We posit that hippocampal place cells encode information about future locations under a transition distribution observed as an agent explores a given (physical or conceptual) space. The encoding of information about the current location, usually associated with place cells, then emerges as a necessary step to achieve t…
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48 results for “Place cells”
Place Cells as Multi-Scale Position Embeddings: Random Walk Transition Kernels for Path Planningq-bio.NC
Model place cells as spatial embeddings for efficient path planning and cognitive map construction.
problem Encoding spatial navigation in the hippocampus.
method Model place cells using spectral decomposition of multi-step random walk transition kernels, inducing sparsity and adjacency.
result Place cells encode spatial information through non-negativity and inner-product structure, forming a cognitive map.
Random walks on cell complexes link to Laplacians and Novikov-Shubin invariants.
problem Computing Novikov-Shubin invariants for complex cell structures.
method Construct random walks on cell complexes, relate to Laplacians, and use return probabilities.
result Novikov-Shubin invariants can be recovered from random walk return probabilities.
A soap film is actually a thin solid fluid bounded by two surfaces of opposite orientation. It is natural to model the film using one polyhedron for each side. Two problems are to get the polyhedra for both sides to be in the same place without canceling each other out and to model triple junctions without introducing …
A central problem to understanding intelligence is the concept of generalisation. This allows previously learnt structure to be exploited to solve tasks in novel situations differing in their particularities. We take inspiration from neuroscience, specifically the hippocampal-entorhinal system known to be important for…
A novel method detects multiple mitosis events and mitigates annotation gaps in phase-contrast microscopy.
problem Detecting multiple mitosis events and handling annotation gaps in closely placed cells.
method Estimating a spatiotemporal likelihood map via 3DCNN to detect multiple mitosis events and mitigate annotation gaps.
result Our method outperformed compared methods in terms of F1-score using a challenging dataset.
In data science, determining proximity between observations is critical to many downstream analyses such as clustering, information retrieval and classification. However, when the underlying structure of the data probability space is unclear, the function used to compute similarity between data points is often arbitrar…
Unsupervised text encoding models have recently fueled substantial progress in NLP. The key idea is to use neural networks to convert words in texts to vector space representations based on word positions in a sentence and their contexts, which are suitable for end-to-end training of downstream tasks. We see a striking…
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 present a neuro-mathematical model for geometrical optical illusions (GOIs), a class of illusory phenomena that consists in a mismatch of geometrical properties of the visual stimulus and its associated percept. They take place in the visual areas V1/V2 whose functional architecture have been modelled in previous wo…
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…
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.
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.
Humans and animals show remarkable flexibility in adjusting their behaviour when their goals, or rewards in the environment change. While such flexibility is a hallmark of intelligent behaviour, these multi-task scenarios remain an important challenge for machine learning algorithms and neurobiological models alike. We…
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.
Review of Single-cell RNA-seq Data Clustering for Cell Type Identification and Characterizationq-bio.GN
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become the central component to identify and characterize novel cell types and gene exp…
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 …
Hippocampal dentate granule cells are among the few neuronal cell types generated throughout adult life in mammals. In the normal brain, new granule cells are generated from progenitors in the subgranular zone and integrate in a typical fashion. During the development of epilepsy, granule cell integration is profoundly…
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
problem Challenges in extracting smooth, low-dimensional representations from noisy single-cell data.
method Builds on PCS framework to develop NESS, a stable machine learning approach.
result NESS consistently yields useful biological insights across diverse single-cell datasets.
New model clusters cells and individuals, revealing genetic influences on cell types.
problem Clustering nested data with group-level and observation-level variables.
method Nested Atoms Model (NAM), Bayesian nonparametric approach.
result Identifies clusters of genetically similar individuals with homogeneous cell-type profiles.
Cell-based NAS search spaces are redundant and lack novelty.
problem Redundancy and lack of novelty in cell-based neural architecture search.
method Empirical analysis of architectures from popular cell-based search spaces.
result Randomly sampled architectures can match or outperform state-of-the-art results.
For a finite family of 3-dimensional almost contact metric manifolds with closed the structure form is described a construction of an almost contact metric manifold, where the members of the family are building blocks - cells. Obtained manifold share many properties of cells. One of the more important are nullity c…
Understanding and reasoning about places and their relationships are critical for many applications. Places are traditionally curated by a small group of people as place gazetteers and are represented by an ID with spatial extent, category, and other descriptions. However, a place context is described to a large extent…
HSSE framework embeds single-cell RNA-seq data at multiple scales.
problem Capturing heterogeneous local structure in single-cell RNA-seq data.
method Hierarchical sheaf spectral embedding (HSSE) framework.
result HSSE achieves competitive or improved performance in single-cell RNA-seq data representation learning.
