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staff:morris:graphkerneldatasets [2020-03-20 23:45] (current)
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 +<color #​ed1c24>​**The website is now located at [[http://​graphlearning.io]]**</​color>​
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 +
 +===== Benchmark Data Sets for Graph Kernels =====
 +
 +This page contains collected benchmark data sets for the evaluation of graph kernels. The data sets were collected by [[http://​www.ml.informatik.tu-darmstadt.de/​|Kristian Kersting]], [[staff:​kriege|Nils M. Kriege]], [[staff:​morris|Christopher Morris]], [[staff:​mutzel|Petra Mutzel]], and [[http://​sites.wustl.edu/​neumann|Marion Neumann]] with partial support of the 
 +[[http://​www.dfg.de/​en/​|German Science Foundation]] (DFG) within the [[http://​sfb876.tu-dortmund.de/​index.html?​p-selected=%27news%27|Collaborative Research Center
 +SFB 876]] "//​Providing Information by Resource-Constrained Data Analysis//",​ [[http://​sfb876.tu-dortmund.de/​SPP/​sfb876-a6.html|project A6]] "//​Resource-efficient Graph Mining//"​.
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 +  * **02.03.2020:​** Added three new data sets from [29].
 +  * **14.01.2020:​** Added twenty-four new data sets from [24].
 +  * **28.08.2019:​** Added twenty-two new data sets from [28].
 +  * **09.07.2019:​** Added two new data sets from [27].
 +  * **23.10.2018:​** Added five new data sets from [26].
 +  * **13.02.2018:​** Added Cuneiform data set from [25].
 +  * **11.05.2017:​** Added twelve new data sets from [24].
 +  * **17.06.2016:​** Added Synthie data set from [21].
 +  * **10.05.2016:​** Added eight new data sets from [16].
 +  * **19.04.2016:​** Added FRANKENSTEIN data set from [15].
 +  *   ​**13.04.2016:​** Added SYNTHETICnew data set from [3,10].
 +  *   ​**08.04.2016:​** Added six new data sets from [14].
 +
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 +^**Name**^**Source**^**Statistics**|||^**Labels/​Attributes**|||^**Download (ZIP)**|
 +^         ​| ​         |//Num. of Graphs//​|//​Num. of Classes//​|//​Avg. Number of Nodes//​|//​Avg. Number of Edges//​|//​Node Labels//​|//​Edge Labels//​|//​Node Attr. (Dim.)//​|//​Edge Attr. (Dim.)//|
 +^AIDS|[16,​17]| 2000 |2|15.69|16.20|+|+|+ (4)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​AIDS.zip|AIDS]]|
 +^alchemy_dev|[29]| 99776 |R (12)|9.71|10.02|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​alchemy_dev.zip|alchemy_dev]]|
 +^alchemy_test|[29]| 15760 |--|11.25|11.76|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​alchemy_test.zip|alchemy_test]]|
 +^alchemy_valid|[29]| 3951 |R (12)|11.25|11.77|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​alchemy_valid.zip|alchemy_valid]]|
 +^BZR|[7]| 405 |2|35.75|38.36|+|--|+ (3)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​BZR.zip|BZR]]|
 +^BZR_MD|[7,​23]| 306 |2|21.30|225.06|+|+|--|+ (1)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​BZR_MD.zip|BZR_MD]]|
 +^COIL-DEL|[16,​18]| 3900 |100| 21.54 | 54.24 |--|+|+ (2)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​COIL-DEL.zip|COIL-DEL]]|
 +^COIL-RAG|[16,​18]| 3900 |100| 3.01 | 3.02 |--|--|+ (64)|+ (1)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​COIL-RAG.zip|COIL-RAG]]|
 +^COLLAB|[14]| 5000 |3|74.49 | 2457.78|--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​COLLAB.zip|COLLAB]]|
 +^COLORS-3|[27]|10500|11|61.31|91.03|--|--|+ (4)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​COLORS-3.zip|COLORS-3]]|
 +^COX2|[7]| 467 |2|41.22 |43.45|+|--|+ (3)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​COX2.zip|COX2]]|
 +^COX2_MD|[7,​23]| 303 |2|26.28|335.12|+|+|--|+ (1)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​COX2_MD.zip|COX2_MD]]|
 +^Cuneiform|[25]| 267 |30|21.27|44.80|+|+|+ (3)|+ (2)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Cuneiform.zip|Cuneiform]]|
