arXiv subjects
Publications and source records attributed to Niharika Chakrabarty Paul.
We show that tree tensor network varieties, including tensor train varieties, are general Markov models associated to spaced trees. This allows us to prove that the prime ideals of these varieties are generated by minors of matrix flattenings. In the case of tensor train varieties, we discuss whether these minors form a Gröbner basis and provide a combinatorial method to compute the degree for order $3$ tensor trains.
We investigate the toric geometry of two families of generalised determinantal varieties arising from permutations: Matrix Schubert varieties ($\overline{X_w}$) and Kazhdan-Lusztig varieties ($\mathcal{N}_{v,w}$). Matrix Schubert varieties can be written as $\overline{X_w} = Y_w \times \mathbb C^d$, where $d$ is maximal. We are especially interested in the structure and complexity of these varieties $Y_w$ and $\mathcal{N}_{v,w}$ under the so-called usual torus actions. In the case when $Y_w$ is toric, we provide a full characterisation of the simple reflections $s_i$ that render ${Y_{w \cdot s_i}}$ toric, as well as the corresponding changes to the weight cone. For Kazhdan-Lusztig varieties, we consider how moving one of the two permutations $v,w$ along a chain in the Bruhat poset affects their complexity. Additionally, we study the complexity of these varieties, for permutations $v$ and $w$ of a specific structure. Finally, we consider the links between these determinantal varieties and two classes of statistical models; namely conditional independence and quasi-independence models.
Phylogenetic invariants are equations that vanish on algebraic varieties associated with Markov processes that model molecular substitutions on phylogenetic trees. For practical applications, it is essential to understand these equations across a wide range of substitution models. Recent work has shown that, for equivariant models, phylogenetic invariants can be derived from those of the general Markov model by restricting to the linear space defined by the model (namely, the space of mixtures of distributions on the model). Following this philosophy, we describe the space of mixtures and phylogenetic invariants for time-reversible models that are not equivariant. Specifically, we study two submodels of the Tamura-Nei nucleotide substitution model (Felsenstein 81 and 84) using an orthogonal change of basis recently introduced for algebraic time-reversible models. For tripods, we prove that the algebraic variety of each submodel coincides with the variety of Tamura-Nei intersected with the linear space of the submodel. In the case of quartets, we show that it is an irreducible component of this intersection. Moreover, we demonstrate that it suffices to consider only the binomial equations defining the linear space, which correspond to the natural symmetries of the model in the new coordinates. For each submodel, we explicitly provide equations defining a local complete intersection that characterizes the phylogenetic variety on a dense open subset containing the biologically relevant points.
We investigate the geometry of a family of log-linear statistical models called quasi-independence models. The toric fiber product is useful for understanding the geometry of parameter inference in these models because the maximum likelihood degree is multiplicative under the TFP. We define the coordinate toric fiber product, or cTFP, and give necessary and sufficient conditions under which a quasi-independence model is a cTFP of lower-order models. We show that the vanishing ideal of every 2-way quasi-independence model with ML-degree 1 can be realized as an iterated toric fiber product of linear ideals. We also classify which Lawrence lifts of 2-way quasi-independence models are cTFPs and give a necessary condition under which a $k$-way model has ML-degree 1 using its facial submodels.