Semantic similarity

Semantic similarity or semantic relatedness is a concept whereby a set of documents or terms within term lists are assigned a metric based on the likeness of their meaning / semantic content.

Concretely, this can be achieved for instance by defining a topological similarity, by using ontologies to define a distance between words (a naive metric for terms arranged as nodes in a directed acyclic graph like a hierarchy would be the minimal distance—in separating edges—between the two term nodes), or using statistical means such as a vector space model to correlate words and textual contexts from a suitable text corpus (co-occurrence).

Taxonomy

The concept of semantic similarity is more specific than semantic relatedness, as the latter includes concepts as antonymy and meronymy, while similarity does not . However, much of the literature uses these terms interchangeably, along with terms like semantic distance. In essence, semantic similarity, semantic distance, and semantic relatedness all mean, "How much does term A have to do with term B?" The answer to this question is usually a number between -1 and 1, or between 0 and 1, where 1 signifies extremely high similarity/relatedness, and 0 signifies little-to-none.

Visualisation

An intuitive way of visualising the semantic similarity of terms is by grouping together closer related terms and spacing more distantly related ones wider apart. This is also common - if sometime subconscious - practice for mind maps and concept maps.

Applications

Biomedical Informatics

Semantic similarity measures have been applied and developed in biomedical ontologies, namely, the Gene Ontology (GO). They are mainly used to compare genes and proteins based on the similarity of their functions rather than on their sequence similarity, but they are also being extended to other bioentities, such as chemical compounds and diseases.

These comparisons can be done using tools freely available on the web:

• ProteInOn can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of UniProt proteins and to get the information content and calculate the functional semantic similarity of GO terms.
• CMPSim provides a functional similarity measure between chemical compounds and metabolic pathways using ChEBI based semantic similarity measures.
• CESSM provides a tool for the automated evaluation of GO-based semantic similarity measures.

GeoInformatics

Similarity is also applied to find similar geographic features or feature types:

• SIM-DL similarity server can be used to compute similarities between concepts stored in geographic feature type ontologies.
• Geo-Net-PT Similarity Calculator can be used to compute how well related two geographic concepts are in the Geo-Net-PT ontology.

Linguistics

Several metrics use WordNet: (+) humanly constructed; (−) humanly constructed (not automatically learned), cannot measure relatedness between multi-word term, non-incremental vocabulary

Measures

Topological similarity

There are essentially two types of approaches that calculate topological similarity between ontological concepts:

• Edge-based: which use the edges and their types as the data source;
• Node-based: in which the main data sources are the nodes and their properties.

Other measures calculate the similarity between ontological instances:

• Pairwise: measure functional similarity between two instances by combining the semantic similarities of the concepts they represent
• Groupwise: calculate the similarity directly not combining the semantic similarities of the concepts they represent

Some examples:

Edge-based

• Pekar, Viktor; Staab, Steffen (2002). "Taxonomy learning". 1: 1. doi:10.3115/1072228.1072318. {{cite journal}}: Cite journal requires |journal= (help)
• Cheng, J; Cline, M; Martin, J; Finkelstein, D; Awad, T; Kulp, D; Siani-Rose, MA (2004). "A knowledge-based clustering algorithm driven by Gene Ontology". Journal of biopharmaceutical statistics. 14 (3): 687–700. doi:10.1081/BIP-200025659. PMID 15468759.
• Wu, H; Su, Z; Mao, F; Olman, V; Xu, Y (2005). "Prediction of functional modules based on comparative genome analysis and Gene Ontology application". Nucleic acids research. 33 (9): 2822–37. doi:10.1093/nar/gki573. PMC 1130488. PMID 15901854.
• Del Pozo, Angela; Pazos, Florencio; Valencia, Alfonso (2008). "Defining functional distances over Gene Ontology". BMC Bioinformatics. 9: 50. doi:10.1186/1471-2105-9-50. PMC 2375122. PMID 18221506.{{cite journal}}: CS1 maint: unflagged free DOI (link)
• IntelliGO: Benabderrahmane, Sidahmed; Smail Tabbone, Malika; Poch, Olivier; Napoli, Amedeo; Devignes, Marie-Domonique. (2010). "IntelliGO: a new vector-based semantic similarity measure including annotation origin". Biomed Central. 11: 588. doi:10.1186/1471-2105-11-588. PMID 21122125.{{cite journal}}: CS1 maint: unflagged free DOI (link)

Node-based

• Resnik
  • based on the notion of information content
• Lin
• Jiang and Conrath
• GraSM: Graph-based Similarity Measure

Pairwise

• maximum of the pairwise similarities
• composite average in which only the best-matching pairs are considered (best-match average)

Groupwise

• Jaccard index
• simGIC
• simLP
• simUI

Statistical similarity

• LSA (Latent semantic analysis) (+) vector-based, adds vectors to measure multi-word terms; (−) non-incremental vocabulary, long pre-processing times
• PMI (Pointwise mutual information) (+) large vocab, because it uses any search engine (like Google); (−) cannot measure relatedness between whole sentences or documents
• SOC-PMI (Second-order co-occurrence pointwise mutual information) (+) sort lists of important neighbor words from a large corpus; (−) cannot measure relatedness between whole sentences or documents
• GLSA (Generalized Latent Semantic Analysis) (+) vector-based, adds vectors to measure multi-word terms; (−) non-incremental vocabulary, long pre-processing times
• ICAN (Incremental Construction of an Associative Network) (+) incremental, network-based measure, good for spreading activation, accounts for second-order relatedness; (−) cannot measure relatedness between multi-word terms, long pre-processing times
• NGD (Normalized Google distance) (+) large vocab, because it uses any search engine (like Google); (−) cannot measure relatedness between whole sentences or documents
• ESA (Explicit Semantic Analysis) based on Wikipedia and the ODP
• n° of Wikipedia (noW), inspired by the game Six Degrees of Wikipedia, is a distance metric based on the hierarchical structure of Wikipedia. A directed-acyclic graph is first constructed and later, Dijkstra's shortest path algorithm is employed to determine the noW value between two terms as the geodesic distance between the corresponding topics (i.e. nodes) in the graph. Demo is available here.
• VGEM (Vector Generation of an Explicitly-defined Multidimensional Semantic Space) (+) incremental vocab, can compare multi-word terms (−) performance depends on choosing specific dimensions
• BLOSSOM (Best path Length On a Semantic Self-Organizing Map) (+) uses a Self Organizing Map to reduce high dimensional spaces, can use different vector representations (VGEM or word-document matrix), provides 'concept path linking' from one word to another (−) highly experimental, requires nontrivial SOM calculation
• SimRank

See also

• Terminology extraction
• Coherence (linguistics)
• Analogy
• Semantic differential

References

• Sidahmed Benabderrahmane, Malika Smail-Tabbone, Olivier Poch, Amedeo Napoli and Marie-Dominique Devignes, (2010). IntelliGO: a new vector-based semantic similarity measure including annotation origin. Biomed Central, Volume 11.

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External links

• Measures of Semantic Relatedness (MRS)
• WordNet-Similarity, an open source package for computing the similarity and relatedness of concepts found in WordNet
• List of related literature
• WordNet::Similarity (using WordNet as an ontology)
• WordNet Explorer (interactive graphic WordNet database editor)
• Similarity-based Learning Methods for the Semantic Web (C. d'Amato, PhD Thesis)
• Survey on Semantic Similarity Measures (C. d'Amato, S. Staab, N. Fanizzi, EKAW 2008, Springer-Verlag)
• Algorithm, Implementation and Application of the SIM-DL Similarity Server (Introduction to the SIM-DL Similarity Server)