 +^DBLP_v1|[26]|19456|2 |10.48|19.65|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​DBLP_v1.zip|DBLP_v1]]|
 +^DHFR|[7]| 467 |2|42.43|44.54|+|--|+ (3)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​DHFR.zip|DHFR]]|
 +^DHFR_MD|[7,​23]| 393 |2|23.87| 283.01|+|+|--|+ (1)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​DHFR_MD.zip|DHFR_MD]]|
 +^ER_MD|[7,​23]| 446 |2| 21.33| 234.85 | +|+|--|+ (1)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​ER_MD.zip|ER_MD]]|
 +^DD|[6,22]| 1178 |2|284.32| 715.66|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​DD.zip|DD]]|
 +^ENZYMES|[4,​5]| 600 |6|32.63 | 62.14|+|--|+ (18)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​ENZYMES.zip|ENZYMES]]|
 +^Fingerprint|[16,​19]| 2800 |4|5.42 | 4.42|--|--|+ (2)|+ (2)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Fingerprint.zip|Fingerprint]]|
 +^FIRSTMM_DB|[11,​12,​13]| 41 |11|1377.27| 3074.10|+|--|+ (1) |+ (2)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​FIRSTMM_DB.zip|FIRSTMM_DB]]|
 +^FRANKENSTEIN|[15]| 4337 | 2 |16.90| 17.88 |--|--|+ (780) |--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​FRANKENSTEIN.zip|FRANKENSTEIN]]|
 +^IMDB-BINARY|[14]| 1000 |2| 19.77 | 96.53 |--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​IMDB-BINARY.zip|IMDB-BINARY]]|
 +^IMDB-MULTI|[14]| 1500 |3| 13.00 | 65.94 |--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​IMDB-MULTI.zip|IMDB-MULTI]]|
 +^KKI|[26]|83|2 |26.96|48.42|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​KKI.zip|KKI]]|
 +^Letter-high|[16]| 2250 |15| 4.67 |4.50 |--|--|+ (2)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Letter-high.zip|Letter-high]]|
 +^Letter-low|[16]| 2250 |15| 4.68 |3.13 |--|--|+ (2)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Letter-low.zip|Letter-low]]|
 +^Letter-med|[16]| 2250 |15| 4.67 |4.50 |--|--|+ (2)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Letter-med.zip|Letter-med]]|
 +^MCF-7|[28]| 27770 |2|26.39| 28.52 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MCF-7.zip|MCF-7]]|
 +^MCF-7H|[28]| 27770 |2|47.30| 49.43 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MCF-7H.zip|MCF-7H]]|
 +^MOLT-4|[28]| 39765 |2|26.09| 28.13 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MOLT-4.zip|MOLT-4]]|
 +^MOLT-4H|[28]| 39765 |2|46.70| 48.73 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MOLT-4H.zip|MOLT-4H]]|
 +^Mutagenicity|[16,​20]| 4337 |2| 30.32 | 30.77 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Mutagenicity.zip|Mutagenicity]]|
 +^MSRC_9|[13]| 221 |8|40.58| 97.94 |+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MSRC_9.zip|MSCR_9]]|
 +^MSRC_21|[13]| 563 |20|77.52|198.32|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MSRC_21.zip|MSRC_21]]|
 +^MSRC_21C|[13]| 209 |20|40.28 | 96.60|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MSRC_21C.zip|MSRC_21C]]|
 +^MUTAG|[1,​23]| 188 |2|17.93|19.79|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​MUTAG.zip|MUTAG]]|
 +^NCI1|[8,​9,​22]| 4110 |2|29.87|32.30|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​NCI1.zip|NCI1]]|
 +^NCI109|[8,​9,​22]| 4127 |2|29.68| 32.13 |+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​NCI109.zip|NCI109]]|
 +^NCI-H23|[28]| 40353 |2|26.07| 28.10 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​NCI-H23.zip|NCI-H23]]|
 +^NCI-H23H|[28]| 40353 |2|46.67| 48.69 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​NCI-H23H.zip|NCI-H23H]]|
 +^OHSU|[26]|79|2 |82.01|199.66|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​OHSU.zip|OHSU]]|
 +^OVCAR-8|[28]| 40516 |2|26.07| 28.10 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​OVCAR-8.zip|OVCAR-8]]|
 +^OVCAR-8H|[28]| 40516 |2|46.67| 48.70 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​OVCAR-8H.zip|OVCAR-8H]]|
 +^P388|[28]| 41472 |2|22.11| 23.55 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​P388.zip|P388]]|
