We briefly describe each of the four topics: Schubert Calculus, Schubert Cell, Schubert Cycle, and Schubert Polynomials.
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48 results for “cell cycle”
New features from early battery cycles predict lifetime with high accuracy.
problem Accurately predicting battery lifetime under varying conditions is challenging due to manufacturing variability and usage-dependent degradation.
method Extracted features from regularly scheduled reference performance tests and used them to predict battery lifetime using a hierarchical Bayesian regression model.
result Demonstrated a lifetime prediction of in-distribution cells with 15.1% mean absolute percentage error using only the first 15% of data.
Improved GPLVM model for single-cell RNA-seq data.
problem Lack of effective scalable models for clustering cell types in large-scale single-cell RNA-seq data.
method Introduces amortized stochastic variational Bayesian GPLVM (BGPLVM) tailored for single-cell RNA-seq.
result Matches the performance of scVI on synthetic and real-world datasets and reveals more interpretable latent structures.
Euler's theorem extended to complex structures.
problem Generalizing Euler's theorem to complex structures.
method Analyzing strongly connected, pure -dimensional regular CW-complexes.
result Evenness of cells is equivalent to generalized cycle decomposition and traversability.
SRCA reduces high-dimensional data to lower dimensions while preserving geometric structures.
problem High-dimensional datasets with underlying geometric structures.
method Spherical Rotation Component Analysis (SRCA) incorporating geometric loss functions.
result SRCA provides a low-rank spherical representation of data with general theoretic guarantees.
Study homology of periodic cell complexes using quotient spaces and spectral sequences.
problem Quantifying homology in periodic cell complexes.
method Finite representation of periodic cell complexes, Mayer-Vietoris spectral sequence.
result Full recovery of homology generators for -periodic graphs.
This article introduces proximal planar vortex 1-cycles, resembling the structure of vortex atoms introduced by William Thomson (Lord Kelvin) in 1867 and recent work on the proximity of sets that overlap either spatially or descriptively. Vortex cycles resemble Thomson's model of a vortex atom, inspired by P.G. Tait's …
A closed formula is obtained for the integral of tautological classes over the locus of hyperelliptic Weierstraß points in the moduli space of curves. As a corollary, a relation between Hodge integrals is obtained. The calculation utilizes the homeomorphism between the moduli…
CTEF fits ellipsoids to noisy data in any dimension.
problem Fitting ellipsoids to noisy data in arbitrary dimensions.
method Uses the Cayley transform to fit ellipsoids.
result CTEF outperforms other methods, especially when data are not uniformly distributed.
New method learns cell trajectories from multiple snapshots.
problem Inferring cell trajectories from limited, single-time-point data.
method Multi-marginal Schrödinger Bridges with iterative reference refinement.
result Effective in capturing long-term dependencies and learning from multiple time points.
The paper introduces a new metric to quantify uncertainty's impact on multiple objectives.
problem Quantifying the impact of uncertainty on multiple objectives in complex systems.
method Proposes the mean multi-objective cost of uncertainty (multi-objective MOCU) to quantify uncertainty.
result Demonstrates the effectiveness of the multi-objective MOCU in real-world applications.
We study Lagrangian embeddings of a class of two-dimensional cell complexes into the complex projective plane. These cell complexes, which we call pinwheels, arise naturally in algebraic geometry as vanishing cycles for quotient singularities of type (Wahl singularities). We show that …
In this paper, we propose a novel application of Generative Adversarial Networks (GAN) to the synthesis of cells imaged by fluorescence microscopy. Compared to natural images, cells tend to have a simpler and more geometric global structure that facilitates image generation. However, the correlation between the spatial…
This article introduces vortex nerve complexes in CW (Closure finite Weak) topological spaces, which first appeared in works by P. Alexandroff, H. Hopf and J.H.C. Whitehead during the 1930s. A vortex nerve is a CW complex containing one or more intersecting path-connected cycles. Each vortex nerve has its own distincti…
This article introduces planar ribbons, Vergili ribbon complexes and ribbon nerves in Alexandroff-Hopf-Whitehead CW (Closure finite Weak) topological spaces. A {\em planar ribbon} (briefly, {ribbon}) in a CW space is the closure of a pair of nesting, non-concentric filled cycles that includes the boundary but does not …
This is the first of two papers in which we prove that a cell model of the moduli space of curves with marked points and tangent vectors at the marked points acts on the Hochschild co--chains of a Frobenius algebra. We also prove that a there is dg--PROP action of a version of Sullivan Chord diagrams which acts on the …
Betti Numbers of Prodsimplicial Complexes for Directed Graphs with Applications to Word Reductionsmath.CO
Study of Betti numbers in prodsimplicial complexes for directed graphs, focusing on DNA recombination.
