Related papers: Computing phylogenetic invariants for time-reversi…
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model…
Invariant manifolds provide the geometric structures for describing and understanding dynamics of nonlinear systems. The theory of invariant manifolds for both finite and infinite dimensional autonomous deterministic systems, and for…
Invariant theory is concerned with functions that do not change under the action of a given group. Here we communicate an approach based on tensor networks to represent polynomial local unitary invariants of quantum states. This graphical…
We propose an extension of the classical variational theory of evolution equations that accounts for dynamics also in possibly non-reflexive and non-separable spaces. The pivoting point is to establish a novel variational structure, based…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Representations learnt through deep neural networks tend to be highly informative, but opaque in terms of what information they learn to encode. We introduce an approach to probabilistic modelling that learns to represent data with two…
Alignment between non-rigid stretchable structures is one of the most challenging tasks in computer vision, as the invariant properties are hard to define, and there is no labeled data for real datasets. We present unsupervised neural…
Let $\mathbf{K}$ be a field and $\phi$, $\mathbf{f} = (f_1, \ldots, f_s)$ in $\mathbf{K}[x_1, \dots, x_n]$ be multivariate polynomials (with $s < n$) invariant under the action of $\mathcal{S}_n$, the group of permutations of $\{1, \dots,…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
An enumerative invariant theory in Algebraic Geometry, Differential Geometry, or Representation Theory, is the study of invariants which 'count' $\tau$-(semi)stable objects $E$ with fixed topological invariants $[E]=\alpha$ in some…
We study configuration space integral formulas for Milnor's homotopy link invariants, showing that they are in correspondence with certain linear combinations of trivalent trees. Our proof is essentially a combinatorial analysis of a…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Intrinsic time-dependent invariants are constructed for classical, flat, homogeneous, anisotropic cosmology with a massless scalar material source. Invariance under the time reparameterization-induced canonical symmetry group is displayed…
This paper presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are…
We construct knot invariants categorifying the quantum knot variants for all representations of quantum groups. We show that these invariants coincide with previous invariants defined by Khovanov for sl_2 and sl_3 and by Mazorchuk-Stroppel…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
Using several numerical invariants, we study a partition of the space of line arrangements in the complex projective plane, given by the intersection lattice types. We offer also a new characterization of the free plane curves using the…
We consider tilings of Euclidean spaces by polygons or polyhedra, in particular, tilings made by a substitution process, such as the Penrose tilings of the plane. We define an isomorphism invariant related to a subgroup of rotations and…
Time reversal symmetry is studied in a space with noncommutativity of coordinates and noncommutativity of momenta of canonical type. The circular motion is examined as an apparent example of time reversal symmetry breaking in the space. On…