Latent semantic structure indexing: Difference between revisions

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'''Latent Semanticsemantic Structurestructure Indexingindexing''' ('''LaSSI)''') is a technique for calculating chemical similarity derived from [[Latentlatent semantic analysis]] (LSA).

LaSSI was developed at [[Merck & Co.]] and patented in 2007<ref>{{Cite [web |url=http://patft.uspto.gov/netacgi/nph-Parser?patentnumber=7219020] |title=United States Patent: 7219020 |access-date=2007-10-07 |archive-date=2017-12-02 |archive-url=https://web.archive.org/web/20171202052848/http://patft.uspto.gov/netacgi/nph-Parser?patentnumber=7219020 |url-status=dead }}</ref> by Richard Hull, Eugene Fluder, Suresh Singh, Robert Sheridan, Robert Nachbar and Simon Kearsley.

== Overview ==

LaSSI is similar to LSA in that it involves the construction of an occurrence matrix from a corpus of items and the application of [[singular value decomposition]] to that matrix to derive latent features. What differs is that the occurrence matrix represents the frequency of two- and three-dimensional chemical descriptors (rather than natural language terms) found within a [[chemical database]] of chemical structures. This process derives latent chemical structure concepts that can be used to calculate chemical similarities and [[structure-activitystructure–activity relationship]]s for [[drug discovery]].

== References ==

{{Reflist}}

* Hull, R.D., Fluder, E.M., Singh, S.B., Nachbar, R.B., Sheridan, R.P. and Kearsley, S.K. (2001) "Latent semantic structure indexing (LaSSI) for defining chemical similarity." J Med Chem, 2001 Apr 12;44(8):1177-841177–84. {{doi|10.1021/jm000393c}}

* Hull, R.D., Singh, S.B., Nachbar, R.B., Sheridan, R.P., Kearsley, S.K. and Fluder, E.M. (2001) "Chemical similarity searches using latent semantic structure indexing (LaSSI) and comparison to TOPOSIM." J Med Chem, 2001 Apr 12;44(8):1185-911185–91.

* Singh, S.B., Sheridan, R.P., Fluder, E.M. and Hull, R.D. (2001) "Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining." J Med Chem, 2001 May 10;44(10):1564-751564–75.

[[Category:Cheminformatics]]

* Hull, R.D., Singh, S.B., Nachbar, R.B., Sheridan, R.P., Kearsley, S.K. and Fluder, E.M. (2001) "Chemical similarity searches using latent semantic structure indexing (LaSSI) and comparison to TOPOSIM." J Med Chem, 2001 Apr 12;44(8):1185-91.

[[Category:Drug discovery]]

* Singh, S.B., Sheridan, R.P., Fluder, E.M. and Hull, R.D. (2001) "Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining." J Med Chem, 2001 May 10;44(10):1564-75.