diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..b424e9c Binary files /dev/null and b/.DS_Store differ diff --git a/.idea/NetworkClustering.iml b/.idea/NetworkClustering.iml new file mode 100755 index 0000000..24643cc --- /dev/null +++ b/.idea/NetworkClustering.iml @@ -0,0 +1,12 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100755 index 0000000..d64b8fb --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100755 index 0000000..94a25f7 --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/.idea/workspace.xml b/.idea/workspace.xml new file mode 100755 index 0000000..dddee21 --- /dev/null +++ b/.idea/workspace.xml @@ -0,0 +1,753 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a_array_ext + _betweennness_virtual + a_array_av + var VirtualAdj = a_array_ext(alink_o, av)[0]; + 10 + class + graph + links + svg_graph + line_g + line_gline_g + takeaname + tree_mapingv3 + State + 3 + : 3 + numNode = + console.log + update_group + + + + + + + + + + + true + DEFINITION_ORDER + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + project + + + + + + + + + + + + + + + + project + + + true + + + + DIRECTORY + + false + + + + + + + + + + + 1486928402360 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + file://$PROJECT_DIR$/scripts/math_script.js + 889 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/README.md b/README.md old mode 100644 new mode 100755 index c9d5777..b347610 --- a/README.md +++ b/README.md @@ -1,12 +1,50 @@ -# NetworkClustering -Implementing network clustering algorithms. +# Algorithms for detecting community structure in networks +In this project, we implement algorithms for detecting community structure in networks. +Our web application is available at [Victor Hugo Dataset](https://alex-nguyen.github.io/VictorHugo/)|[Biological Pathway Literature](https://alex-nguyen.github.io/ClusteringIndex500/). -Out web application is available at [online demo](http://hexagon.esy.es/). +### Exploring Topics and Events in Political Blogs +The following image shows the top 100 terms in nearly 100,000 political blog posts in last 10 years (from 2006 to 2015). Terms are color-coded by clusters (generated by our algorithm). The red dashed slider on the left controls the cut-off value for cluster formation. Terms appear together in the same political blogs are connected by links. The link thickness indicates the frequency of collocated terms. -# References +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/text_100.png) + +### Finding Patterns in the IMDB Co-Star Network +The following image shows community structure for the top 100 actors from [IMDB database](http://www.imdb.com/interfaces) in movies rated 8.5 stars or higher. Links connect co-actors in the same movies and color-coded by thier clusters. + +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/imdb_125.png) + +### Protein interactions in Biological Pathway Literature +The following image shows community structure for 125 proteins selected from various Pathway Commons index cards. In particular, a link connects two proteins/complexes if they interact. Nodes are colored by community formation. + +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/IndexCards.png) + +### Author Collaboration in Visualization Publications +The following image shows collaboration network of the top 100 researchers from [Visualization Publication Data Collection](http://www.vispubdata.org/site/vispubdata/). Links connect authors of the same paper. Link thickness highlights the number of papers that they published together. + +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/vis_100.png) + +### Zachary's Karate Club +The following image shows contains the network of friendships between the 34 members of a karate club at a US university, as described by Wayne Zachary in 1977. Dataset at [UCI Network Data Repository](https://networkdata.ics.uci.edu/data.php?id=105). + +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/karate.png) + +### Jazz Musicians network +The following image shows the collaboration network between Jazz musicians. Each node is a Jazz musician and an edge denotes that two musicians have played together in a band from [Koblenz Network Collection](http://konect.uni-koblenz.de/networks/arenas-jazz). + +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/Jazz musician.png) + +### American College Football +The following image shows the network of American football games +between Division IA colleges during regular season Fall 2000, as compiled +by M. Girvan and M. Newman. Dataset: [UCI Network Data Repository](https://networkdata.ics.uci.edu/data.php?id=5). + +![ScreenShot](https://github.com/iDataVisualizationLab/NetworkClustering/blob/master/figures/football.png) + +### References http://journals.aps.org/pre/abstract/10.1103/PhysRevE.69.066133 http://journals.aps.org/pre/abstract/10.1103/PhysRevE.69.026113 http://www.tandfonline.com/doi/abs/10.1080/0022250x.2001.9990249 + +http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022557 diff --git a/convert.html b/convert.html new file mode 100755 index 0000000..4198f24 --- /dev/null +++ b/convert.html @@ -0,0 +1,183 @@ + + + + + \ No newline at end of file diff --git a/data/IMDB_Graph.js b/data/IMDB_Graph.js new file mode 100644 index 0000000..d23ab9b --- /dev/null +++ b/data/IMDB_Graph.js @@ -0,0 +1,26 @@ +var chart = c3.generate({ + data: { + x : 'x', + columns: [['x','250','500','750','1000'], + ['Brandes', 4.356, 16.637, 44.490,94.430], + ['Virtual Node', 8.461, 30.195, 75.712, 131.875], + ['Random Sampling', 2.404, 4.326, 7.219, 9.746] + ], + type: 'bar' + }, + + size: { + width: 700 + + }, + bar: { + width: { + ratio: 0.5 // this makes bar width 50% of length between ticks + } + + // or + //width: 100 // this makes bar width 100px + } +});/** + * Created by vinhtngu on 2/22/17. + */ diff --git a/data/IndexCards.json b/data/IndexCards.json deleted file mode 100644 index dfc864b..0000000 --- a/data/IndexCards.json +++ /dev/null @@ -1,839 +0,0 @@ -{ -"nodes": [ - {"id": "0", "name": "Lysyl hydroxylases", "group": 1}, - {"id": "1", "name": "Procollagen galactosyltransferases", "group": 1}, - {"id": "2", "name": "p300", "group": 1}, - {"id": "3", "name": "HS", "group": 1}, - {"id": "4", "name": "KAT3A", "group": 1}, - {"id": "5", "name": "H31", "group": 1}, - {"id": "6", "name": "H32", "group": 1}, - {"id": "7", "name": "Ca2+", "group": 1}, - {"id": "8", "name": "HDAC1/2 deacetylase complexes", "group": 1}, - {"id": "9", "name": "HDAC8", "group": 1}, - {"id": "10", "name": "HDAC10", "group": 1}, - {"id": "11", "name": "NOTC1", "group": 1}, - {"id": "12", "name": "GHRL", "group": 1}, - {"id": "13", "name": "TMED2", "group": 1}, - {"id": "14", "name": "OPSD", "group": 1}, - {"id": "15", "name": "Procollagen N-proteinases", "group": 1}, - {"id": "16", "name": "PCOLCEs", "group": 1}, - {"id": "17", "name": "Procollagen C-proteinases", "group": 1}, - {"id": "18", "name": "PRMT6", "group": 1}, - {"id": "19", "name": "HMT2", "group": 1}, - {"id": "20", "name": "CPLX1", "group": 1}, - {"id": "21", "name": "BTK", "group": 1}, - {"id": "22", "name": "TRPs", "group": 1}, - {"id": "23", "name": "GLUC", "group": 1}, - {"id": "24", "name": "SARA", "group": 1}, - {"id": "25", "name": "INS", "group": 1}, - {"id": "26", "name": "Src family tyrosine kinases (SFKs)", "group": 1}, - {"id": "27", "name": "NA", "group": 1}, - {"id": "28", "name": "MIB/NEURL", "group": 1}, - {"id": "29", "name": "CD14", "group": 1}, - {"id": "30", "name": "FA9", "group": 1}, - {"id": 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