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Using Answer Set Programming to Simulate the Interplay of Taxonomic and Nomenclatural Change. Nico Franz 1 , Joohyung Lee 2 & Chao Zhang 2 1 School of Life Sciences, Arizona State University 2 CIDSE Automated Reasoning Group, ASU

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slide1

Using Answer Set Programming to

Simulate the Interplay of Taxonomic

and Nomenclatural Change

Nico Franz1, Joohyung Lee2 & Chao Zhang2

1 School of Life Sciences, Arizona State University

2 CIDSE Automated Reasoning Group, ASU

TDWD 2013 Annual Conference, Florence, Italy

Semantics for Biodiversity – Formal Models and Ontologies

November 01, 2013

Slides @ http://taxonbytes.org/tdwg-2013-using-asp-to-simulate-the-interplay-of-taxonomic-and-nomenclatural-change

slide2

Question – are the

rules of nomenclature

logically tractable?

slide3

Core principles embodied in the Code of Zoological Nomenclature

  • Binominal Nomenclature
    • The scientific name of a species, and not of a taxon at any other rank, is a combination of two names.
  • Priority
    • The valid name of a taxon is the oldest available name applied to it.
  • Coordination
    • Within the [family, genus, species] group, a name established for a taxon at any rank is simultaneously established with the same author/date for taxa with the same name-bearing type at other ranks in the group.
  • First Reviser
    • The relative precedence of two or more names or nomenclatural acts published on the same date, or of different original spellings of the same name, is determined by the First Reviser.
  • Homonymy
    • The name of each taxon must be unique.
  • Typification
    • Each nominal taxon in the family group, genus group or species group has a name-bearing type fixed to provide the objective standard of reference by which the application of the name is determined.
    • [Gender Agreement]
      • Agreement in grammatical gender between a generic name and Latin or latinized adjectival or participial species-group names combined with it originally or subsequently.

Source: Code On-Line: http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp

slide4

Core principles embodied in the Code of Zoological Nomenclature

  • Binominal Nomenclature
    • The scientific name of a species, and not…
  • Priority
    • The valid name of a taxon is the oldest….
  • Coordination
    • Within the [family, genus, species] group, a name established for a taxon at any rank is simultaneously established with the same author/date for taxa with the same name-bearing type at other ranks in the group.
  • First Reviser
    • The relative precedence of two or more names or nomenclatural acts published on the same date, or of different original spellings of the same name, is determined by the First Reviser.
  • Homonymy
    • The name of each taxon must be unique.
  • Typification
    • Each nominal taxon in the family group, genus group or species group has a name-bearing type fixed to provide the objective standard of reference by which the application of the name is determined.
    • [Gender Agreement]
      • Agreement in grammatical gender between a generic name and Latin or latinized adjectival or participial species-group names combined with it originally or subsequently.

Working hypothesis:

All (6 + 1) Principles are representable in Stable Model Semantics and computable with ASP programs & solvers.

Source: Code On-Line: http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp

slide5

Answer Set Programming reviewed in 10 bullet points

  • Relatively new programming paradigm, not widely used until late 1990s
  • A form of declarative programming based on Stable Model Semantics
  • Combines expressive representation language with efficient solving tools
  • Instead of proving truth/falsity, identifies solutions that satisfy conditions
slide6

Answer Set Programming reviewed in 10 bullet points

  • Relatively new programming paradigm, not widely used until late 1990s
  • A form of declarative programming based on Stable Model Semantics
  • Combines expressive representation language with efficient solving tools
  • Instead of proving truth/falsity, identifies solutions that satisfy conditions
  • Closed World Assumption – what is not known is false (unlike OWL-DL)
  • Can compute non-monotonic reasoning
  • Has the property of elaboration tolerance
  • Excels at modeling complex rules
slide7

Answer Set Programming reviewed in 10 bullet points

  • Relatively new programming paradigm, not widely used until late 1990s
  • A form of declarative programming based on Stable Model Semantics
  • Combines expressive representation language with efficient solving tools
  • Instead of proving truth/falsity, identifies solutions that satisfy conditions
  • Closed World Assumption – what is not known is false (unlike OWL-DL)
  • Can compute non-monotonic reasoning
  • Has the property of elaboration tolerance
  • Excels at modeling complex rules
  • Capable of default reasoning ("by default, X is true"), transition systems
  • Translatable (in part) into First-Order Logic (FOL), Description Logic (DL)
  • More information in the reference list appended to this presentation
slide8

ASP paradigm – set conditions, constraints, ground, identify SMs

Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf

slide9

ASP paradigm – apply to taxonomy/nomenclature change scenario

 Fully specified input taxonomy (t = 0); incl.:

ranked names, priority/type relationships

 At t = 1 (revision), effect a taxonomic change

where 1 species is moved into another genus

Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf

slide10

ASP paradigm – apply to taxonomy/nomenclature change scenario

 Represent: input tree, names, years, ranks…

 Encode: Principles of Nomenclature

 Choice: Select a taxonomic change scenario

Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf

slide11

ASP paradigm – apply to taxonomy/nomenclature change scenario

 Grounding of all domains, variables and

conditions at t = 0 (original) vs. t = 1 (revision)

Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf

slide12

ASP paradigm – apply to taxonomy/nomenclature change scenario

 Inference of Stable Models (taxonomies) and

all concomitant nomenclatural emendations

Source: Eiter, T. 2008. http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf

slide14

Input (original) taxonomy at t = 0 ["9-name/taxon use case"]

  • All type bearing and non-type bearing epithets have different publication years

t = 0

* = type-bearing name

 Transition: exactly 1 species will move to the other genus at t = 1.

