The PubMed dataset consists of 19717 scientific publications from PubMed database pertaining to diabetes classified into one of three classes. The citation network consists of 44338 links. Each publication in the dataset is described by a TF/IDF weighted word vector from a dictionary which consists of 500 unique words.

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The Open Graph Benchmark (OGB) is a collection of realistic, large-scale, and diverse benchmark datasets for machine learning on graphs. OGB datasets are automatically downloaded, processed, and split using the OGB Data Loader. The model performance can be evaluated using the OGB Evaluator in a unified manner. OGB is a community-driven initiative in active development.

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The Reddit dataset is a graph dataset from Reddit posts made in the month of September, 2014. The node label in this case is the community, or “subreddit”, that a post belongs to. 50 large communities have been sampled to build a post-to-post graph, connecting posts if the same user comments on both. In total this dataset contains 232,965 posts with an average degree of 492. The first 20 days are used for training and the remaining days for testing (with 30% used for validation). For features, off-the-shelf 300-dimensional GloVe CommonCrawl word vectors are used.

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The FB15k dataset contains knowledge base relation triples and textual mentions of Freebase entity pairs. It has a total of 592,213 triplets with 14,951 entities and 1,345 relationships. FB15K-237 is a variant of the original dataset where inverse relations are removed, since it was found that a large number of test triplets could be obtained by inverting triplets in the training set.

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DBpedia (from "DB" for "database") is a project aiming to extract structured content from the information created in the Wikipedia project. DBpedia allows users to semantically query relationships and properties of Wikipedia resources, including links to other related datasets.

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The Cora dataset consists of 2708 scientific publications classified into one of seven classes. The citation network consists of 5429 links. Each publication in the dataset is described by a 0/1-valued word vector indicating the absence/presence of the corresponding word from the dictionary. The dictionary consists of 1433 unique words.

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FrameNet is a linguistic knowledge graph containing information about lexical and predicate argument semantics of the English language. FrameNet contains two distinct entity classes: frames and lexical units, where a frame is a meaning and a lexical unit is a single meaning for a word.

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The WN18 dataset has 18 relations scraped from WordNet for roughly 41,000 synsets, resulting in 141,442 triplets. It was found out that a large number of the test triplets can be found in the training set with another relation or the inverse relation. Therefore, a new version of the dataset WN18RR has been proposed to address this issue.

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FB15k-237 is a link prediction dataset created from FB15k. While FB15k consists of 1,345 relations, 14,951 entities, and 592,213 triples, many triples are inverses that cause leakage from the training to testing and validation splits. FB15k-237 was created by Toutanova and Chen (2015) to ensure that the testing and evaluation datasets do not have inverse relation test leakage. In summary, FB15k-237 dataset contains 310,116 triples with 14,541 entities and 237 relation types.

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WN18RR is a link prediction dataset created from WN18, which is a subset of WordNet. WN18 consists of 18 relations and 40,943 entities. However, many text triples are obtained by inverting triples from the training set. Thus the WN18RR dataset is created to ensure that the evaluation dataset does not have inverse relation test leakage. In summary, WN18RR dataset contains 93,003 triples with 40,943 entities and 11 relation types.

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Yet Another Great Ontology (YAGO) is a Knowledge Graph that augments WordNet with common knowledge facts extracted from Wikipedia, converting WordNet from a primarily linguistic resource to a common knowledge base. YAGO originally consisted of more than 1 million entities and 5 million facts describing relationships between these entities. YAGO2 grounded entities, facts, and events in time and space, contained 446 million facts about 9.8 million entities, while YAGO3 added about 1 million more entities from non-English Wikipedia articles. YAGO3-10 a subset of YAGO3, containing entities which have a minimum of 10 relations each.

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PROTEINS is a dataset of proteins that are classified as enzymes or non-enzymes. Nodes represent the amino acids and two nodes are connected by an edge if they are less than 6 Angstroms apart.

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The CiteSeer dataset consists of 3312 scientific publications classified into one of six classes. The citation network consists of 4732 links. Each publication in the dataset is described by a 0/1-valued word vector indicating the absence/presence of the corresponding word from the dictionary. The dictionary consists of 3703 unique words.

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IMDB-BINARY is a movie collaboration dataset that consists of the ego-networks of 1,000 actors/actresses who played roles in movies in IMDB. In each graph, nodes represent actors/actress, and there is an edge between them if they appear in the same movie. These graphs are derived from the Action and Romance genres.

