For leveled spatial graphs, we find a surface embedding that allows cellular embedding.
problem Finding a surface embedding for general spatial graphs is not always possible.
method Define leveled property, decompose graph into subgraphs, and construct surface.
result For leveled spatial graphs with a small number of levels, a surface can always be found.
The paper extends Gaussian processes to model complex interactions in cellular complexes.
problem Capturing topological inductive biases in machine learning models.
method Proposes Gaussian processes on cellular complexes, introducing novel kernels.
result Derives two novel kernels for modeling interactions between cells.
The study embeds graphs on translation surfaces, proving essential-systolic embeddings and estimating surface genera.
problem Embedding graphs on translation surfaces with specific properties.
method Proving essential-systolic embeddings and estimating surface genera.
result Finite graphs admit essential-systolic embeddings on translation surfaces with estimated genera.
CT improves neural network performance on cell complex data.
problem Improving predictive performance of neural networks on complex data.
method Introducing the Cellular Transformer (CT) that generalizes graph-based transformers to cell complexes.
result CT achieves state-of-the-art performance on cell complex datasets without complex enhancements.
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
A new framework for knowledge graph embedding using sheaves.
problem Learning representations for entities and relations in knowledge graphs.
method Using cellular sheaves to describe knowledge graph embeddings with consistency constraints.
result A generalized framework for reasoning about knowledge graph embedding models.
Recently V. Krushkal and D. Renardy generalized the Tutte polynomial from graphs to cell complexes. We show that evaluating this polynomial at the origin gives the number of cellular spanning trees in the sense of A. Duval, C. Klivans, and J. Martin. Moreover, after a slight modification, the Tutte-Krushkal-Renardy pol…
Wavelets model complex interactions in spatial transcriptomics.
problem Capturing higher-order relationships in spatial transcriptomics data.
method Hypergraph diffusion wavelets for representing hyperedges.
result Wavelets effectively represent disease-relevant cellular niches in Alzheimer's disease.
This paper studies compactifications of moduli spaces involving closed Riemann surfaces. The first main result identifies the homeomorphism types of these compactifications. The second main result introduces orbicell decompositions on these spaces using semistable ribbon graphs extending the earlier work of Looijenga.
We compare two combinatorial models for the moduli space of two-dimensional cobordisms: Bödigheimer's radial slit configurations and Godin's admissible fat graphs, producing an explicit homotopy equivalence using a "critical graph" map. We also discuss natural compactifications of these two models, the unilevel harmoni…
CW Networks leverage cell complexes to enhance GNNs, achieving state-of-the-art results on molecular datasets.
problem Graph Neural Networks struggle with long-range interactions and lack principled ways to model higher-order structures.
method CW Networks use cell complexes to decouple computational and input graph structures, enabling flexible hierarchical message passing.
result CW Networks achieve state-of-the-art results on molecular datasets.
In this paper we generalize cellular algebras by allowing different partial orderings relative to fixed idempotents. For these relative cellular algebras we classify and construct simple modules, and we obtain other characterizations in analogy to cellular algebras. We also give several examples of algebras that are re…
This article introduces descriptive cellular homology on cell complexes, which is an extension of J.H.C. Whitehead's CW topology. A main result is that a descriptive cellular complex is a topology on fibres in a fibre bundle. An application of two forms of cellular homology is given in terms of the persistence of shape…
The study classifies cellular pseudomanifolds and their properties.
problem Understanding the structure of cellular pseudomanifolds.
method Analyzing the combinatorial and geometric properties of cellular pseudomanifolds.
result Complete classification of cellular pseudomanifolds with excess < 2, and progress towards excess 2.
The paper studies Morse theory on manifolds with boundaries, constructing cellular structures and estimating critical points.
problem Understanding Morse functions on manifolds with boundaries.
method Constructing a cellular structure and analyzing its algebraic properties.
result Estimation of the number of critical points of a Morse function with boundary conditions.
Research shows finiteness in triangulations with girth constraints.
problem Finiteness of cellular partial triangulations with girth constraints.
method Characterization of sparse graphs and contraction-minimal graphs.
result There are finitely many (3,6)-tight and (3,3)-tight graphs.