 +^P388H|[28]| 41472 |2|40.44| 41.88 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​P388H.zip|P388H]]|
 +^PC-3|[28]| 27509 |2|26.35| 28.49 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PC-3.zip|PC-3]]|
 +^PC-3H|[28]| 27509 |2|47.19| 49.32 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PC-3H.zip|PC-3H]]|
 +^Peking_1|[26]|85|2 |39.31|77.35|+|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Peking_1.zip|Peking_1]]|
 +^PTC_FM|[2,​23]| 349 |2|14.11|14.48|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PTC_FM.zip|PTC_FM]]|
 +^PTC_FR|[2,​23]| 351 |2|14.56| 15.00|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PTC_FR.zip|PTC_FR]]|
 +^PTC_MM|[2,​23]| 336 |2|13.97 | 14.32|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PTC_MM.zip|PTC_MM]]|
 +^PTC_MR|[2,​23]| 344 |2|14.29| 14.69|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PTC_MR.zip|PTC_MR]]|
 +^PROTEINS|[4,​6]| 1113 |2|39.06|72.82|+|--|+ (1)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PROTEINS.zip|PROTEINS]]|
 +^PROTEINS_full|[4,​6]| 1113 |2|39.06|72.82|+|--|+ (29)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​PROTEINS_full.zip|PROTEINS_full]]|
 +^REDDIT-BINARY|[14]| 2000 |2| 429.63| 497.75 |--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​REDDIT-BINARY.zip|REDDIT-BINARY]]|
 +^REDDIT-MULTI-5K|[14]| 4999 | 5 |508.52 | 594.87 |--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​REDDIT-MULTI-5K.zip|REDDIT-MULTI-5K]]|
 +^REDDIT-MULTI-12K|[14]| 11929 | 11 | 391.41 | 456.89 |--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​REDDIT-MULTI-12K.zip|REDDIT-MULTI-12K]]|
 +^SF-295|[28]| 40271 |2|26.06| 28.08 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SF-295.zip|SF-295]]|
 +^SF-295H|[28]| 40271 |2|46.65| 48.68 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SF-295H.zip|SF-295H]]|
 +^SN12C|[28]| 40004 |2|26.08| 28.11 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SN12C.zip|SN12C]]|
 +^SN12CH|[28]| 40004 |2|46.69| 48.71 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SN12CH.zip|SN12CH]]|
 +^SW-620|[28]| 40532 |2|26.05| 28.08 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SW-620.zip|SW-620]]|
 +^SW-620H|[28]| 40532 |2|46.62| 48.65 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SW-620H.zip|SW-620H]]|
 +^SYNTHETIC|[3]| 300 |2|100.00| 196.00|--|--|+ (1)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SYNTHETIC.zip|SYNTHETIC]]|
 +^SYNTHETICnew|[3,​10]| 300 |2|100.00| 196.25|--|--|+ (1)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​SYNTHETICnew.zip|SYNTHETICnew]]|
 +^Synthie|[21]| 400 |4|95.00| 172.93|--|--|+ (15)|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Synthie.zip|Synthie]]|
 +^Tox21_AhR_training|[24]|8169|2 |18.09|18.50|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AhR_training.zip|Tox21_AhR_training]]|
 +^Tox21_AhR_testing|[24]|272|2 |22.13|23.05|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AhR_testing.zip|Tox21_AhR_testing]]|
 +^Tox21_AhR_evaluation|[24]|607|2 |17.64|18.06|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AhR_evaluation.zip|Tox21_AhR_evaluation]]|
 +^Tox21_AR_training|[24]|9362|2 |18.39|18.84|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AR_training.zip|Tox21_AR_training]]|
 +^Tox21_AR_testing|[24]|292|2 |22.35|23.32|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AR_testing.zip|Tox21_AR_testing]]|
 +^Tox21_AR_evaluation|[24]|585|2 |17.99|18.45|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AR_evaluation.zip|Tox21_AR_evaluation]]|
 +^Tox21_AR-LBD_training|[24]|8599|2 |17.77|18.16|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AR-LBD_training.zip|Tox21_AR-LBD_training]]|
 +^Tox21_AR-LBD_testing|[24]|253|2 |21.85|22.73|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AR-LBD_testing.zip|Tox21_AR-LBD_testing]]|
 +^Tox21_AR-LBD_evaluation|[24]|580|2 |17.09|17.42|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_AR-LBD_evaluation.zip|Tox21_AR-LBD_evaluation]]|
