31 Mart 2010 Çarşamba

Graph of Day 19: Worldcup Visualizations

I found interesting studies of some research group. They visualize world cup history according to some semantics like participations, success etc. using graph layouts.

30 Mart 2010 Salı

Visual Web Mining

During the Internet surfing, found a research website with interesting screens. They aim to visualize the web using appropriate mining techniques. Some of their results are confusing but seems to be beautiful.

Graph of Day 18: Network of Electronic Devices

Network of electronic devices visualized with orthogonal layout.

29 Mart 2010 Pazartesi

Graph of Day 17: Political Networks

They have chosen American politics visualized using Radial-Circular layout.

28 Mart 2010 Pazar

Graph of Day 16: PPI Network 2

Recently, I try to propose a new model for the visualization of PPI networks. The main problem of the model is how to collect subgraphs and how to visualize. There are over 165000 interactions meaning edges and over 6000 nodes. I do not want to code existing algorithms since then the production of subgraphs are done with C++ using OGDF. Interestingly, one of the subgraphs has the property of very high disconnectivity. Here are my first snapshots using Circular and Symmetric layouts in GDE graph editor.



27 Mart 2010 Cumartesi

Graph of Day 15: Map of Science as Graph

Graph of Day 15: The Human Disease Network

Today, I decide to show you different graph, disease network of human is extracted using the tool Diseasome. It is really interesting.

26 Mart 2010 Cuma

Graph of Day 14: Hierarchical Graphs and Trees

Drawing the graph in hierarchic way is well studied drawing paradigm. Sugiyama frameworks and its variants, its each steps are well studied. It is applicable for both drawing graphs and trees.

The most famous tool for obtaining hierarchic graphs is to use graphviz dot program. The samples are;

Grammer tree(Theory of Computation) for a context free languages,

Unix history graph.

As well as dot program, you can use Yed, GoVisual Diagram Editor, Robinviz, Cytoscape and DaVinci tools to draw these types of graphs. You can also use specific libraries OGDF, LEDA, JGraph etc.

24 Mart 2010 Çarşamba

Graph of Day 13: Regularity Network

Today's graph is regularity network. It is one level of looking biological relevance.

They would be very dense, and I obtain one of Biomed journal papers.

You can see this huge graph here.

22 Mart 2010 Pazartesi

Graph of Day 12: Railroad and Metro Maps as Graph

We posted a topic about airline routes as graphs showing the changes in time before. Today, I would like to post similar graphs. Especially, metro maps as graphs are used widely and several research paper published before in leading conferences like Graph Drawing. To draw these graphs, sometimes we draw as it is. For instance, Istanbul metro map, it is not too complicated,

but, railroad map of the entire Europe and its graph is more complicated;

There are also metro maps with good visualizations. For instance, New York metro map as a snapshot:

Producing these graphs and finding some semantics to give importance such as number of passengers, number of freight wagons, number of train routes and showing in the map would be meaningful to analyze the railways. Even, it would be useful to estimate on which route should be invested to utilize more.

21 Mart 2010 Pazar

Graph of Day 11: Protein bound tree

Recently, I attend Chemical Engineering course which is related to bioinformatics and computational biology. It is closer to chemical engineering perspective but also professor tends to integrate our perspective which is almost zero knowledge about some topics :). Protein is formed by amino acids, and each protein is the product of sequence on the genome.

I obtain one protein from PDB, and using matlab, I visualize the protein( 2WTT: P73 Tumor Protein). Interestingly it is a tree structure with atoms and bounds( Figure on the right above ).

Then, when we form complex structure in the form of several proteins. This time we obtain graphs that is formed with several trees. I don't know do people work on it, but analyzing the graphs would be an alternative to sequence matching algorithms. Maybe in the near future, I will have better understanding on these topics.

Same protein with apha helixes;

And just amino acids with different colors;

20 Mart 2010 Cumartesi

Reasons to watch 22 men and one ball

Today, I would like to comment on today's Football game something out of topic of this blog. Actually, it is classic but football is not just a game, it is almost passion for every teenage boys even for girls sometimes. It is also passion for me to watch a football game. The simplicity of the game is apparent; 22 players and one ball, it is like a real time chess. Each teams respond to the opponent team moves while making their own moves as well. I don't know why people start playing football but I believe that the aim is changed a lot and it is not simple as I guess. Did the first football player start playing if he(probably a male , I guess) could see the today's football game? People are going mad in stadiums. We always say that Roman's Ancient Arenas were barbaric, but even now football stadiums could be similar to those arenas. People may die during the matches, players may get hurt and supporters may throw up some pennies to the head of referees. Can you believe that a player may be whistled when it is injured? Do we lose our emotions during the game? In 17 th century, people in Italy, use their mask to hide their identities. Today in stadiums, people do not have masks but they feel free to behave to different. Intentionally, they swear, whistle, shout, fight... Interestingly, as a supporter, we proudly hang some posters to stands as "Welcome to Hell". As I said, we are going far away from simple football game. We increase hospitality although we try to spread a phrase "fair play". Think about the national matches. It is one type of modern wars.

In a conclusion, no matter which happens in the game, I believe we could not give up being interested in football, watching the game, proudly talking about the victories and counting cups. One interesting and bizarre point that comes in my mind is about the number of cups. Do you believe that in Turkcell Super League over 50 seasons, one of the leading team Fenerbahçe(my favorite team as well) has 17 league champions cup. What will happen in 2510? Will we proudly say we have won 17x11 cups( assuming to have same ratio 17/50)? Will we able to? Can you imagine the lifetime of football game? Will human kind reproduce another game? Obviously, who has read that entry in 2010 may not see the next century but I hope today's football will remain with better "fair play" understanding.

