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Abstract

We present Binomials, a package for the computer algebra system Macaulay 2, which specializes well-known algorithms to binomial ideals. These come up frequently in algebraic statistics and commutative algebra, and it is shown that significant speedup of computations like primary decomposition is possible. While central parts of the implemented algorithms go back to a paper of Eisenbud and Sturmfels, we also discuss a new algorithm for computing the minimal primes of a binomial ideal. All decompositions make significant use of combinatorial structure found in binomial ideals, and to demonstrate the power of this approach we show how Binomials was used to compute primary decompositions of commuting birth and death ideals of Evans et al., yielding a counterexample for their conjectures.

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References

  • 4ti2 team (2007). 4ti2—a software package for algebraic, geometric and combinatorial problems on linear spaces. Available at http://www.4ti2.de

  • Altmann K. (2000) The chain property for the associated primes of \({\mathcal{A}}\) -graded ideals. Mathematical Research Letters 7: 565–575

    MATH  MathSciNet  Google Scholar 

  • Bigatti A.M., Scala R.L., Robbiano L. (1999) Computing toric ideals. Journal of Symbolic Computation 27(4): 351–365

    Article  MATH  MathSciNet  Google Scholar 

  • Cox D.A., Little J.B., O’Shea D. (1996) Ideals, varieties, and algorithms (2nd ed.). Undergraduate texts in mathematics. Springer, New York

    Google Scholar 

  • Dickenstein, A., Matusevich, L., Miller, E. (2008). Combinatorics of binomial primary decomposition. Mathematische Zeitschrift (to appear).

  • Drton M., Sturmfels B., Sullivant S. (2009) Lectures on algebraic statistics. Oberwolfach Seminars (Vol. 39). Springer, Birkhäuser, Berlin

    Google Scholar 

  • Eisenbud D. (1995) Commutative algebra: With a view toward algebraic geometry. Graduate texts in mathematics (Vol. 150). Springer, New York

    Google Scholar 

  • Eisenbud D., Sturmfels B. (1996) Binomial ideals. Duke Mathematical Journal 84(1): 1–45

    Article  MATH  MathSciNet  Google Scholar 

  • Eisenbud D., Grayson D.R., Stillman M.E., Sturmfels B. (2001) Computations in algebraic geometry with Macaulay 2. Algorithms and computations in Mathematics (Vol. 8). Springer, New York

    Google Scholar 

  • Evans S., Sturmfels B., Uhler C. (2010) Commuting birth-death processes. Annals of Applied Probability 20(1): 238–266

    Article  MATH  MathSciNet  Google Scholar 

  • Fink, A. (2009). The binomial ideal of the intersection axiom for conditional probabilities. preprint arXiv:09021495

  • Fulton W. (1993) Introduction to toric varieties. Annals of Mathematical Studies. Princeton University Press, Princeton

    Google Scholar 

  • Geiger D., Meek C., Sturmfels B. (2006) On the toric algebra of graphical models. The Annals of Statistics 34(5): 1463–1492

    Article  MATH  MathSciNet  Google Scholar 

  • Gilmer R. (1984) Commutative semigroup rings. University of Chicago Press, Chicago

    MATH  Google Scholar 

  • Hemmecke R., Malkin P. (2009) Computing generating sets of lattice ideals. Journal of Symbolic Computation 44(10): 1493–1476

    Article  MATH  MathSciNet  Google Scholar 

  • Hemmecke R., Morton J., Shiu A., Sturmfels B., Wienand O. (2008) Three counter-examples on semi-graphoids. Combinatorics, Probability and Computation 17: 239–257

    MATH  MathSciNet  Google Scholar 

  • Herzog, J., Hibi, T., Hreinsdóttir, F., Kahle, T., Rauh, J. (2009). Binomial edge ideals and conditional independence statements. Advances in Applied Mathematics (in press).

  • Hoşten S., Sturmfels B. (1995) Grin: An implementation of groebner bases for integer programming. In: Balas E., Clausen J. (eds) Integer Programming and Combinatorial Optimization. Lecture Notes in Computer Science. Springer, Berlin, pp 267–276

    Google Scholar 

  • Hungerford T.W. (1974) Algebra, graduate texts in mathematics (Vol. 73). Springer, New York

    Google Scholar 

  • Latouche G., Ramaswami V. (1999) Introduction to matrix analytic methods in stochastic modeling. Statistics and Applied Probability. SIAM, Philadelphia

    Google Scholar 

  • Miller E., Sturmfels B. (2005) Combinatorial commutative algebra. Graduate texts in mathematics (Vol. 227). Springer, Berlin

    Google Scholar 

  • Ojeda I., Piedra R. (2000) Cellular binomial ideals. primary decomposition of binomial ideals. Journal of Symbolic Computation 30: 383–400

    Article  MATH  MathSciNet  Google Scholar 

Download references

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Correspondence to Thomas Kahle.

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The author is supported by the Volkswagen Foundation.

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Kahle, T. Decompositions of binomial ideals. Ann Inst Stat Math 62, 727–745 (2010). https://doi.org/10.1007/s10463-010-0290-9

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  • DOI: https://doi.org/10.1007/s10463-010-0290-9

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