Data identification for improving gene network inference using computational algebra

Geometric Characterization of Data Sets with Unique Reduced Gröbner Bases

Model selection based on experimental data is an important challenge in biological data science. Particularly when collecting data is expensive or time-consuming, as it is often the case with clinical trial and biomolecular experiments, the problem of selecting information-rich data becomes crucial for creating relevant models. We identify geometric properties of input data that result in an unique algebraic model, and we show that if the data form a staircase, or a so-called linear shift of a staircase, the ideal of the points has a unique reduced Gröbner basis and thus corresponds to a unique model. We use linear shifts to partition data into equivalence classes with the same basis. We demonstrate the utility of the results by applying them to a Boolean model of the well-studied lac operon in E. coli.