problem Analyzing Betti numbers in directed graphs for DNA recombination.
method Custom prodsimplicial complexes for acyclic directed graphs, investigating Betti numbers.
result Investigated Betti numbers and cycles in prodsimplicial complexes for DNA recombination.
Simple rectilinear polygons (i.e. rectilinear polygons without holes or cutpoints) can be regarded as finite rectangular cell complexes coordinatized by two finite dendrons. The intrinsic -metric is thus inherited from the product of the two finite dendrons via an isometric embedding. The rectangular cell complexe…
Metastability of lipid necks via geometric trialitycond-mat.soft
Lipid necks, large curvature bridges, are shown to be metastable.
problem Understanding the energetically prohibitive yet ubiquitous lipid necks in cell membranes.
method Geometric triality approach to demonstrate metastability.
result Lipid necks can exist for finite but potentially long times without stabilizing mechanisms.
A new method learns manifold-valued latents without an encoder.
problem Distorting data with intrinsic non-Euclidean structure.
method Riemannian generative decoder that learns latents directly.
result Learned representations respect the prescribed geometry and capture intrinsic non-Euclidean structure.
Accurately predicting the future capacity and remaining useful life of batteries is necessary to ensure reliable system operation and to minimise maintenance costs. The complex nature of battery degradation has meant that mechanistic modelling of capacity fade has thus far remained intractable; however, with the advent…
This is the second of two papers in which we prove that a cell model of the moduli space of curves with marked points and tangent vectors at the marked points acts on the Hochschild co--chains of a Frobenius algebra. We also prove that a there is dg--PROP action of a version of Sullivan Chord diagrams which acts on the…
Study embeddability of 2-complexes in 4-space, proving Heawood family's excluded minors.
problem Whether a 2-dimensional CW complex embeds in .
method Operations preserving embeddability, constructions of non-preserving transformations, study of 4-flat graphs.
result Prove 78 graphs of Heawood family are excluded minors for 4-flat graphs.
Hyperconnected Relator Spaces. CW Complexes and Continuous Function Paths that are Hyperconnectedmath.GT
This article introduces proximal cell complexes in a hyperconnected space. Hyperconnectedness encodes how collections of path-connected sub-complexes in a Alexandroff-Hopf-Whitehead CW space are near to or far from each other. Several main results are given, namely, a hyper-connectedness form of CW (Closure Finite Weak…
Deep learning model explains breast cancer subtypes using logistic regression.
problem Clarifying the mechanisms of breast cancer subtypes for better treatment.
method Developed a PWL model that generates custom-made logistic regression for each patient.
result The PWL model reveals genes relevant to cell cycle-related pathways.
DPA preserves data distribution in reduced dimensions.
problem Loss of data distribution in dimension reduction.
method DPA combines encoder and decoder to match data distribution.
result DPA successfully reconstructs data distribution.
