-07-02.

Caleydo and Visual Links

VRVis Research Company, Vienna, Austria. 2010-03-11

Caleydo: Design and Evaluation of a Visual Analysis Framework for Gene Expression Data in its Biological Context.

PacificVis 2010, Taipei, Taiwan. Paper presentation, 2010-03-03.

Caleydo: Visualization of Gene Expression Data in the Context of Biological Processes

AUVA Research Center for Traumatology, Vienna, Austria, 2009-02-26.

Novel InfoVis Techniques Applied to Pathways and Gene Expression Data

Institute for Genomics and Bioinformatics, Graz University of Technology, Austria, 2008-07-10.

Teaching and Student Projects

Guest Lectures

Courses at Harvard University

Courses at TU Graz

Mentored Students

I have supervised many student projects on all levels - PhD, bachelor's thesis, master project and master's thesis, both at Harvard and at TU Graz. For a list of previous and ongoing students go here.

Looking for a Project?

Are you a student at Harvard looking for a visualization project? I'm always looking for students to work on web-based visualization or on projects in Caleydo. Just write me!