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.
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.
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.
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.
JojoSCL improves scRNA-seq clustering by reducing intra-cluster dispersion.
problem High dimensionality and sparsity of scRNA-seq data challenge clustering models.
method Integrates shrinkage estimator and contrastive learning for improved clustering.
result JojoSCL outperforms existing methods on ten scRNA-seq datasets.
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.
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.
New method improves clustering accuracy in noisy single-cell data.
problem Challenges in clustering single-cell RNA sequencing data due to noise and variability.
method Latent plug-and-play diffusion framework with input-space steering.
result Improved clustering accuracy on synthetic and real-world single-cell data.
Motivation: Single cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct coun…
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.
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.
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.
Multi-cell cooperative processing with limited backhaul traffic is studied for cellular uplinks. Aiming at reduced backhaul overhead, a sparsity-regularized multi-cell receive-filter design problem is formulated. Both unstructured distributed cooperation as well as clustered cooperation, in which base station groups ar…
The study compares different scRNA sequencing methods using a high-dimensional dataset.
problem To identify unique characteristics of different scRNA sequencing methods.
method Quantitative comparison through clustering analysis of a high-dimensional dataset.
result Identifies unique characteristics associated with different scRNA sequencing methods.
IMPACC improves consensus clustering for bioinformatics data.
problem Consensus clustering's inefficiency and lack of interpretability for large-scale data.
method Ensemble minipatch co-occurrences, adaptive sampling of observations and features.
result Significantly improved accuracy and interpretability with substantial computational savings.
Tree-SNE combines t-SNE and hierarchical clustering for data visualization.
problem Data visualization and clustering in complex datasets.
method Stacked one-dimensional t-SNE embeddings and alpha-clustering.
result Effective hierarchical clustering and visualization of various datasets.
We present a Bayesian hierarchical multi-view mixture model termed Symphony that simultaneously learns clusters of cells representing cell types and their underlying gene regulatory networks by integrating data from two views: single-cell gene expression data and paired epigenetic data, which is informative of gene-gen…
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our cluste…
New hypergraph method improves scRNA-seq clustering.
problem Loss of higher-order information and overestimation in coexpression networks.
method Conceptualizing scRNA-seq data as hypergraphs and proposing novel clustering methods.
result Proposed methods outperform existing methods on simulated and real datasets.
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.
We establish the Gaussian Multi-Bubble Conjecture: the least Gaussian-weighted perimeter way to decompose Rn into q cells of prescribed (positive) Gaussian measure when 2≤q≤n+1, is to use a "simplicial cluster", obtained from the Voronoi cells of q equidistant points. Moreover, we prove that…
Paper proposes a new method for sparse spectral clustering on Stiefel manifold.
problem Sparse spectral clustering on Stiefel manifold with nonsmooth and nonconvex objective.
method Proposes a manifold proximal linear method (ManPL) to solve the original SSC formulation.
result Demonstrates the advantage of ManPL over existing methods on single-cell RNA sequencing data.
Proposes a model for identifying 4G cells with network throughput problems.
problem Challenges in identifying 4G cells with network throughput issues due to network complexity and privacy concerns.
method Data-driven model using clustering and Deep Neural Networks (DNNs). Model parameters are learned from a small number of expert-labeled data. Multiple clustering models capture common features for problematic cells.
result The proposed model outperforms a simple classifier in identifying cells with network throughput problems.
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been…
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.
Extracting an understanding of the underlying system from high dimensional data is a growing problem in science. Discovering informative and meaningful features is crucial for clustering, classification, and low dimensional data embedding. Here we propose to construct features based on their ability to discriminate bet…
Dynamic cell-free networks reduce complexity in serving many devices with distributed APs and DRL.
problem Designing efficient cell-free networks with many devices and APs.
method Dynamic architecture, SIC, DAS, DRL for optimization.
result DRL significantly improves performance in dynamic cell-free networks.
BanditPAM clusters data faster than traditional methods.
problem Efficiently clustering large datasets with arbitrary distance metrics.
method Inspired by multi-armed bandits, reduces PAM complexity from O(n2) to O(nlogn). result Matches state-of-the-art clustering loss with up to 4x faster results and 200x fewer distance computations.
New methods detect continuous variation in single-cell data.
problem Continuous variation within and between cell types not detected by discrete analyses.
method Three topologically motivated mathematical methods for unsupervised feature selection.
result Detect additional biologically meaningful genes with coherent expression patterns.