 Since there are 4 species, this yields 4 Stable Models.

slide15

Model 1:O. secundus moves into Agenus

  • Requires new higher-level synonymies, "cascading", new names, new types

t = 0

t = 1

 Required nomenclatural changes; O. secundus is a type bearer.

slide16

Model 2:A. tertiusmoves into Ogenus

  • Non-type bearer – 1 taxonomic change ↔ 1 new combination

t = 0

t = 1

slide17

Model 3:O. quartusmoves into Agenus

  • Non-type bearer – 1 taxonomic change ↔ 1 new combination

t = 0

t = 1

slide18

Model 4:A. primus "moves" [Ogenus spp. ingressintoAgenus]

  • Most dramatic nomenclatural adjustments – A. primus is globally oldest type

t = 0

t = 1

 Two species (names) – secundus & quartus – move into Agenus.

slide19

Modeling in ASP

Does it work? It does.

slide20

Current ASP program properly resolves all 4 models*

* Output optics notwithstanding; actual tree visualization in progress.

slide21

Conclusion – ASP can logically represent key rules of nomenclature

  • Binominal Nomenclature
    • The scientific name of a species, and not…
  • Priority
    • The valid name of a taxon is the oldest….
  • Coordination
    • Within the [family, genus, species] group, a name established for a taxon at any rank is simultaneously established with the same author/date for taxa with the same name-bearing type at other ranks in the group.
  • First Reviser
    • The relative precedence of two or more names or nomenclatural acts published on the same date, or of different original spellings of the same name, is determined by the First Reviser.
  • Homonymy
    • The name of each taxon must be unique.
  • Typification
    • Each nominal taxon in the family group, genus group or species group has a name-bearing type fixed to provide the objective standard of reference by which the application of the name is determined.
    • [Gender Agreement]
      • Agreement in grammatical gender between a generic name and Latin or latinized adjectival or participial species-group names combined with it originally or subsequently.

= Principles currently modeled.

Extension of Priority.

Likely feasible.

Likely feasible.

slide23

Next up – improved output visualization, more complex cases

  • "20-name/taxon use case" can include 36 *one-species-moves* permutations
  • Compute, tabulate, visualize complete set of nomenclatural changes for each
  • At the genus level, moving entire non-type genera requires no name change
slide24

Conclusions & outlook

This work is a novel representation of the Principles of Nomenclature in a formal logic system with default conditions and transitional properties.

The model can be elaborated to include an increasing wide range of taxonomic / nomenclatural change scenarios, and specific rule exceptions.

ASP could be utilized to validate proposed nomenclatural emendations or infer additional required changes, and implemented in a nomenclatoral repository such as ZooBank.

In complex change scenarios, ASP could be used to perform optimizations and minimize nomenclatural instability given the need to move one or more taxa.

slide25

Acknowledgments

  • TDWG 2013 Symposiumorganizers – John Deck, Mark Schildhauer, Ramona Walls
  • Stanley Blum, David Patterson, Richard Pyle – nomenclatural use case input
  • Euler team, UC Davis – BertramLudäscher, MingminChen – ASP support

https://sols.asu.edu

http://taxonbytes.org

slide26

What is ASP? – introductory reading list & links

Brewka, G., T. Either & M. Truszczyński. 2011. Answer set programming at a glance. Communications of the ACM 54: 92-103. Available at

http://people.scs.carleton.ca/~bertossi/KR11/material/communications201112ASP.pdf

Eiter, T. 2008. Answer Set Programming in a nutshell. Available at

http://gradlog.informatik.uni-freiburg.de/gradlog/slides_ak/eiter_asp.pdf

Gelfond, M. 2008. Answer sets; pp. 285-316. In: van Harmelen, F., V. Lifschitz & B. Porter. Handbook of Knowledge Representation. Elsevier. Available at

http://www.depts.ttu.edu/cs/research/krlab/pdfs/papers/gel07b.pdf

Gebser, M., B. Kaufmann, R. Kaminski, M. Ostrowski, T. Schaub & M. Schneider. 2011. Potassco: the Potsdam Answer Set Solving Collection. Available at http://www.cs.uni-potsdam.de/wv/pdfformat/gekakaosscsc11a.pdf

Lifschitz, V. 2008. What is Answer Set Programming? Available at

http://www.cs.utexas.edu/~ai-lab/pubs/wiasp.pdf

Potassco Group website: http://potassco.sourceforge.net/ (programs, tutorials)