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Bridget McInnes Ted Pedersen Ying Liu Genevieve B. Melton Serguei Pakhomov

Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity. Bridget McInnes Ted Pedersen Ying Liu Genevieve B. Melton Serguei Pakhomov. Objective of this work. Develop and evaluate a method than can

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Bridget McInnes Ted Pedersen Ying Liu Genevieve B. Melton Serguei Pakhomov

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  1. Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity Bridget McInnes Ted Pedersen Ying Liu Genevieve B. Melton Serguei Pakhomov

  2. Objective of this work • Develop and evaluate a method than can disambiguate terms in biomedical text by exploiting similarity information extrapolated from the Unified Medical Language System • Evaluate the efficacy of Information Content-based similarity measures over path-based similarity measures for Word Sense Disambiguation, WSD

  3. Word Sense Disambiguation Word sense disambiguation is the task of determining the appropriate sense of a term given context in which it is used. TERM:tolerance Drug Tolerance Immune Tolerance

  4. Word Sense Disambiguation Word sense disambiguation is the task of determining the appropriate sense of a term given context in which it is used. Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance Immune Tolerance

  5. Sense inventory: Unified Medical Language System • Unified Medical Language Sources (UMLS) • Semantic Network • Metathesaurus • ~1.7 million biomedical and clinical concepts; integrated semi-automatically • CUIs (Concept Unique Identifiers), linked: • Hierarchical: PAR/CHD and RB/RN • Non-hierarchical: SIB, RO • Sources viewed together or independently • Medical Subject Heading (MSH) • SPECIALIST Lexicon • Biomedical and clinical terms, including variants

  6. Word Sense Disambiguation Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance: C0013220 Immune Tolerance: C0020963 Concept Unique Identifiers: CUIs

  7. SenseRelatealgorithm • Each possible sense of a target word is assigned a score [sum similarity between it and its surrounding terms] • Assign target word the sense with highest score • Proposed by Patwardhan and Pedersen 2003 using WordNet • UMLS::SenseRelate is a modification of this algorithm using information from the UMLS NEXT UP: an example

  8. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer

  9. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance: C0013220 Immune Tolerance: C0020963

  10. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance: C0013220 Immune Tolerance: C0020963 Busprione: C0006462 Morphine: C0026549 Mice: C0026809 Skin cancer: C0007114

  11. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance: C0013220 Immune Tolerance: C0020963 0.11 0.09 0.09 0.16 Busprione: C0006462 Morphine: C0026549 Mice: C0026809 Skin cancer: C0007114

  12. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance Score = 0.09 + 0.09 + 0.16 + 0.11 = 0.45 Drug Tolerance: C0013220 Immune Tolerance: C0020963 0.11 0.09 0.09 0.16 Busprione: C0006462 Morphine: C0026549 Mice: C0026809 Skin cancer: C0007114

  13. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance Score = 0.09 + 0.09 + 0.16 + 0.11 = 0.45 Drug Tolerance: C0013220 Immune Tolerance: C0020963 0.11 0.09 0.09 0.04 0.09 0.05 0.16 0.09 Busprione: C0006462 Morphine: C0026549 Mice: C0026809 Skin cancer: C0007114

  14. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance Score = 0.09 + 0.09 + 0.16 + 0.11 = 0.45 Immune Tolerance Score = 0.09 + 0.09 + 0.05 + 0.05 = 0.27 Drug Tolerance: C0013220 Immune Tolerance: C0020963 0.11 0.09 0.09 0.04 0.09 0.05 0.16 0.09 Busprione: C0006462 Morphine: C0026549 Mice: C0026809 Skin cancer: C0007114

  15. SenseRelate Example Busprione attenuates tolerance to morphine in mice with skin cancer Drug Tolerance Score = 0.09 + 0.09 + 0.16 + 0.11 = 0.45 Immune Tolerance Score = 0.09 + 0.09 + 0.05 + 0.05 = 0.27 Drug Tolerance: C0013220 Immune Tolerance: C0020963 0.11 0.09 0.09 0.04 0.09 0.05 0.16 0.09 Busprione: C0006462 Morphine: C0026549 Mice: C0026809 Skin cancer: C0007114

