An official website of the United States government
Abstract MotivationModel organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this cross-species transfer, sequence similarity does not imply functional similarity, and thus, several current approaches incorporate protein–protein interactions to help map findings between species. Existing transfer methods either formulate the alignment problem as a matching problem which pits network features against known orthology, or more recently, as a joint embedding problem. ResultsWe propose a novel state-of-the-art joint embedding solution: Embeddings to Network Alignment (ETNA). ETNA generates individual network embeddings based on network topological structure and then uses a Natural Language Processing-inspired cross-training approach to align the two embeddings using sequence-based orthologs. The final embedding preserves both within and between species gene functional relationships, and we demonstrate that it captures both pairwise and group functional relevance. In addition, ETNA’s embeddings can be used to transfer genetic interactions across species and identify phenotypic alignments, laying the groundwork for potential opportunities for drug repurposing and translational studies. Availability and implementationhttps://github.com/ylaboratory/ETNA
more »
« less
This content will become publicly available on February 5, 2026
Joint transitivity for linear iterates
Abstract We establish sufficient and necessary conditions for the joint transitivity of linear iterates in a minimal topological dynamical system with commuting transformations. This result provides the first topological analogue of the classical Berend and Bergelson joint ergodicity criterion in measure-preserving systems.
more »
« less
- Award ID(s):
- 2247331
- PAR ID:
- 10587128
- Editor(s):
- Donoso, S; Koutsogiannis, A; Sun, W
- Publisher / Repository:
- Cambridge University Press
- Date Published:
- Journal Name:
- Forum of Mathematics, Sigma
- Volume:
- 13
- ISSN:
- 2050-5094
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
In this work, we examine the topological phases of the spring-mass lattices when the spatial inversion symmetry of the system is broken and prove the existence of edge modes when two lattices with different topological phases are glued together. In particular, for the one-dimensional lattice consisting of an infinite array of masses connected by springs, we show that the Zak phase of the lattice is quantized, only taking the value 0 or . We also prove the existence of an edge mode when two semi-infinite lattices with distinct Zak phases are connected. For the two-dimensional honeycomb lattice, we characterize the valley Chern numbers of the lattice when the masses on the lattice vertices are uneven. The existence of edge modes is proved for a joint honeycomb lattice formed by gluing two semi-infinite lattices with opposite valley Chern numbers together.more » « less
-
Abstract Topological metals are conducting materials with gapless band structures and nontrivial edge-localized resonances. Their discovery has proven elusive because traditional topological classification methods require band gaps to define topological robustness. Inspired by recent theoretical developments that leverage techniques from the field ofC∗-algebras to identify topological metals, here, we directly observe topological phenomena in gapless acoustic crystals and realize a general experimental technique to demonstrate their topology. Specifically, we not only observe robust boundary-localized states in a topological acoustic metal, but also re-interpret a composite operator—mathematically derived from theK-theory of the problem—as a new Hamiltonian whose physical implementation allows us to directly observe a topological spectral flow and measure the topological invariants. Our observations and experimental protocols may offer insights for discovering topological behaviour across a wide array of artificial and natural materials that lack bulk band gaps.more » « less
-
Abstract Topological field‐effect transistor is a revolutionary concept that physical fields are used to switch on and off quantum topological states of the condensed matter. Although this emerging concept has been explored in electronics, how to realize it in the acoustic realm remains elusive. In this work, a class of magnetoactive acoustic topological transistors capable of on‐demand switching on and off topological states and reconfiguring topological edges with external magnetic fields is presented. The key mechanism is to harness magnetic fields to tune air‐cavity volumes within acoustic chambers, thus breaking or preserving the inversion symmetry to manifest or conceal the quantum valley Hall effect. To switch the topological transport beyond the in‐plane routes, a magneto‐tuned non‐topological band gap to allow or forbid the wave transport out‐of‐plane is harnessed. With the reversible magnetic control, on‐demand switching of topological routes to realize topological field‐effect waveguides and wave regulators is demonstrated. Analogous to the impact of semiconductor transistors on modern electronics, this work may expand the scope of topological acoustics by achieving unprecedented functions in acoustic modulation.more » « less
-
Abstract We prove Farber’s conjecture on the stable topological complexity of configuration spaces of graphs. The conjecture follows from a general lower bound derived from recent insights into the topological complexity of aspherical spaces. Our arguments apply equally to higher topological complexity.more » « less