 +^Tox21_ARE_training|[24]|7167|2 |16.28|16.52|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ARE_training.zip|Tox21_ARE_training]]|
 +^Tox21_ARE_testing|[24]|234|2 |21.99|22.91|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ARE_testing.zip|Tox21_ARE_testing]]|
 +^Tox21_ARE_evaluation|[24]|552|2 |17.01|17.33|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ARE_evaluation.zip|Tox21_ARE_evaluation]]|
 +^Tox21_aromatase_training|[24]|7226|2 |17.50|17.79|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_aromatase_training.zip|Tox21_aromatase_training]]|
 +^Tox21_aromatase_testing|[24]|214|2 |21.65|22.36|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_aromatase_testing.zip|Tox21_aromatase_testing]]|
 +^Tox21_aromatase_evaluation|[24]|528|2 |16.74|16.99|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_aromatase_evaluation.zip|Tox21_aromatase_evaluation]]|
 +^Tox21_ATAD5_training|[24]|9091|2 |17.89|18.30|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ATAD5_training.zip|Tox21_ATAD5_training]]|
 +^Tox21_ATAD5_testing|[24]|272|2 |21.99|22.89|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ATAD5_testing.zip|Tox21_ATAD5_testing]]|
 +^Tox21_ATAD5_evaluation|[24]|619|2 |17.68|18.11|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ATAD5_evaluation.zip|Tox21_ATAD5_evaluation]]|
 +^Tox21_ER_training|[24]|7697|2 |17.58|17.94|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ER_training.zip|Tox21_ER_training]]|
 +^Tox21_ER_testing|[24]|265|2 |22.16|23.13|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ER_testing.zip|Tox21_ER_testing]]|
 +^Tox21_ER_evaluation|[24]|515|2 |17.66|18.10|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ER_evaluation.zip|Tox21_ER_evaluation]]|
 +^Tox21_ER-LBD_training|[24]|8753|2 |18.06|18.47|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ER-LBD_training.zip|Tox21_ER-LBD_training]]|
 +^Tox21_ER-LBD_testing|[24]|287|2 |22.28|23.23|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ER-LBD_testing.zip|Tox21_ER-LBD_testing]]|
 +^Tox21_ER-LBD_evaluation|[24]|599|2 |17.75|18.17|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_ER-LBD_evaluation.zip|Tox21_ER-LBD_evaluation]]|
 +^Tox21_HSE_training|[24]|8150|2 |16.72|17.04|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_HSE_training.zip|Tox21_HSE_training]]|
 +^Tox21_HSE_testing|[24]|267|2 |22.07|23.00|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_HSE_testing.zip|Tox21_HSE_testing]]|
 +^Tox21_HSE_evaluation|[24]|607|2 |17.61|18.01|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_HSE_evaluation.zip|Tox21_HSE_evaluation]]|
 +^Tox21_MMP_training|[24]|7320|2 |17.49|17.83|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_MMP_training.zip|Tox21_MMP_training]]|
 +^Tox21_MMP_testing|[24]|238|2 |21.68|22.55|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_MMP_testing.zip|Tox21_MMP_testing]]|
 +^Tox21_MMP_evaluation|[24]|541|2 |16.67|16.88|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_MMP_evaluation.zip|Tox21_MMP_evaluation]]|
 +^Tox21_p53_training|[24]|8634|2 |17.79|18.19|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_p53_training.zip|Tox21_p53_training]]|
 +^Tox21_p53_testing|[24]|269|2 |22.14|23.04|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_p53_testing.zip|Tox21_p53_testing]]|
 +^Tox21_p53_evaluation|[24]|613|2 |17.34|17.72|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_p53_evaluation.zip|Tox21_p53_evaluation]]|
 +^Tox21_PPAR-gamma_training|[24]|8184|2 |17.23|17.55|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_PPAR-gamma_training.zip|Tox21_PPAR-gamma_training]]|
 +^Tox21_PPAR-gamma_testing|[24]|267|2 |22.04|22.93|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_PPAR-gamma_testing.zip|Tox21_PPAR-gamma_testing]]|
 +^Tox21_PPAR-gamma_evaluation|[24]|602|2 |17.38|17.77|+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Tox21_PPAR-gamma_evaluation.zip|Tox21_PPAR-gamma_evaluation]]|