  16. Sense Relate Assumption An ambiguous word is often used in the sense that is most similar to the sense of the terms that surround it

  17. SenseRelate Components • Identifying the concepts of surrounding terms • Calculating semantic similarity

  18. Use the SPECIALIST LEXICON to identify the terms and map the terms doing a string match to the MRCONSO table in the UMLS Identifying the concepts of the surrounding terms

  19. Use the SPECIALIST LEXICON to identify the terms and map the terms doing a string match to the MRCONSO table in the UMLS Identifying the concepts of the surrounding terms Busprione attenuates tolerance to morphine in mice with skin cancer

  20. Use the SPECIALIST LEXICON to identify the terms and map the terms doing a string match to the MRCONSO table in the UMLS Identifying the concepts of the surrounding terms Busprione attenuates tolerance to morphine in mice with skin cancer ... skin cancer skin grafting skin disease ... SPECIALIST LEXICON

  21. Use the SPECIALIST LEXICON to identify the terms and map the terms doing a string match to the MRCONSO table in the UMLS Identifying the concepts of the surrounding terms Busprione attenuates tolerance to morphine in mice with skin cancer ... skin cancer C0007114 skin grafting C0037297 skin disease C0037274 ... ... skin cancer skin grafting skin disease ... SPECIALIST LEXICON MRCONSO

  22. Semantic Similarity Measures • Path-based measures • Path • Wu and Palmer • Leacock and Chodorow • Ngyuen and Al-Mubaid • Information content (IC)-based measures • Resnik • Lin • Jiang and Conrath

  23. Path-based similarity measures • Use only the path information obtained from a taxonomy

  24. Path-based similarity measures • Use only the path information obtained from a taxonomy • Path measure • sim(c1,c2) = 1 / minpath(c2,c2) • where minpath is the shortest path between the two concepts

  25. Path-based similarity measures • Use only the path information obtained from a taxonomy • Path measure • sim(c1,c2) = 1/minpath(c2,c2) • where minpath is the shortest path between the two concepts • Wu and Palmer, 1994 • sim(c1,c2) = (2*depth(LCS(c2,c2))) / (depth(c1)+depth(c2)) • where LCS is the least common subsumer of the two concepts

  26. Path-based similarity measures • Use only the path information obtained from a taxonomy • Path measure • sim(c1,c2) = 1/ minpath(c2,c2) • where minpath is the shortest path between the two concepts • Wu and Palmer, 1994 • sim(c1,c2) = (2*depth(LCS(c2,c2))) / (depth(c1)+depth(c2)) • where LCS is the least common subsumer of the two concepts • Leacock and Chodorow, 1998 • sim(c1,c2) = -log( minpath(c1,c2) / (2D) ) • where D is the total depth of the taxonomy

  27. Path-based similarity measures • Use only the path information obtained from a taxonomy • Path measure • sim(c1,c2) = 1/ minpath(c2,c2) • where minpath is the shortest path between the two concepts • Leacock and Chodorow, 1998 • sim(c1,c2) = -log( minpath(c1,c2) / (2D) ) • where D is the total depth of the taxonomy • Wu and Palmer, 1994 • sim(c1,c2) = (2*depth(LCS(c2,c2))) / (depth(c1)+depth(c2)) • where LCS is the least common subsumer of the two concepts • Nyguen and Al-Mubaid, 2006 • sim(c1,c2) = log ( (2 + minpath(c1,c2) - 1) * (D - depth(LCS(c1,c2))) )

  28. Path-based Similarity Measures Disease: C0012634 Drug Related Disorder: C0277579 Neoplasm: C1302761 Neoplastic Disease: C1882062 Drug Tolerance: C0013220 Malignant Neoplasm: C0006826 USE ONLY THE PATH INFORMATION OBTAINED FROM A TAXONOMY Skin cancer: C0007114

  29. Information content-based Measures • Incorporate the probability of the concepts • IC = -log(P(concept))

  30. Information content-based Measures • Incorporate the probability of the concepts • IC = -log(P(concept)) • P(concept) • Calculated by summing the probability of the concept and the probability of its descendants • Probabilities are obtained from an external corpus

  31. Information content-based Measures • Incorporate the probability of the concepts • IC = -log(P(concept) • Resnik, 1995 • sim(c1,c2) = IC(LCS(c1,c2))

