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Modeling Alzheimer’s Disease research claims, evidence, and arguments from a biology research paper-ISSA-2018-07-05

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Presentation: Jodi Schneider and Novejot Sandhu, “Modeling Alzheimer’s Disease Reseach Claims, Evidence, and Arguments from a Biology Research Paper.” 9th International Conference on Argumentation, International Society for the Society of Argumentation, Amsterdam, Netherlands, July 5, 2018

Abstract: Argument visualization may help make research papers easier to understand, which could both speed quality assessment within a discipline and help build interdisciplinary knowledge networks. This paper presents a case study of the arguments in a single high-profile paper on Alzheimer's disease research. Within this one paper, we analyze and hand-annotate the main claim, which is supported by 4 subclaims, in turn supported by data, methods, and materials. We also investigate how the paper imports and uses knowledge claims from other research papers. We create a specialized argument-based knowledge representation called a micropublication. In future work, we will investigate automatic argumentation mining for experimental biology research papers. Our long-term vision is to create literature-scale claim-argument networks that help more quickly use new knowledge about human health.

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Modeling Alzheimer’s Disease research claims, evidence, and arguments from a biology research paper-ISSA-2018-07-05

  1. 1. ModelingAlzheimer’sDiseaseReseach Claims,Evidence,andArgumentsfroma BiologyResearchPaper Jodi Schneider, Novejot Sandhu ISSA ISSA – Amsterdam – 2018-07-05
  2. 2. Theoretical Framework • Scientific paper as an argument
  3. 3. Theoretical Framework • Scientific paper as an argument – “Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods.” (Clark, Ciccarese, Goble 2014). Clark, Tim, Paolo N. Ciccarese, and Carole A. Goble. "Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications." Journal of biomedical semantics 5.1 (2014): 28.
  4. 4. Theoretical Framework • Scientific paper as an argument – “Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods.” (Clark, Ciccarese, Goble 2014) • Micropublications model Clark, Tim, Paolo N. Ciccarese, and Carole A. Goble. "Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications." Journal of biomedical semantics 5.1 (2014): 28.
  5. 5. Micropublications Model [Clark, Ciccarese, Goble (2014) Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications.] 5
  6. 6. Micropublications Model [Clark, Ciccarese, Goble (2014) Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications] 6
  7. 7. 4. Create a Micropublication 3. Identify the Reasoning 2. Annotate using http://hypothes.is 1. Identify a scientific research paper Approach
  8. 8. Step 1: Choose Our Data
  9. 9. Uh-Oh, It’s Complex! Neurofibrillary tangles advance from layer II of the entorhinal cortex (EC-II) toward limbic and association cortices as Alzheimer’s disease evolves. However, the mechanism involved in this hierarchical pattern of disease progression is unknown. We describe a transgenic mouse model ….
  10. 10. Step 2: Annotate the Article Conclusion What we know about Alzheimer's What is hypothesize d to be true
  11. 11. Step 3: Identify the Reasoning • Central Argument – Tau & tangles lead to neurodegeneration • Support – Data from 4 experimental studies using a mouse model. – Citation of outside experiments.
  12. 12. Step 4: Create a micropublication
  13. 13. Step 4: Create a micropublication A mouse model of tau pathology is used to understand the mechanism and progression of Alzheimer's disease (C0). 1. Tau pathology is age-dependent in mice (C1). 2. Human Tau is propagated synaptically in mice (C2). 3. Mouse Tau is recruited by Human Tau to aggregate (C3). 4. Tau pathology results in neurodegeneration which is accompanied by gliosis (C4).
  14. 14. Experimental data supporting claim 4 Claim Data Methods Materials
  15. 15. Experimental data supporting claim 4
  16. 16. Experimental data supporting claim 4 Data
  17. 17. Experimental data supporting claim 4 Claim Data
  18. 18. Experimental data supporting claim 4 Claim Data Methods
  19. 19. Experimental data supporting claim 4 Claim Data Methods Materials
  20. 20. Claim Data Methods Materials Citation of outside experiments supporting claim 4
  21. 21. Claim Data Methods Materials Citation of outside experiments supporting claim 4