Graph of Day 10: Air Traffic Graph

Air traffic graphs are special graphs. There are some visualization methodologies and effort to manage air traffic using these visualizations. Recently, we have more information about US air traffic graphs and we can easily find good graphs and its visualizations. These graphs are perfect for macro view of traffic.

Visualization techniques of these graphs generally rely on determined node positions and curved edges. Generally, edge clustering is done. In the literature, you can easily detect several research paper about the visualization of air traffic.

Futhermore, rather than graphs and its visualizations, there are also computational geometry approaches to manage air routes, attitudes, etc. These are also challenging research areas.

18 Mart 2010 Perşembe

Graph of Day 9: Hairball

Some graph visualizations may turn into "hairball" ( in Turkish: Saç yumağı) when the corresponding graph is too dense. The graph at the side is human protein-protein interactions graphs. Over 25000 genes and its corresponding product protein exist in Human. Its interactions which corresponds to edges are even more than 100000 depending on the interaction types. BIOGRID is one the database that I knew for the PPI networks. Finally, the aim of the visualization system should be rescuing from this hairball results.

17 Mart 2010 Çarşamba

Graph of Day 8: Level by Level Visualization

Today, I would like to mention about the graph abstraction and visualization with several levels. We are now able to visualize the huge graphs at one window. There are some examples which were posted before like the Internet Graph. However, when you look at the whole layout, you could not easily detect useful semantics which is too complicated to understand. So we need an abstraction or visualize within the levels methodology in order to give both details and general perspective.

Abstraction can be done in several ways. One way is clustering. Clustering may occur due to the nature of the graph or it may be done intentionally. One of the widely used algorithm is MCL(Markov Clustering Algorithm) and publicly available. This clustering can be useful to divide the graph into pieces. Furthermore, one can use some filtering methodologies to relax the layout production and view.

Also, visualization within levels is also important. When you level the problem, you can use different layouts for different levels in order to make the visualization semantically. In Robinviz we have done this methodology. We proposed a visualization solution for biclustering using another paradigm called Protein-Protein Interactions network. One central view shows the relations between biclusters and peripheral views shows the corresponding PPI graph.

It is also interesting fact that biological interaction data has also several levels. PPI's are one aspect. The lower aspect molecular interactions which I am now working on their visualizations, is also at one level depth.

Anyway, the total visualization system for these interactions using graph drawing is exciting research that could be perfect for biologist :). However, it is really though business.

16 Mart 2010 Salı

Graph of Day 7: Biological Networks and Cytoscape

Biological networks have several types such as Protein Protein Interaction networks, Molecular Interaction Networks, Regulatory Networks etc. Then after 2000 with the increase in both network numbers and sizes, the new society emerged whom have concentrated on these networks especially originated from graph visualization and drawing researchers.

One of the main tool is Cytoscape. It is well supported and widely used. There are some other tools among them we also provide a tool for the visualization of biclusters and protein-protein interaction networks which is called robinviz.

The sample ppi graph using Cytoscape can be found here.

15 Mart 2010 Pazartesi

Graph of Day 6: Social Networks and Analysis

Today I would like to mention about the graphs of social networks. Social network graphs could have some interesting property that could not easily be generated by random graph generators. There are so many tools and graphs for both academic researches and business challenges. The one that I know is Pajek and it is widely used. I guess that it is free but there are also commercial tools for both analysis and visualization. For example, Sentinel Visualizer is one of them and the graph of today is here.

There is still much more work to do. Especially due to the availability of social structures like facebook, twitter, I believe that visualization would take increasing attention in research community.

10 Mart 2010 Çarşamba

Graph of Day 5: Small World Graph; visualized with Radial Layout

Radial Layouts are special drawing of graphs, that show both hierarchy and centrality. It is like a Sugiyama framework and in one of the published papers, I have seen the radial adaptation of this framework. The aim of radial layouts is to draw graph by introducing layers for the graph and drawing each layer on a circle with less crossings and less bends.

9 Mart 2010 Salı

Graph of Day 4: Small World Graph; visualized with sugiyama framework

Small world graphs are also special graphs. Especially, rather than graph drawings, it is widely used in order to model communities in complex systems. The graph in the picture is created using VisOne tool which is available as binary executable. You can test just creating a small world graph and then run layered layout based on sugiyama framework.

8 Mart 2010 Pazartesi

Graph of Day 3: The Internet Graph

I don't know why we need so large graphs but the interesting thing is that we have also the graph of the Internet. Can you imagine the number of nodes? Even more interesting some people are tried to visualize these graphs.

You really need a good computation power or you need to model abstraction of the whole graph. Luckily, we have some graph clustering methods and we are able to manipulate visual clues, using the current research.

One sample graph can be found here.

7 Mart 2010 Pazar

Graph of Day 2: Clustered Orthogonal Graph

Orthogonal Graphs are interesting graph types. I am able to work on some orthogonal graphs due to my research project. I am not able to go further beyond the application but they are widely used in VLSI design, biological pathway drawings etc.

Clustered means it gives an importance to draw clusters close during the drawing. To begin the theory you can follow this link and to try you can install Go Visual Diagram Editor

And the graph of today is

6 Mart 2010 Cumartesi

Graph of Day 1: GO Graph

Recently, I have decided to publish some graphs that I worked in the past and might I work in the future. The first graph is related to bioinformatics. You can obtain similar one using these web based application. Interestingly, GO categories has a graph eventually. It is hierarchical. The parent node is the super-set of its leaf nodes meaning that each genes in leaf nodes are also inside the parent nodes.

Sample graph is below;