1. Taxonomy-Based Glyph Design– with a Case Study on
Visualizing Workflows of Biological Experiments
Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jim Davies and Min Chen
University of Oxford, UK
2. The Road Map…
Aid quicker exploration and comparison of experimental workflows for
biologists performing experiments and curators who validate them.
3. Glyph: A glyph is a small visual object composed of a number
Getting there of visual channels which can be used independently as well as
constructively to depict attributes of a data record.
e.g. Chernoff Faces e.g. Glyph based on rectangles using color and
Image Sources: http://kspark.kaist.ac.kr/Human orientation.
%20Engineering.files/Chernoff/Chernoff%20Faces.htm
Healey, C et al. Perceptually-Based Brush Strokes for
Nonphotorealistic Visualization 2004
4. Some of the ~4000 concepts
labeling
But, we have a problem… nucleic acid extraction
hybridization
feature extraction
bioassay data transformation
Growth
We have 21,000 studies with > 500,000 individual cultured cells
saccharomyces cerevisiae scr101
experiments giving > 60 processes (actions on pool
materials) and >4000 inputs/outputs to those image acquisition
behavioral stimulus
processes. purify
pcr amplification
normalization
Creating 1000s of glyphs for each individual concept lowess group normalization
is simply not scalable. extraction
Scanning
feature extraction and analysis
We need a systematic process for glyph creation based immunoprecipitation
compound based treatment
on the properties of these concepts. transformation protocol
linear amplification
fresh frozen tissue
saccharomyces cerevisiae bqs252.
exponential growth in ypd.
5. Solution outline
Create a taxonomy Order Visual Channels… Map taxonomy to visual channels.
A structured hierarchical arrangement Color > shape > size > We can create a glyph for items
of concepts. orientation > texture. based on the position in taxonomy.
One or more concepts represented by
leaf nodes And provide design Higher levels in the taxonomy will
guidelines. command better visual channels.
7. Creating the taxonomy…input format
In each scheme, there are sub-classifications (4 in S1).
If a concept can be classified with this classification, it is assigned a 1, otherwise 0.
8. Creating the taxonomy…general workings
The algorithm runs recursively,
selecting each best scheme S
and attempting to sub-classify
each classification C
But how do we select the best
scheme?
9. Metric 1: Coverage
100% coverage yields value of 1
The more concepts a scheme can classify, the better.
11. Metric 3: Sub tree balance
Low standard deviation in number of concepts in each classification yields value closer to 1
A balanced tree is desirable and prevents a tree from having excessive height (greater height = need for more visual channels).
12. Metric 4: Number of Subclasses
Low number of classes yields value close to 1
Schemes with a high number of subclasses are penalized since a high number of subclasses would mean a high number of
levels to map to with the selected visual channels.
Only consider subclasses that are used.
13. Application to our case study
We have 8 schemes shown here, focusing mainly on processes.
14. Application to our case study
We have 21,000 biological studies with > 500,000 individual
experiments giving > 60 processes (actions on materials) and
>4000 inputs/outputs to those processes.
1. Concepts were extracted
2. Categories were created by a domain expert.
3. Taxonomy algorithm applied.
4. Taxonomy on the right created >>
Next we attempt to order visual channels and
create design guidelines.
18. Associative Selective Ordered Quantitative
facilitate grouping of all facilitate selection of one facilitate visual permits extraction of ratios
elements of a variable category of data and ignore ranking of data: without the need to inspect a
despite differing values: others: legend:
texture, color, orientation texture, color, orientation, texture, color & planar & size.
and shape. shape, planar, size & size.
brightness.
20. Visual Hierarchy
In particular we look at:
1.top-down (global);
2.salient feature detection of edges, points and colors.
Since they are most relevant to overview level processing of a scene.
[Palmer 77, Navon 77, Shor 71, Love 99, Kinchla 79]
23. Visual Mapping
Select design options based on the guidelines and the
level of the classification in the taxonomy and map the
scheme to selected Visual Channels and structure
C1 C3 C2
In Vitro In Vivo In Silico
25. Crush test.
Schemes high up in the taxonomy should be distinguishable at low resolution...overview level.
We should be able to distinguish high-
level classes in the taxonomy even at
low resolutions.
27. Contributions
1. Systematic Approach For Glyph Design
• Ordering of concepts
• Ordering of visual channels according to
psychological literature
• Mapping between them
2. Application
• Biological Metadata
• Biological Workflows
In biological experiment workflows, we are showing the biological materials and protocols enacted on materials which result in some data files…e.g. DNA sequence data, protein expression data, etc. The current representation is the representation on the left. It does not facilitate pattern discovery/recognition and requires zooming in to get any information about the nodes. In other words, it is absent of a valid overview level visualization. Our solution is to use glyphs to replace these text-labeled boxes with glyphs. The presence of iconic memory was introduced by Sperling in 1960. It is shown to facilitate rapid comparison between glyphs in the same display, whereas the effect is less so for text.
Sperling, 1960 - The presence of iconic memory may facilitate rapid comparison between glyphs in the same display, whereas it is less so for texts.
In our problem domain, we have the following numbers at our disposal. >4,000 qualitative terms
Taxonomy and visual channels. Through formulating a glyphs representation based on the taxonomy, we implicitly construct rules for how a glyph is constructed.
Animate.
The first metric for selecting a scheme is the coverage.
Same coverage but Scheme 1 is better for potential use.
Make fair comparison with 3 each side.
When mapped to more abstract visual channels, e.g. color, too many mappings are hard to learn. Unless the color is metaphoric.
Move information about concepts in to earlier slide.
Move information about concepts in to earlier slide.
Move information about concepts in to earlier slide.
I will simply show how we built this table but relatively briefly. If you want more information, you can read the paper and/or speak to me throughout the course of the meeting.
Pop-out effect We looked at many sources of literature on pop-out effectThe power of Visual Channels differ in their ability to contribute to pop out effect. Integral/Separable Visual Channels Some visual channels do not interact well with others, for instance, motion & flicker or width and height are common examples of what are termed integral dimensions .
There are a few theories on how we process information in the visual hierarchy. Local, Global, middle-out and salient feature detection. Some disagreement over exact mechanism used. In our work we focus mainly on the top-down and salient feature detection theories since the glyphs will often be small in relation to the overall visualization.
In Particular domain-specific metaphor... Learning, recognition + memorizing… “ Natural mappings ” [Siirtola 02] between data and their visual counterparts can make it easier for users to infer meaning from the glyph with less effort required to learn and remember them.
We have the taxonomic order and the visual channel order, now we can map between them.
Explain the first level mapping in more detail.
Animate creation of the tree.
Because of the ordering, the top level in the taxonomy will be distinguishable even at low levels.
Franks and Bransford’s study on transformation of prototypes suggested that humans can learn to recognize glyphs by rules consciously as well as unconsciously.
We’ve provided a rule based encoding Franks and Bransford’s study on transformation of prototypes suggested that humans can learn to recognize glyphs by rules consciously as well as unconsciously.