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In particular, MUTAG is a collection of nitroaromatic compounds and the goal is to predict their mutagenicity on Salmonella typhimurium. Input graphs are used to represent chemical compounds, where vertices stand for atoms and are labeled by the atom type (represented by one-hot encoding), while edges between vertices represent bonds between the corresponding atoms. It includes 188 samples of chemical compounds with 7 discrete node labels.

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COLLAB is a scientific collaboration dataset. A graph corresponds to a researcher’s ego network, i.e., the researcher and its collaborators are nodes and an edge indicates collaboration between two researchers. A researcher’s ego network has three possible labels, i.e., High Energy Physics, Condensed Matter Physics, and Astro Physics, which are the fields that the researcher belongs to. The dataset has 5,000 graphs and each graph has label 0, 1, or 2.

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The NCI1 dataset comes from the cheminformatics domain, where each input graph is used as representation of a chemical compound: each vertex stands for an atom of the molecule, and edges between vertices represent bonds between atoms. This dataset is relative to anti-cancer screens where the chemicals are assessed as positive or negative to cell lung cancer. Each vertex has an input label representing the corresponding atom type, encoded by a one-hot-encoding scheme into a vector of 0/1 elements.

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IMDB-MULTI is a relational dataset that consists of a network of 1000 actors or actresses who played roles in movies in IMDB. A node represents an actor or actress, and an edge connects two nodes when they appear in the same movie. In IMDB-MULTI, the edges are collected from three different genres: Comedy, Romance and Sci-Fi.

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The DBLP is a citation network dataset. The citation data is extracted from DBLP, ACM, MAG (Microsoft Academic Graph), and other sources. The first version contains 629,814 papers and 632,752 citations. Each paper is associated with abstract, authors, year, venue, and title. The data set can be used for clustering with network and side information, studying influence in the citation network, finding the most influential papers, topic modeling analysis, etc.

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MoleculeNet is a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance.

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ENZYMES is a dataset of 600 protein tertiary structures obtained from the BRENDA enzyme database. The ENZYMES dataset contains 6 enzymes.

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The data was collected from the English Wikipedia (December 2018). These datasets represent page-page networks on specific topics (chameleons, crocodiles and squirrels). Nodes represent articles and edges are mutual links between them. The edges csv files contain the edges - nodes are indexed from 0. The features json files contain the features of articles - each key is a page id, and node features are given as lists. The presence of a feature in the feature list means that an informative noun appeared in the text of the Wikipedia article. The target csv contains the node identifiers and the average monthly traffic between October 2017 and November 2018 for each page. For each page-page network we listed the number of nodes an edges with some other descriptive statistics.

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SNAP is a collection of large network datasets. It includes graphs representing social networks, citation networks, web graphs, online communities, online reviews and more.

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REDDIT-BINARY consists of graphs corresponding to online discussions on Reddit. In each graph, nodes represent users, and there is an edge between them if at least one of them respond to the other’s comment. There are four popular subreddits, namely, IAmA, AskReddit, TrollXChromosomes, and atheism. IAmA and AskReddit are two question/answer based subreddits, and TrollXChromosomes and atheism are two discussion-based subreddits. A graph is labeled according to whether it belongs to a question/answer-based community or a discussion-based community.

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CLUSTER is a node classification tasks generated with Stochastic Block Models, which is widely used to model communities in social networks by modulating the intra- and extra-communities connections, thereby controlling the difficulty of the task. CLUSTER aims at identifying community clusters in a semi-supervised setting.

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PATTERN is a node classification tasks generated with Stochastic Block Models, which is widely used to model communities in social networks by modulating the intra- and extra-communities connections, thereby controlling the difficulty of the task. PATTERN tests the fundamental graph task of recognizing specific predetermined subgraphs.

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The Materials Project is a collection of chemical compounds labelled with different attributes. The labelling is performed by different simulations, most of them at DFT level of theory.

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PTC is a collection of 344 chemical compounds represented as graphs which report the carcinogenicity for rats. There are 19 node labels for each node.

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WebKB is a dataset that includes web pages from computer science departments of various universities. 4,518 web pages are categorized into 6 imbalanced categories (Student, Faculty, Staff, Department, Course, Project). Additionally there is Other miscellanea category that is not comparable to the rest.

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Orkut is a social network dataset consisting of friendship social network and ground-truth communities from Orkut.com on-line social network where users form friendship each other.

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Reddit-5K is a relational dataset extracted from Reddit.

