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…
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A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
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48 results for “cell profiling”
A novel criterion selects optimal distance metrics for cell profile analysis.
problem Determining the most accurate distance metric for high-dimensional cell profiles.
method Generalized proposition and corollaries to evaluate and select distance metrics.
result Wasserstein and cosine similarity metrics are optimal for general cases.
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.
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.
Modeling curvature-sensitive cells in visual cortex using manifold geometry.
problem Understanding how curvature influences cell function in the visual cortex.
method Developed a 4D manifold with canonical Engel structure to represent orientation, position, curvature, and scale.
result Characterized curvature-sensitive receptive profiles using left-invariant generators of the Engel structure.
Elastic co-clustering improves clustering of single-cell genomic data.
problem Improving clustering performance of single-cell genomic datasets.
method Elastic coupled co-clustering in an unsupervised transfer learning framework.
result Our algorithm significantly improves clustering performance over traditional methods.
Modeling curvature-sensitive cells in visual cortex with geometric structures.
problem Understanding the functional architecture of curvature-sensitive cells in the visual cortex.
method Geometric model based on Engel structure and SIM(2) symmetry.
result Identified SIM(2) as the natural symmetry group for curvature-sensitive cells.
New model generates realistic single-cell gene expression data.
problem Generating realistic single-cell gene expression profiles is challenging.
method scLDM, a latent diffusion model using Diffusion Transformers and linear interpolants.
result Superior performance in generating realistic single-cell gene expression data.
Tissue heterogeneity is a major confounding factor in studying individual populations that cannot be resolved directly by global profiling. Experimental solutions to mitigate tissue heterogeneity are expensive, time consuming, inapplicable to existing data, and may alter the original gene expression patterns. Here we a…
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…
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.
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However,…
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…
Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq dataq-bio.QM
Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has …
CR-UOT improves matching of heterogeneous single-cell omics profiles.
problem Matching nonnegative finite Radon measures across heterogeneous spaces.
method Cost-regularized unbalanced optimal transport (CR-UOT) framework.
result CR-UOT improves alignment of heterogeneous single-cell omics profiles.
Recent developments in high throughput profiling of individual neurons have spurred data driven exploration of the idea that there exist natural groupings of neurons referred to as cell types. The promise of this idea is that the immense complexity of brain circuits can be reduced, and effectively studied by means of i…
With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and prop…
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical investigations. In the study, we will be using the dataset collected by the authors of Sys…
Paper finds new criteria for conjugate points in fluid flows.
problem Finding conjugate points in steady 2D Euler flows.
method Develops a new sufficient criterion for conjugate points, applies to any rotational cell, and uses a general construction of steady fluid surfaces.
result Improves on existing criteria and captures all known conjugate points in rotational cells.
Study identifies biomarkers for lung cancer in female non-smokers.
problem Identifying prognostic biomarkers for stage III NSCLC in non-smoking females.
method Gene expression profiling and XGBoost machine learning algorithm.
result Top biomarkers validated in literature, with AUC score of 0.835.
SnapMMD forecasts cell differentiation outcomes from snapshot data.
problem Forecasting cell differentiation outcomes from limited snapshot data.
method SnapMMD learns dynamics by directly fitting the joint distribution of state measurements and observation time with MMD loss, allowing for unknown and state-dependent volatilities.
result SnapMMD delivers accurate forecasts and an R2-style statistic for diagnosing fit.
Transcriptomics response of SK-N-AS cells to methamidophos (an acetylcholine esterase inhibitor) exposure was measured at 10 time points between 0.5 and 48 h. The data was analyzed using a combination of traditional statistical methods and novel machine learning algorithms for detecting anomalous behavior and infer cau…
scICML integrates multi-omics data from single cells using co-clustering.
problem High noise and sparsity in multi-omics data from single cells.
method Information-theoretic co-clustering-based multi-view learning.
result Improves clustering performance and provides biological insights.
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for technical effects that may erroneously set some observations of gene expression leve…
Gene expression profiles have been widely used to characterize patterns of cellular responses to diseases. As data becomes available, scalable learning toolkits become essential to processing large datasets using deep learning models to model complex biological processes. We present an autoencoder to capture nonlinear …
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.
TransST improves spatial transcriptomics data analysis by identifying cell clusters and biomarkers.
problem Low resolution and insufficient sequencing depth in spatial transcriptomics data.
method Transfer learning framework to adaptively leverage external cell-labeled information.
result TransST successfully identifies five biologically meaningful cell clusters and separates adipose tissues from connective issues.