Quantum cellular automata form a homology theory.
problem Understanding the topological structure of quantum cellular automata.
method Formal properties of coarse homology theories.
result Quantum cellular automata naturally form the degree-zero part of a coarse homology theory.
This survey paper begins with the description of the duality between arc systems and ribbon graphs embedded in a punctured surface. Then we explain how to cellularize the moduli space of curves in two different ways: using Jenkins-Strebel differentials and using hyperbolic geometry. We also briefly discuss how these tw…
We present a construction of cellular BF theory (in both abelian and non-abelian variants) on cobordisms equipped with cellular decompositions. Partition functions of this theory are invariant under subdivisions, satisfy a version of the quantum master equation, and satisfy Atiyah-Segal-type gluing formula with respect…
Optimizes natural frequencies of cellular composites with various microstructures.
problem Designing cellular composites with diverse microstructures for maximizing natural frequencies.
method Data-driven topology optimization with a latent-variable Gaussian process model.
result Cellular designs with multiclass microstructures achieve higher natural frequencies.
We give examples of harmonic cellular maps between negatively curved manifolds which are not diffeomorphisms but are homotopic to diffeomorphisms.
A deep learning model for traffic forecasting in telecommunication networks.
problem Complex spatial-temporal dependency in traffic forecasting.
method Spatio-Temporal Hybrid Graph Convolutional Network (STHGCN) combining GRUs and hybrid-GCN.
result The proposed model outperforms classical and state-of-the-art methods.
The notion of cellular stratified spaces was introduced in a joint work of the author with Basabe, González, and Rudyak [1009.1851] with the aim of constructing a cellular model of the configuration space of a sphere. In particular, it was shown that the classifying space (order complex) of the face poset of a totally …
Study immersions of punctured 4-manifolds for quantum automata applications.
problem Existence of immersions between specific 4-manifolds.
method Analyzing immersions of punctured 4-manifolds to establish a partial order.
result Established a partial order on closed 4-manifolds via immersions.
New architectures improve topological deep learning's ability to capture complex data features.
problem Current TDL architectures struggle with fundamental topological and metric invariants.
method Developed multi-cellular networks (MCN) and scalable MCN (SMCN) to enhance expressivity.
result SMCN outperforms HOMP and expressive graph methods in learning topological properties.
In this work we develop a cellular equivariant homology functor and apply it to prove an equivariant Euler-Poincare formula and an equivariant Lefschetz theorem.
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
Partial recovery of node mappings between correlated graphs is possible under specific conditions.
problem Recovering a one-to-one mapping between nodes of two correlated graphs with a fraction of correct matches.
method Analyzing the graph isomorphism problem as a noisy version, considering Erdős-Rényi graphs, and providing conditions for partial recovery.
result Necessary and sufficient conditions for partial recovery of node mappings in correlated graphs are given.
Machine learning algorithms can be fooled by small well-designed adversarial perturbations. This is reminiscent of cellular decision-making where ligands (called antagonists) prevent correct signalling, like in early immune recognition. We draw a formal analogy between neural networks used in machine learning and model…
New findings on hyperbolicity of augmented links in thickened surfaces.
problem Proving hyperbolicity of links in thickened surfaces.
method Extending hyperbolicity results to generalized augmented cellular alternating links.
result Generalized augmented cellular alternating links in thickened surfaces are hyperbolic.
Solves challenges of drone communication in cellular networks.
problem Interference from drones to base stations in cellular networks.
method Derived analytical models, formulated optimization problem, transformed into machine learning problem, solved using deep reinforcement learning.
result Optimal handover and resource management policies for drones in cellular networks.
TrajectoryNet models dynamic cellular trajectories using optimal transport.
problem Modeling continuous and non-linear paths in dynamic processes.
method Continuous normalizing flows linked to dynamic optimal transport.
result TrajectoryNet improves interpolation of cellular distributions.