  32. Information content-based Measures • Incorporate the probability of the concepts • IC = -log(P(concept) • Resnik, 1995 • sim(c1,c2) = IC(LCS(c2,c2)) • Jiang and Conrath, 1997 • sim(c1,c2) = 1 / (IC(c1)+IC(c2) – 2* IC(LCS(c1,c2))

  33. Information content-based Measures • Incorporate the probability of the concepts • IC = -log(P(concept) • Resnik, 1995 • sim(c1,c2) = IC(LCS(c2,c2)) • Jiang and Conrath, 1997 • sim(c1,c2) = 1 ÷ (IC(c1)+IC(c2) – 2* IC(LCS(c1,c2)) • Lin, 1998 • sim(c1,c2) = (2*IC(LCS(c2,c2))) / (IC(c1)+IC(c2))

  34. IC-based similarity measures PATH INFORMATION PROBABILITY OF CONCEPTS Disease: C0012634 EXTERNAL CORPUS Drug Related Disorder: C0277579 Neoplasm: C1302761 + Drug Tolerance: C0013220 Neoplastic Disease: C1882062 Malignant Neoplasm: C0006826 Skin cancer: C0007114

  35. Experimental Framework • Use open-source UMLS::Similarity package to obtain the similarity between the terms and possible senses in the SenseRelate algorithm • Path information: parent/child relations in MSH source • Information content: calculated using the UMLSonMedline dataset created by NLM • Consists of concepts from 2009AB UMLS and the frequency they occurred in Medline using the Essie Search Engine (Ide et al 2007) • Medline: database of citations of biomedical/clinical articles

  36. Evaluation Data: MSH WSD • MSH-WSD dataset (Jimeno-Yepes, et al 2011) • 203 target words (ambiguous word) from Medline • 106 terms e.g. tolerance • 88 acronyms e.g. CA (calcium, california) • 9 mixtures e.g. bat (brown adipose tissue) • Each target word contains ~187 instances (Medline abstracts) • abstract = ~ 500 words • Each target word in the instances assigned a concept from MSH by exploiting the manually assigned MSH concepts assigned to the abstract • Average of 2.08 possible senses per target word • Majority sense over all the target words is 54.5%

  37. Results a c c u r a c y baseline lch wup res jcn lin path nam Path-based IC-based

  38. Comparison across subsets of msh-wsd a c c u r a c y

  39. Comparison across subsets of msh-wsd a c c u r a c y

  40. Comparison across subsets of msh-wsd a c c u r a c y

  41. Comparison across subsets of msh-wsd a c c u r a c y

  42. Comparison across subsets of msh-wsd a c c u r a c y

  43. Window sizes • Use the terms surrounding the target word within a specified window: 1, 2, 5, 10, 25, 50, 60, 70 WINDOW SIZE = 2 Busprione attenuates tolerance to morphine in mice with skin_cancer

  44. Comparison of window sizes for lin a c c u r a c y window size

  45. Surrounding terms Not all terms have a concept in the UMLS therefore Not all surrounding terms in the window mapped to CUIs

  46. Window sizes versus mapped terms n u m b e r o f m a p p i n g s window size

  47. Future work: mapping Terms • Currently looking at mapping the terms to CUIs using information from the concept mapping system MetaMap • Obtain the terms from MetaMap and do a dictionary look up in MRCONSO • Hypothesis – the terms obtained by MetaMap are more accurate than using the SPECIALIST Lexicon • Obtain the CUIs from MetaMap • Hypothesis – the CUIs obtained by MetaMap will be more accurate than the dictionary look-up

  48. Objective #1 Develop and evaluate a method than can disambiguate terms in biomedical text by exploiting similarity information extrapolated from the UMLS • UMLS::SenseRelatestatistically significantly higher disambiguation accuracy than the baseline • On par with previous unsupervised methods for terms

  49. Objective #2 Evaluate the efficacy of IC-based similarity measures over path-based measures on a secondary task • There is no statistically significant difference between the accuracies obtained by the IC-based measures • There is a statistically significant difference between the IC-based measures and the path-based measures

  50. Take home message: An ambiguous word is often used in the sense that is most similar to the sense of the concepts of the terms that surround it

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