On the minimization of the Willmore energy under a constraint on total mean curvature and areamath.DG
Study minimizes Willmore energy with constraints on surface properties.
problem Minimizing Willmore energy under specific surface properties.
method Adapting Keller-Mondino-Rivière, Bauer-Kuwert, and Ndiaye-Schätzle methods.
result Existence of smooth minimizers for a broad range of constraints.
In this study, we present Flatsomatic - a Variational Auto Encoder (VAE) optimized to compress somatic mutations that allow for unbiased data compression whilst maintaining the signal. We compared two different neural network architectures for the VAE: Multilayer Perceptron (MLP) and bidirectional LSTM. The somatic pro…
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this rev…
Emergence of Grid-like Representations by Training Recurrent Networks with Conformal Normalizationq-bio.NC
The paper studies how grid cell patterns emerge in neural networks.
problem Understanding how grid cells in the brain form hexagonal firing patterns.
method Training recurrent neural networks with conformal normalization of velocity inputs.
result Conformal normalization is crucial for the emergence of hexagonal grid patterns in neural networks.
METASET selects diverse unit cells for efficient data-driven metamaterial design.
problem Imbalanced datasets in unit cells can bias data-driven metamaterial design.
method METASET uses similarity metrics and DPPs to select diverse subsets of unit cells.
result Smaller, diverse subsets improve search process and structural performance.
Analysis of somatic mutation profiles from cancer patients is essential in the development of cancer research. However, the low frequency of most mutations and the varying rates of mutations across patients makes the data extremely challenging to statistically analyze as well as difficult to use in classification probl…
LOT framework embeds high-dimensional cell data into interpretable Euclidean space.
problem Lack of interpretable methods for high-dimensional cell data.
method Adapts Linear Optimal Transport (LOT) to irregular point clouds.
result Accurate and interpretable classification and synthetic data generation.
Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific, isolated biomedical properties. In this work, we propose a new cross-modal small mole…
In this paper we present a novel model of the primary visual cortex (V1) based on orientation, frequency and phase selective behavior of the V1 simple cells. We start from the first level mechanisms of visual perception: receptive profiles. The model interprets V1 as a fiber bundle over the 2-dimensional retinal plane …
Study discovers patterns in insulin needs for T1D patients.
problem Finding the right insulin dose and time for T1D patients is challenging.
method Used OpenAPS Data Commons dataset and time series techniques like matrix profile and multi-variate clustering.
result Identified temporal patterns in insulin needs driven by factors like carbohydrates and possibly others.
A Large-Scale Comparative Analysis of Imputation Methods for Single-Cell RNA Sequencing Dataq-bio.GN
A comprehensive benchmark of 15 scRNA-seq imputation methods across various datasets and analyses.
problem Imputation of single-cell RNA sequencing data to recover latent transcriptional signals.
method Evaluation of 15 imputation methods across 30 datasets and 6 downstream analyses.
result Traditional methods generally outperform DL-based methods in scRNA-seq data analysis.
Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an opportunity to apply machine learning methods for this purpose. In addition to cytotoxi…
Minimalistic model captures head direction system properties.
problem Representing head direction system in a high-dimensional space.
method A minimalistic representation model of the rotation group U(1), including fully connected and convolutional versions.
result Emergence of Gaussian-like tuning profiles and 2D circle geometry in both model versions.
Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be captured from images, from which similarities between different drug compounds appli…
V1 cortex reconstructs images as Poisson equation solutions with varying weights.
problem Reconstructing images from V1 cortical cell receptive profiles.
method Solves a heterogeneous Poisson equation with varying weights representing neural connectivity.
result Reconstructions converge to homogeneous solutions using homogenization techniques.
This paper proposes a representational model for image pairs such as consecutive video frames that are related by local pixel displacements, in the hope that the model may shed light on motion perception in primary visual cortex (V1). The model couples the following two components: (1) the vector representations of loc…
Confirms isoperimetric conjectures on R^n and S^n for q ≤ min(5, n+1).
problem Minimizing total perimeter among bubbles enclosing prescribed volume.
method Tandem consideration of R^n and S^n, Möbius geometry, conformal Killing fields.
result Spherical interfaces and connected cells in minimizers, resolving Heppes conjecture.
We present the extention and application of a new unsupervised statistical learning technique--the Partition Decoupling Method--to gene expression data. Because it has the ability to reveal non-linear and non-convex geometries present in the data, the PDM is an improvement over typical gene expression analysis algorith…
Switched latent force models for reverse-engineering transcriptional regulation in gene expression dataphysics.bio-ph
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult …
In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure i…