 +^TRIANGLES|[27]|45000|10|20.85|32.74|--|--|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​TRIANGLES.zip|TRIANGLES]]|
 +^TWITTER-Real-Graph-Partial|[26]|144033|2 |4.03|4.98|+|--|--|+ (1)|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​TWITTER-Real-Graph-Partial.zip|TWITTER-Real-Graph-Partial]]|
 +^UACC257|[28]| 39988 |2|26.09| 28.12 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​UACC257.zip|UACC257]]|
 +^UACC257H|[28]| 39988 |2|46.68| 48.71 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​UACC257H.zip|UACC257H]]|
 +^Yeast|[28]| 79601 |2|21.54| 22.84 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​Yeast.zip|Yeast]]|
 +^YeastH|[28]| 79601 |2|39.44| 40.74 |+|+|--|--|[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​YeastH.zip|YeastH]]|
 +^ | ||||||||| | 
 +^//All Data Sets// | |||||||||[[https://​ls11-www.cs.tu-dortmund.de/​people/​morris/​graphkerneldatasets/​DS_all.zip|DS_all]]|
 +
 +R(N) are regression datasets with N tasks per graph.
 +==== File Format ====
 +
 +The data sets have the following //format// (replace **DS** by the name of the data set):
 +
 +<WRAP box>
 +
 +Let 
 +  * n = total number of nodes
 +  * m = total number of edges
 +  * N = number of graphs
 +
 +  - **DS_A.txt (m lines):** sparse (block diagonal) adjacency matrix for all graphs, each line corresponds to (row, col) resp. (node_id, node_id). //All graphs are undirected. Hence, DS_A.txt contains two entries for each edge.//
 +  - **DS_graph_indicator.txt (n lines):** column vector of graph identifiers for all nodes of all graphs, the value in the i-th line is the graph_id of the node with node_id i
 +  - **DS_graph_labels.txt (N lines):** class labels for all graphs in the data set, the value in the i-th line is the class label of the graph with graph_id i
 +  - **DS_node_labels.txt (n lines):** column vector of node labels, the value in the i-th line corresponds to the node with node_id i
 +
 +
 +
 +There are //optional files// if the respective information is available:
 +
 +  * **DS_edge_labels.txt (m lines; same size as DS_A_sparse.txt):​** labels for the edges in DS_A_sparse.txt ​
 +  * **DS_edge_attributes.txt (m lines; same size as DS_A.txt):​** attributes for the edges in DS_A.txt ​
 +  * **DS_node_attributes.txt (n lines):** matrix of node attributes, the comma seperated values in the i-th line is the attribute vector of the node with node_id i
 +  * **DS_graph_attributes.txt (N lines):** regression values for all graphs in the data set, the value in the i-th line is the attribute of the graph with graph_id i
 +
 +<WRAP center ​  ​100%>​
 +</​WRAP>​
 +
 +
 +
 +</​WRAP>​
 +
 +==== Deep Learning Libraries ====
 +
 +The datasets can also be accessed using [[https://​pytorch-geometric.readthedocs.io/​en/​latest/​modules/​datasets.html|PyTorch Geometric]] and the [[https://​docs.dgl.ai/​api/​python/​data.html|Deep Graph Library]].
 +
 +==== Citing this Website ====
 +We encourage you to refer to our website at http://​graphkernels.cs.tu-dortmund.de if you have used the data sets for your publication. Please use the following BibTeX citation:
 +
 +  @misc{KKMMN2016,​
 +    title  = {Benchmark Data Sets for Graph Kernels},
 +    author = {Kristian Kersting and Nils M. Kriege and Christopher Morris and Petra Mutzel and Marion Neumann},
 +    year   = {2016},
 +    url    = {http://​graphkernels.cs.tu-dortmund.de}
 +  }
 +
 +If your bibliography style does not support the url field, you may use this alternative:​
 +
 +  @misc{KKMMN2016,​
 +    title  = {Benchmark Data Sets for Graph Kernels},
 +    author = {Kristian Kersting and Nils M. Kriege and Christopher Morris and Petra Mutzel and Marion Neumann},
 +    year   = {2016},
 +    note   = {\url{http://​graphkernels.cs.tu-dortmund.de}}
 +  }
 +
 +
 +==== Bibliography ====
 +
 +[1] Debnath, A.K., Lopez de Compadre, R.L., Debnath, G., Shusterman, A.J., and Hansch, C.