Cluster LOCO: A model-agnostic feature importance score for interpreting cluster outputs
problem Interpreting and auditing cluster outputs
method Cluster LOCO (Leave-One-Covariate-Out)
result More reliably recovers informative features than existing methods
Proposes selective inference for testing differences in means between clusters.
problem Inflated type I error rate when testing differences in means between clusters.
method Selective inference approach to control selective type I error rate.
result Controls selective type I error rate by accounting for data-driven cluster definition.
New method uses dendrograms for better mixture model selection and clustering.
problem Selecting the correct number of components in finite mixture models.
method Hierarchical clustering tree derived from overfitted latent mixing measures.
result Consistently selects the true number of mixing components and optimal convergence rate for parameter estimation.
Generates infinite-depth hierarchical clusters from few examples.
problem Inadequate finite-sample clustering methods for fine-scale hierarchical structures.
method Classification fields generated by a local refinement rule, approximated by predictors.
result Learned predictors can approximate infinite-depth hierarchical structures.
New methods for visualizing multi-view data improve clustering accuracy.
problem Visualizing multi-view data for better understanding of samples.
method Extensions of manifold learning methods (t-SNE, LLE, ISOMAP) for multi-view data.
result Improved clustering accuracy of multi-view data.
Study of generalized double Bruhat cells and their integrations.
problem Understanding and integrating generalized double Bruhat cells in Lie groups.
method Integrating Poisson groupoids to symplectic double groupoids, relating to fission spaces of irregular singularities.
result Explicit integrations of Poisson groupoids and Morita equivalence of double groupoids.
Flow cytometry is a high-throughput technology used to quantify multiple surface and intracellular markers at the level of a single cell. This enables to identify cell sub-types, and to determine their relative proportions. Improvements of this technology allow to describe millions of individual cells from a blood samp…
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.
There are various algorithms and methodologies used for automated screening of cervical cancer by segmenting and classifying cervical cancer cells into different categories. This study presents a critical review of different research papers published that integrated AI methods in screening cervical cancer via different…
Clustering high-dimensional data, such as images or biological measurements, is a long-standingproblem and has been studied extensively. Recently, Deep Clustering has gained popularity due toits flexibility in fitting the specific peculiarities of complex data. Here we introduce the Mixture-of-Experts Similarity Variat…
We consider the use of the Joint Clustering and Matching (JCM) procedure for the supervised classification of a flow cytometric sample with respect to a number of predefined classes of such samples. The JCM procedure has been proposed as a method for the unsupervised classification of cells within a sample into a numbe…
Selective inference controls Type I error in k-means clustering tests.
problem Inflated Type I error in classical hypothesis tests for k-means clusters.
method Selective inference approach to control Type I error.
result Proposes a computable finite-sample p-value for selective inference.
A novel multi-resolution cluster detection (MCD) method is proposed to identify irregularly shaped clusters in space. Multi-scale test statistic on a single cell is derived based on likelihood ratio statistic for Bernoulli sequence, Poisson sequence and Normal sequence. A neighborhood variability measure is defined to …
We establish the Gaussian Double-Bubble Conjecture: the least Gaussian-weighted perimeter way to decompose Rn into three cells of prescribed (positive) Gaussian measure is to use a tripod-cluster, whose interfaces consist of three half-hyperplanes meeting along an (n−2)-dimensional plane at 120∘ …
This paper deals with unsupervised clustering with feature selection. The problem is to estimate both labels and a sparse projection matrix of weights. To address this combinatorial non-convex problem maintaining a strict control on the sparsity of the matrix of weights, we propose an alternating minimization of the Fr…
sgdGMF efficiently estimates generalized matrix factorization models for single-cell RNA sequencing data.
problem Challenges in dimensionality reduction for large single-cell RNA sequencing datasets.
method Scalable adaptive stochastic gradient descent algorithm for generalized matrix factorization models.
result sgdGMF outperforms existing methods in scalability and accuracy for large datasets.
We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data w…
Unsupervised clustering of curves according to their shapes is an important problem with broad scientific applications. The existing model-based clustering techniques either rely on simple probability models (e.g., Gaussian) that are not generally valid for shape analysis or assume the number of clusters. We develop an…
VampPrior Mixture Model improves clustering in DLVMs.
problem Simplicity of standard priors in DLVMs leads to poor clustering performance.
method Leverages VampPrior concepts to fit a Bayesian GMM prior in a VAE.
result VMM achieves highly competitive clustering performance on benchmark datasets.