In the recent years, Riemannian shape analysis of curves and surfaces has found several applications in medical image analysis. In this paper we present a numerical discretization of second order Sobolev metrics on the space of regular curves in Euclidean space. This class of metrics has several desirable mathematical …
We give an algorithm to compute the integer cohomology groups of any real partial flag manifold, by computing the incidence coefficients of the Schubert cells. For even flag manifolds we determine the integer cohomology groups, by proving that any torsion class has order 2 (generalizing a result of Ehresmann). We conje…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental cycles, from day/night to seasonal. Transcriptional regulatory networks are one…
Infinite presentations are given for all of the higher Torelli groups of once-punctured surfaces. In the case of the classical Torelli group, a finite presentation of the corresponding groupoid is also given, and finite presentations of the classical Torelli groups acting trivially on homology modulo N are derived for …
Topology-enhanced loss improves 3D object reconstruction from 2D images.
problem Challenges in reconstructing 3D objects from 2D images, especially capturing shape information.
method Integrates multi-scale topological features into the reconstruction loss using cubical complexes and optimal transport distance.
result Topology-aware loss substantially improves 3D reconstruction quality.
To each oriented closed combinatorial manifold we assign the set (with repetitions) of isomorphism classes of links of its vertices. The obtained transformation L is the main object of study of the present paper. We pose a problem on the inversion of the transformation L. We shall show that this problem is closely rela…
Algorithm constructs and classifies weaving diagrams using combinatorial methods.
problem Classifying unique weaving diagrams with over/under information.
method Systematic algorithm based on tiling and crossing matrices.
result Classification of periodic structures based on minimum crossings.
Kernel testing compares cell states in single-cell data.
problem Comparing non-linear cell states in single-cell data.
method Kernel-based testing framework for non-linear distribution comparison.
result Identifies subtle population variations in cell states.
We consider collections of disjoint simple closed curves in a compact orientable surface which decompose the surface into pairs of pants. The isotopy classes of such curve systems form the vertices of a 2-complex, whose edges correspond to certain simple moves in which only one curve changes, and whose 2-cells correspo…
Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterizationq-bio.GN
This study reviews and evaluates clustering methods for single-cell RNA-seq data.
problem Identifying and characterizing novel cell types from single-cell RNA-seq data.
method Review and performance comparison of clustering methods.
result Performance comparison experiments on two datasets.
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer vision and machine learning methods, analysis of multi-label samples (region containi…
Forest Fire Clustering discovers cell types from single-cell data.
problem Discovering cell types from large-scale single-cell sequencing data.
method Iterative label propagation and parallelized Monte Carlo simulation.
result Forest Fire Clustering outperforms state-of-the-art methods on diverse benchmarks.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
Matching cells over time has long been the most difficult step in cell tracking. In this paper, we approach this problem by recasting it as a classification problem. We construct a feature set for each cell, and compute a feature difference vector between a cell in the current frame and a cell in a previous frame. Then…
Structures of optimal discrete gradient vector fields on surface with one or two critical cellsmath.DS
The study identifies all possible vector field structures on specific 2D shapes.
problem Optimal discrete gradient vector fields on surfaces with 1-2 critical cells.
method Analysis of discrete vector fields on 2D shapes with minimal critical cells.
result All possible structures of discrete Morse functions on specified shapes.
Stochastic networks are a plausible representation of the relational information among entities in dynamic systems such as living cells or social communities. While there is a rich literature in estimating a static or temporally invariant network from observation data, little has been done toward estimating time-varyin…
New model identifies cell-specific genes for cancer prognosis.
problem No statistical model to integrate multiscale cancer data.
method Bayesian generalized promotion time cure models (GPTCMs).
result Improves cancer prognosis by identifying cell-specific genes.
MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.
problem Selecting informative genes from large single-cell RNA-seq datasets is challenging and computationally intensive.
method MarkerMap is a generative model that identifies minimal gene sets explaining cell type variability.
result MarkerMap outperforms existing methods in both supervised and unsupervised marker selection.
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.
New metric scores perturbations across populations, not cells, improving model comparison.
problem Single-cell perturbation data overlaps, making per-cell accuracy unreliable.
method Average per-cell probability vectors over all cells of a perturbation to form a population profile and rank candidate perturbations.
result Classifier Discrimination Score (CDS) identifies true perturbation more reliably than pseudobulk-based scores.
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profil…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of …