  22. 22. Citation of outside experiments supporting claim 4 • Claim 4 is supported by the biomarker materials, which are justified by a chain of citations – “PSD-95, a postsynaptic marker that has been reported to decrease early in neurodegeneration (Zhao et al., 2006)”. – Zhao in turn cites Lacor et al. 2004
  23. 23. Future Work • Mine arguments by first extracting methods from experimental research articles. • First: automatically extract methods and manually infer the knowledge claims that the method COULD support. • Later: characterize the types of claims authorized by the method.
  24. 24. Applications • Argument-based information retrieval • Generate summaries of the argument • Audit argument networks
  25. 25. Teufel, S. (2014). Scientific Argumentation Detection as Limited-domain Intention Recognition. In ArgNLP 2014 Frontiers and Connections between Argumentation Theory and Natural Language Processing. http://ceur-ws.org/Vol- 1341/paper14.pdf Teufel’s model
  26. 26. Using Array tomography with two different indicators red (post) PSD and green (pre) synapsin I proteins to identify the densities of pre and post synaptic structures.
  27. 27. [Clark, Ciccarese, Goble (2014) Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications]
  28. 28. Mapping Scholarship
  29. 29. “[Y]ou can transform a fact into fiction or a fiction into fact just by adding or subtracting references” - Bruno Latour Latour, Bruno. Science in action: How to follow scientists and engineers through society. Harvard University Press, 1987. p33
  30. 30. Funded grants with citation bias & citation distortion. Greenberg, Steven A. "How citation distortions create unfounded authority: analysis of a citation network." BMJ 339 (2009): b2680. https://doi.org/10.1136/bmj.b2680
  31. 31. Citing fake science harms people A paper about a clinical trial for renal disease was retracted because: “‘the trial had not been approved by the ethics committee, the involvement of a statistician could not be verified, [and] the trial was not a double-blind study, because Dr Nakao knew the treatment allocation’.” “Nevertheless, the COOPERATE study was cited by 173 review articles and 58 secondary clinical studies that enrolled a total of 35,929 patients.” “The harm done by COOPERATE is thus 4-fold: • patients were enrolled in an experimental therapy for a condition which already had an accepted therapy; • time, energy and money were wasted by patients and investigators; • false information pervaded the literature; • and combination therapy was accepted more quickly and used more widely than it might have been otherwise.” Steen, R. G. (2011). Retractions in the medical literature: how many patients are put at risk by flawed research?. Journal of Medical Ethics, 37(11), 688-692.
  32. 32. Citing fake science harms people A paper about a clinical trial for renal disease was retracted because: “‘the trial had not been approved by the ethics committee, the involvement of a statistician could not be verified, [and] the trial was not a double-blind study, because Dr Nakao knew the treatment allocation’.” “Nevertheless, the COOPERATE study was cited by 173 review articles and 58 secondary clinical studies that enrolled a total of 35,929 patients.” “The harm done by COOPERATE is thus 4-fold: • patients were enrolled in an experimental therapy for a condition which already had an accepted therapy; • time, energy and money were wasted by patients and investigators; • false information pervaded the literature; • and combination therapy was accepted more quickly and used more widely than it might have been otherwise.” Steen, R. G. (2011). Retractions in the medical literature: how many patients are put at risk by flawed research?. Journal of Medical Ethics, 37(11), 688-692.
  33. 33. Take away messages • Biomedicine has evolved multiple approaches for managing and appraising individual papers and bodies of “facts”. • Citations come in many shapes and sizes. • Citations may support “facts” – as part of a larger scientific fabric that includes data, evidence, arguments. • Powermove: identify the critical supports (think Jenga)
  34. 34. Take away messages • Network analysis may help identify problematic citation practices. • Modeling arguments can help identify the robustness of a claimed “fact”. • Semantic models could enable inference- based reasoning and citation network querying. • Relevant citation corpora exist.

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