 +[[http://​www.ncbi.nlm.nih.gov/​pubmed/​1995902|Structure-activity relationship of mutagenic aromatic and heteroaromatic nitro compounds.
 +Correlation with molecular orbital energies and hydrophobicity]]. J. Med. Chem. 34(2):​786-797 (1991).
 +
 +[2] Helma, C., King, R. D., Kramer, S., and Srinivasan, A. [[https://​doi.org/​10.1093/​bioinformatics/​17.1.107|The Predictive Toxicology Challenge 2000–2001]]. Bioinformatics,​ 2001, 17, 107-108. URL: [[http://​www.predictive-toxicology.org/​ptc|www.predictive-toxicology.org/​ptc]]
 +
 +[3] Feragen, A., Kasenburg, N., Petersen, J., de Bruijne, M., Borgwardt, K.M.: [[http://​papers.nips.cc/​paper/​5155-scalable-kernels-for-graphs-with-continuous-attributes.pdf|Scalable
 +kernels for graphs with continuous attributes]]. In: C.J.C. Burges, L. Bottou, Z. Ghahramani, K.Q. Weinberger (eds.) NIPS, pp. 216-224 (2013).
 +
 +[4] K. M. Borgwardt, C. S. Ong, S. Schoenauer, S. V. N. Vishwanathan,​ A. J. Smola, and H. P. 
 +Kriegel. [[http://​bioinformatics.oxfordjournals.org/​content/​21/​suppl_1/​i47.full.pdf+html|Protein function prediction via graph kernels]]. Bioinformatics,​ 21(Suppl 1):​i47–i56, ​
 +Jun 2005.
 +
 +[5] I. Schomburg, A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, and D. Schomburg. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​14681450|Brenda, ​
 +the enzyme database: updates and major new developments]]. Nucleic Acids Research, 32D:​431–433,​ 2004.
 +
 +[6] P. D. Dobson and A. J. Doig. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​12850146|Distinguishing enzyme structures from non-enzymes without ​
 +alignments]]. J. Mol. Biol., 330(4):​771–783,​ Jul 2003.
 +
 +[7] Sutherland, J. J.; O'​Brien,​ L. A. & Weaver, D. F. [[http://​www.ncbi.nlm.nih.gov/​pubmed/​14632439|Spline-fitting with a
 +genetic algorithm: a method for developing classification structure-activity
 +relationships]]. J. Chem. Inf. Comput. Sci., 2003, 43, 1906-1915.
 +
 +[8] N. Wale and G. Karypis. [[http://​ieeexplore.ieee.org/​xpls/​abs_all.jsp?​arnumber=4053093&​tag=1|Comparison of descriptor spaces for chemical compound retrieval and 
 +classification]]. In Proc. of ICDM, pages 678–689, Hong Kong, 2006.
 +
 +[9] [[http://​pubchem.ncbi.nlm.nih.gov]]
 +
 +[10] http://​image.diku.dk/​aasa/​papers/​graphkernels_nips_erratum.pdf
 +
 +[11] M. Neumann, P. Moreno, L. Antanas, R. Garnett, K. Kersting. [[http://​www-kd.iai.uni-bonn.de/​pubattachments/​716/​neumann2013mlg_grasping.pdf|Graph Kernels for 
 +Object Category Prediction in Task-Dependent Robot Grasping]]. Eleventh Workshop ​
 +on Mining and Learning with Graphs (MLG-13), Chicago, Illinois, USA, 2013.
 +
 +[12] [[http://​www.first-mm.eu/​data.html]]
 +
 +[13] M. Neumann, R. Garnett, C. Bauckhage, and K. Kersting. [[http://​link.springer.com/​article/​10.1007%2Fs10994-015-5517-9|Propagation kernels: efficient graph kernels from propagated information]].Machine Learning, 102(2):​209–245,​ 2016
 +
 +[14] Pinar Yanardag and S.V.N. Vishwanathan. 2015. [[http://​dl.acm.org/​citation.cfm?​id=2783417|Deep Graph Kernels]]. In Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, ACM, New York, NY, USA, 1365-1374. ​
 +
 +[15] Francesco Orsini, Paolo Frasconi, and Luc De Raedt. 2015 [[http://​www.ijcai.org/​Proceedings/​15/​Papers/​528.pdf|Graph invariant kernels]]. In Proceedings of the 24th International Conference on Artificial Intelligence (IJCAI'​15),​ Qiang Yang and Michael Wooldridge (Eds.). AAAI Press 3756-3762.