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Wiki-CS is a Wikipedia-based dataset for benchmarking Graph Neural Networks. The dataset is constructed from Wikipedia categories, specifically 10 classes corresponding to branches of computer science, with very high connectivity. The node features are derived from the text of the corresponding articles. They were calculated as the average of pretrained GloVe word embeddings (Pennington et al., 2014), resulting in 300-dimensional node features.

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The AMiner Dataset is a collection of different relational datasets. It consists of a set of relational networks such as citation networks, academic social networks or topic-paper-autor networks among others.

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Tudataset: A collection of benchmark datasets for learning with graphs

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The Reuters-21578 dataset is a collection of documents with news articles. The original corpus has 10,369 documents and a vocabulary of 29,930 words.

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Friendster is an on-line gaming network. Before re-launching as a game website, Friendster was a social networking site where users can form friendship edge each other. Friendster social network also allows users form a group which other members can then join. The Friendster dataset consist of ground-truth communities (based on user-defined groups) and the social network from induced subgraph of the nodes that either belong to at least one community or are connected to other nodes that belong to at least one community.

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The set is based on the ZINC Clean Leads collection. It contains 4,591,276 molecules in total, filtered by molecular weight in the range from 250 to 350 Daltons, a number of rotatable bonds not greater than 7, and XlogP less than or equal to 3.5. We removed molecules containing charged atoms or atoms besides C, N, S, O, F, Cl, Br, H or cycles longer than 8 atoms. The molecules were filtered via medicinal chemistry filters (MCFs) and PAINS filters.

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The Slashdot dataset is a relational dataset obtained from Slashdot. Slashdot is a technology-related news website know for its specific user community. The website features user-submitted and editor-evaluated current primarily technology oriented news. In 2002 Slashdot introduced the Slashdot Zoo feature which allows users to tag each other as friends or foes. The network cotains friend/foe links between the users of Slashdot. The network was obtained in February 2009.

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AIDS is a graph dataset. It consists of 2000 graphs representing molecular compounds which are constructed from the AIDS Antiviral Screen Database of Active Compounds. It contains 4395 chemical compounds, of which 423 belong to class CA, 1081 to CM, and the remaining compounds to CI.

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The Epinions dataset is built form a who-trust-whom online social network of a general consumer review site Epinions.com. Members of the site can decide whether to ''trust'' each other. All the trust relationships interact and form the Web of Trust which is then combined with review ratings to determine which reviews are shown to the user. It contains 75,879 nodes and 50,8837 edges.

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This corpus includes annotations of cancer-related PubMed articles, covering 3 full papers (PMID:24651010, PMID:11777939, PMID:15630473) as well as the result sections of 46 additional PubMed papers. The corpus also includes about 1000 sentences each from the BEL BioCreative training corpus and the Chicago Corpus.

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GAP is a graph processing benchmark suite with the goal of helping to standardize graph processing evaluations. Fewer differences between graph processing evaluations will make it easier to compare different research efforts and quantify improvements. The benchmark not only specifies graph kernels, input graphs, and evaluation methodologies, but it also provides optimized baseline implementations. These baseline implementations are representative of state-of-the-art performance, and thus new contributions should outperform them to demonstrate an improvement. The input graphs are sized appropriately for shared memory platforms, but any implementation on any platform that conforms to the benchmark's specifications could be compared. This benchmark suite can be used in a variety of settings. Graph framework developers can demonstrate the generality of their programming model by implementing all of the benchmark's kernels and delivering competitive performance on all of the benchmark's gra

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Node classification on Penn94

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The Long Range Graph Benchmark (LRGB) is a collection of 5 graph learning datasets that arguably require long-range reasoning to achieve strong performance in a given task. The 5 datasets in this benchmark can be used to prototype new models that can capture long range dependencies in graphs.

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MMKG is a collection of three knowledge graphs for link prediction and entity matching research. Contrary to other knowledge graph datasets, these knowledge graphs contain both numerical features and images for all entities as well as entity alignments between pairs of KGs. While MMKG is intended to perform relational reasoning across different entities and images, previous resources are intended to perform visual reasoning within the same image.

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RadGraph is a dataset of entities and relations in radiology reports based on our novel information extraction schema, consisting of 600 reports with 30K radiologist annotations and 221K reports with 10.5M automatically generated annotations.

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node classification on genius

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Arxiv HEP-TH (high energy physics theory) citation graph is from the e-print arXiv and covers all the citations within a dataset of 27,770 papers with 352,807 edges. If a paper i cites paper j, the graph contains a directed edge from i to j. If a paper cites, or is cited by, a paper outside the dataset, the graph does not contain any information about this. The data covers papers in the period from January 1993 to April 2003 (124 months).

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