PPLRE Nearest Neighbor Algorithm: Difference between revisions
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** For the sentence "''[PROTEINa'' virA'']'' encodes a ''[LOCATIONa'' membrane-bound'']'' sensor kinase protein and ''[PROTEINb'' virG'']'' encodes a ''[LOCATIONb'' cytoplasmic'']'' regulator protein." (ref: [[PPLRE Corpus 8611.a.2]]) [[the algorithm]] can clearly extract the two correct relations (''PL(PROTEINa, LOCATIONa)'' and ''PL(PROTEINb, LOCATIONb)'' and with a distance containt also avoid the other two incorrect permutations. | ** For the sentence "''[PROTEINa'' virA'']'' encodes a ''[LOCATIONa'' membrane-bound'']'' sensor kinase protein and ''[PROTEINb'' virG'']'' encodes a ''[LOCATIONb'' cytoplasmic'']'' regulator protein." (ref: [[PPLRE Corpus 8611.a.2]]) [[the algorithm]] can clearly extract the two correct relations (''PL(PROTEINa, LOCATIONa)'' and ''PL(PROTEINb, LOCATIONb)'' and with a distance containt also avoid the other two incorrect permutations. | ||
** For the sentence "In [[this study]], ''[ORGANISM ''Escherichia coli'']'' ''[PROTEIN ''TonB'']'' was found to be distributed in sucrose density gradients approximately equally between the ''[LOCATIONa'' cytoplasmic membrane'']'' and the ''[LOCATIONb'' outer membrane'']'' fractions, while two proteins with which it is known to interact, ''[PROTEINb'' ExbB'']'' and ''[PROTEINc'' ExbD'']'', as well as the ''[PROTEINd'' NADH'']'' oxidase activity characteristic of the ''[LOCATION'' cytoplasmic membrane'']'', were localized in the ''[LOCATION'' cytoplasmic membrane'']'' fraction." a word-based distance function would identify nine relations: ''[[OP]](ORGANISM,PROTEINa)'', ''[[OP]](ORGANISM,PROTEINb)'', ''[[OP]](ORGANISM,PROTEINc)'', ''[[OP]](ORGANISM,PROTEINd)'', ''[[PL]](PROTEINa,LOCATIONa)'', ''[[PL]](PROTEINb,LOCATIONa)'', ''[[PL]](PROTEINc,LOCATIONa)'', ''[[PL]](PROTEINd,LOCATIONa)''. Notice that one of the relations is missed (''[[PL]](PROTEINa,LOCATIONb)'') bust also that many of the invalid permuations are not returned. | ** For the sentence "In [[this study]], ''[ORGANISM ''Escherichia coli'']'' ''[PROTEIN ''TonB'']'' was found to be distributed in sucrose density gradients approximately equally between the ''[LOCATIONa'' cytoplasmic membrane'']'' and the ''[LOCATIONb'' outer membrane'']'' fractions, while two proteins with which it is known to interact, ''[PROTEINb'' ExbB'']'' and ''[PROTEINc'' ExbD'']'', as well as the ''[PROTEINd'' NADH'']'' oxidase activity characteristic of the ''[LOCATION'' cytoplasmic membrane'']'', were localized in the ''[LOCATION'' cytoplasmic membrane'']'' fraction." a word-based distance function would identify nine relations: ''[[OP]](ORGANISM,PROTEINa)'', ''[[OP]](ORGANISM,PROTEINb)'', ''[[OP]](ORGANISM,PROTEINc)'', ''[[OP]](ORGANISM,PROTEINd)'', ''[[PL]](PROTEINa,LOCATIONa)'', ''[[PL]](PROTEINb,LOCATIONa)'', ''[[PL]](PROTEINc,LOCATIONa)'', ''[[PL]](PROTEINd,LOCATIONa)''. Notice that one of the relations is missed (''[[PL]](PROTEINa,LOCATIONb)'') bust also that many of the invalid permuations are not returned. | ||
* <B>See</U>:</B> [[PPLRE Project]], [[Nearest Neighbor Algorithm]] | * <B>See</U>:</B> [[PPLRE Project]], [[Nearest Neighbor Algorithm]]. | ||
---- | ---- | ||
__NOTOC__ | __NOTOC__ | ||
[[Category:Concept]] | [[Category:Concept]] | ||
Latest revision as of 05:19, 28 November 2023
The PPLRE Nearest Neighbor Algorithm is a Binary Relation Recognition Algorithm developed for the PPLRE Project that is based on the Nearest Neighbor Algorithm in that it locates nearest pairs of Entities and identifies them as being in an OP() or PL() relation.
- Context:
- The current version is PPLRE Nearest Neighbor Algorithm v1.0.
- Performance onthe PPLRE Evaluation Task is competitive PPLRE Evaluation - Nearest Neighbor.
- Distance Metric: Currently makes use of a Token-based Distance Metric.
- Tie-breaks: If there is a tie then neither wins.
- Confidence Score: Currently ranges from [1.0 better, 0.0 worse) and is based on 1) the inverse of the Distance Metric and 2) whether the two enties are nearest neighbors to each other.
- Example(s):
- For the sentence "[PROTEINa virA] encodes a [LOCATIONa membrane-bound] sensor kinase protein and [PROTEINb virG] encodes a [LOCATIONb cytoplasmic] regulator protein." (ref: PPLRE Corpus 8611.a.2) the algorithm can clearly extract the two correct relations (PL(PROTEINa, LOCATIONa) and PL(PROTEINb, LOCATIONb) and with a distance containt also avoid the other two incorrect permutations.
- For the sentence "In this study, [ORGANISM Escherichia coli] [PROTEIN TonB] was found to be distributed in sucrose density gradients approximately equally between the [LOCATIONa cytoplasmic membrane] and the [LOCATIONb outer membrane] fractions, while two proteins with which it is known to interact, [PROTEINb ExbB] and [PROTEINc ExbD], as well as the [PROTEINd NADH] oxidase activity characteristic of the [LOCATION cytoplasmic membrane], were localized in the [LOCATION cytoplasmic membrane] fraction." a word-based distance function would identify nine relations: OP(ORGANISM,PROTEINa), OP(ORGANISM,PROTEINb), OP(ORGANISM,PROTEINc), OP(ORGANISM,PROTEINd), PL(PROTEINa,LOCATIONa), PL(PROTEINb,LOCATIONa), PL(PROTEINc,LOCATIONa), PL(PROTEINd,LOCATIONa). Notice that one of the relations is missed (PL(PROTEINa,LOCATIONb)) bust also that many of the invalid permuations are not returned.
- See: PPLRE Project, Nearest Neighbor Algorithm.