 +
 +[16] Riesen, K. and Bunke, H.: [[http://​link.springer.com/​chapter/​10.1007%2F978-3-540-89689-0_33|IAM Graph Database Repository for Graph Based Pattern Recognition and Machine Learning]]. In: da Vitora Lobo, N. et al. (Eds.), SSPR&​SPR 2008, LNCS, vol. 5342, pp. 287-297, 2008.
 +
 +[17] [[https://​wiki.nci.nih.gov/​display/​NCIDTPdata/​AIDS+Antiviral+Screen+Data|AIDS Antiviral Screen Data (2004)]]
 +
 +[18] S. A. Nene, S. K. Nayar and H. Murase. [[http://​www.cs.columbia.edu/​CAVE/​software/​softlib/​coil-100.php|Columbia Object Image Library (]]COIL-100),​ Technical Report, Department of Computer Science, Columbia University CUCS-006-96,​
 +Feb. 1996.
 +
 +[19] [[http://​www.nist.gov/​srd/​nistsd4.cfm|NIST Special Database 4]]
 +
 +[20] Jeroen Kazius, Ross McGuire and, and Roberta Bursi. [[http://​pubs.acs.org/​doi/​abs/​10.1021/​jm040835a|Derivation and Validation of Toxicophores for Mutagenicity Prediction]],​ Journal of Medicinal Chemistry 2005 48 (1), 312-320 ​
 +
 +[21] Christopher Morris, Nils M. Kriege, Kristian Kersting, Petra Mutzel. Faster Kernels for Graphs with Continuous Attributes via Hashing, IEEE International Conference on Data Mining (ICDM) 2016
 +
 +[22] Nino Shervashidze,​ Pascal Schweitzer, Erik Jan van Leeuwen, Kurt Mehlhorn, and Karsten M. Borgwardt. 2011. [[http://​www.jmlr.org/​papers/​volume12/​shervashidze11a/​shervashidze11a.pdf|Weisfeiler-Lehman Graph Kernels]]. J. Mach. Learn. Res. 12 (November 2011), 2539-2561. ​
 +
 +[23] Nils Kriege, Petra Mutzel. 2012. [[http://​icml.cc/​2012/​papers/​542.pdf|Subgraph Matching Kernels for Attributed Graphs]]. International Conference on Machine Learning ​ 2012.
 +
 +[24] [[https://​tripod.nih.gov/​tox21/​challenge/​data.jsp|Tox21 Data Challenge 2014]]
 +
 +[25] Nils M. Kriege, Matthias Fey, Denis Fisseler, Petra Mutzel, Frank Weichert. [[http://​proceedings.mlr.press/​v88/​kriege18a.html|Recognizing Cuneiform Signs Using Graph Based Methods]]. International Workshop on Cost-Sensitive Learning (COST), SIAM International Conference on Data Mining (SDM) 2018, 31-44, ''​[[https://​arxiv.org/​abs/​1802.05908|arXiv:​1802.05908]]''​.
 +
 +[26] [[https://​github.com/​shiruipan/​graph_datasets|A Repository of Benchmark Graph Datasets for Graph Classification]]
 +
 +[27] Boris Knyazev, Graham W. Taylor, Mohamed R. Amer. [[https://​arxiv.org/​abs/​1905.02850|Understanding Attention and Generalization in Graph Neural Networks]]
 +
 +[28] [[https://​sites.cs.ucsb.edu/​~xyan/​dataset.htm|Chemical DataSets]]
 +
 +[29] [[https://​arxiv.org/​abs/​1906.09427|Alchemy:​ A Quantum Chemistry Dataset for Benchmarking AI Models]]
 +
 +
 +==== Contact ====
 +
 +<WRAP info box 100%>
 +If you have any questions regarding the data sets or are interested in adding your graph data, please write an email to christopher.morris{{:​staff:​at.gif|}}tu-dortmund.de.
 +</​WRAP>​
 +
  
 
Last modified: 2020-03-20 23:45 (external edit)
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