Researchers infer gene activity in dividing cells, accounting for protein inheritance and division history.
problem Inferring protein production kinetics in dividing cells due to protein inheritance and division history.
method Adapted conditional normalizing flows to approximate intractable likelihoods from simulated data.
result Glc3 gene is mostly inactive under stress, with brief and transient expression.
SimCD simultaneously clusters cells and identifies differential gene expression in scRNA-seq data.
problem Separate clustering and differential expression analysis for scRNA-seq data leads to suboptimal results.
method Develops SimCD, a unified hierarchical gamma-negative binomial model for simultaneous cell clustering and differential expression analysis.
result SimCD outperforms existing methods in discovering cell clusters and capturing dynamic expression changes.
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second approach is to use machine learning to discriminate cell types based on th…
Two simple homotopy equivalent 2-complexes K2 and L2 are related by an algebraic criterion of their corresponding presentations as stated in [HoMeSier]. Frank Quinn set it into a topological context (see [Qu1]) and call these 2-complexes related by an s-move. Using elementary 3-expansions, K2 extends to 3-cells in K3 r…
We construct a small regular cellular decomposition of the Fulton MacPherson operad that is compatible with the operad composition. The cells are indexed by trees with edges of two colors and vertices labelled by cells of the cacti operad. We compute the generating functions counting the cells, that are algebrai…
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.
Despite fluorescent cell-labelling being widely employed in biomedical studies, some of its drawbacks are inevitable, with unsuitable fluorescent probes or probes inducing a functional change being the main limitations. Consequently, the demand for and development of label-free methodologies to classify cells is strong…
The moduli space of Riemann surfaces with at least two punctures can be decomposed into a cell complex by using a particular family of ribbon graphs called Nakamura graphs. We distinguish the moduli space with all punctures labelled from that with a single labelled puncture. In both cases, we describe a cell decomposit…
Neural network predicts electrochemical cell faults with 53% less error.
problem Predicting faults in electrochemical cells to avoid safety hazards and reduce costs.
method Self-supervised encoder-decoder neural network that learns degradation from operating conditions.
result Predicted voltage with 53% less error than parametric models, 64% faster fault prediction.
New system constructs cell-type taxonomy across multiple samples.
problem Challenges in matching clusters from different datasets.
method Combines Optimal Transport with Relaxed Marginal Constraints (OT-RMC) for simultaneous alignment of clusters across multiple samples.
result Highly accurate annotation of cell types and sample-level feature extraction.
Generalising a seminal result of Epstein and Penner for cusped hyperbolic manifolds, Cooper and Long showed that each decorated strictly convex projective cusped manifold has a canonical cell decomposition. Penner used the former result to describe a natural cell decomposition of decorated Teichmüller space of puncture…
SMAI framework tests and integrates single-cell data alignability.
problem Lack of a rigorous statistical test for alignability and distortion during alignment.
method Spectral manifold alignment and inference (SMAI) framework.
result SMAI outperforms existing methods in alignability testing and integration.
Combinatorics of embeddingsmath.GT
We offer the following explanation of the statement of the Kuratowski graph planarity criterion and of 6/7 of the statement of the Robertson-Seymour-Thomas intrinsic linking criterion. Let us call a cell complex 'dichotomial' if to every cell there corresponds a unique cell with the complementary set of vertices. Then …
Minimal example found for two finite CW-complexes sharing a common covering.
problem Finding the minimum number of 2-cells in two finite CW-complexes that share a common covering.
method Constructing an almost minimal example with two 2-cells in each complex.
result Minimal example with two 2-cells in each complex.
We present a conditional generative model to learn variation in cell and nuclear morphology and the location of subcellular structures from microscopy images. Our model generalizes to a wide range of subcellular localization and allows for a probabilistic interpretation of cell and nuclear morphology and structure loca…
Multi-StyleGAN simulates live cell microscopy imagery.
problem Costly and complex live cell experiments.
method Generative adversarial network (GAN) synthesizing multi-domain time-lapse images.
result Captures biophysical factors and time dependencies in cell imagery.
Cellina uses supervised disentanglement to predict cell behavior in tissues.
problem Querying counterfactuals on tissue graphs
method Cellina framework using supervised disentanglement
result Outperforms spatially-informed and non-spatial competitors