Consider a planar, bounded, m-connected region Ω, and let $\bordΩ$ be its boundary. Let T be a cellular decomposition of $Ω\cup\bordΩ$, where each 2-cell is either a triangle or a quadrilateral. From these data and a conductance function we construct a canonical pair (S,f) where S is a genus (m−1)…
CURIE uses cellular automata to detect concept drift in data streams.
problem Detecting changes in data distribution (concept drift) in data streams.
method CURIE represents data stream distribution in a cellular automata grid and uses its neighborhood rule to detect changes.
result CURIE, when hybridized with base learners, performs competitively in detection metrics and classification accuracy.
Deep learning identifies transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity.
problem Understanding how SARS-CoV-2 varies in infecting and causing severe COVID-19.
method Developed a new approach to generating self-supervised edge features, using Graph Attention Networks (GAT) and Set Transformer.
result Achieved state-of-the-art performance in predicting disease state of individual cells using single-cell RNA sequencing data.
FC-GAGA forecasts traffic using a novel gating mechanism.
problem Forecasting multivariate time-series, especially with graph relationships.
method Learnable fully connected hard graph gating mechanism for fully connected time-series forecasting.
result Competitive or better performance than existing algorithms without graph knowledge.
Electron Cryo-Tomography (ECT) allows 3D visualization of subcellular structures at the submolecular resolution in close to the native state. However, due to the high degree of structural complexity and imaging limits, the automatic segmentation of cellular components from ECT images is very difficult. To complement an…
Classifies fake surfaces up to complexity 5.
problem Classifying fake surfaces for low-dimensional topology.
method Derived properties of fake surfaces, classified up to complexity 5.
result Proved conjectures about fake surfaces up to complexity 5.
Polynomials derived from Heegaard diagrams for 3-manifolds.
problem Creating polynomial invariants for 3-manifolds.
method Using Heegaard diagrams and cellularly embedded graphs to define polynomials.
result Finiteness of minimal Heegaard graphs for a fixed manifold enables polynomial definition.
Proposes GFMMD for comparing signals on graphs.
problem Computing distances between distributions on graphs.
method Graph Fourier MMD (GFMMD) using optimal witness functions.
result Analytical solution and embedding of distributions.
The paper optimizes UAV path and power for QoS in cellular networks.
problem Optimizing UAV path and power for QoS in cellular networks.
method Apprenticeship learning via deep inverse reinforcement learning (IRL) combined with Q-learning and DRL.
result The proposed method achieves expert-level performance and maintains performance in unseen situations.
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here we present OhmNet, a hierarchy-aware unsupervised node feature le…
We show that tree almost automorphism groups, including Neretin groups, satisfy the analogue of the F∞-finiteness condition in the world of totally disconnected groups: They possess a cellular action on a contractible cellular complex such that the stabilizers are open and compact and the restriction of the act…
We analyze oversquashing in topological message-passing using relational structures.
problem Oversquashing in topological message-passing remains understudied.
method A unifying axiomatic framework that bridges graph and topological message-passing.
result Potential to advance topological deep learning.
New method enhances graph neural networks using contractions and hourglass persistence.
problem Limitations of traditional persistent homology in graph neural networks.
method Hourglass Persistence, Contraction Homology, contractions as a topological operation.
result Hourglass Persistence boosts expressivity, learnability, and stability in graph representation learning.
We study the problem of computing the homology of the configuration spaces of a finite cell complex X. We proceed by viewing X, together with its subdivisions, as a subdivisional space--a kind of diagram object in a category of cell complexes. After developing a version of Morse theory for subdivisional spaces, we …
This paper develops a discrete theory of real Riemann surfaces using quad-graphs and linear discretization.
problem Constructing a discrete theory of real Riemann surfaces.
method Using quad-graphs and linear discretization of Cauchy-Riemann equations, constructing a symplectic homology basis.
result The discrete period matrix has the same canonical decomposition as in the smooth setting.
Proposes CXNs for neural network computations on cell complexes.
problem Performing neural network computations on complex topological spaces.
method Introduces a message passing scheme and a unified encoder-decoder framework for cell complexes.
result Generalizes message passing to cell complexes and provides a cell2vec representation.