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.
Energy-efficient detection of natural errors in deep networks.
problem Deep networks lack error detection capability without additional energy costs.
method Append RACs at hidden layers to detect natural errors with early classification termination.
result Early classification termination reduces energy consumption.
New estimator for joint entropy outperforms existing methods in various distributions.
problem Estimating joint entropy in high-dimensional spaces.
method Partitioned sample spacing (PSS) for nonparametric estimation.
result PSS consistently outperforms k-NN and normalizing flow methods.
Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing differential gene regulation. Recent studies either failed to capture combinatorial effects…
JEPA fails to improve language model performance when fine-tuning.
problem Improving language model performance through latent representation learning.
method Testing various training-time auxiliaries on natural-language-to-regex generation.
result No auxiliary improves cross-entropy gradient cosine with decoder visibility.
LSTM improves cross-network recommendations by capturing user preference changes and irregular time intervals.
problem Offline cross-network recommender solutions fail to capture user preference changes and dynamic environments.
method Proposes a multi-layered LSTM network with attention mechanisms, higher order interactions, and time-aware gates.
result The model consistently outperforms state-of-the-art in accuracy, diversity, and novelty.
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.
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…
AuxiLearn combines auxiliary tasks into a single loss function.
problem Improving neural network performance on a main task using auxiliary tasks.
method Implicit differentiation to learn a network that combines auxiliary tasks into a single coherent objective function.
result AuxiLearn consistently outperforms competing methods in various tasks and domains.
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.
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.
New method uses correlated auxiliary feedback to reduce regret in parameterized bandits.
problem Reducing regret in parameterized bandits with correlated auxiliary feedback.
method Develops a reward estimator using auxiliary feedback with tight confidence bounds.
result Shows significant reduction in regret compared to standard methods.
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.
In-N-Out improves model robustness to out-of-distribution data.
problem Learning robust models with few in-distribution labeled examples.
method Pre-training with auxiliary information and self-training with pseudolabels.
result In-N-Out outperforms auxiliary inputs or outputs alone on both in-distribution and OOD error.
Aux-NAS uses auxiliary labels to improve primary task performance without extra inference cost.
problem Improving primary task performance using auxiliary labels without increasing inference cost.
method Architecture-based approach with a flexible asymmetric structure for primary and auxiliary tasks, using Neural Architecture Search (NAS) to evolve networks with only primary-to-auxiliary connections.
result Achieves improved performance on multiple tasks without increasing inference cost.
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 …
Learning with auxiliary tasks can improve the ability of a primary task to generalise. However, this comes at the cost of manually labelling auxiliary data. We propose a new method which automatically learns appropriate labels for an auxiliary task, such that any supervised learning task can be improved without requiri…
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…
Researchers identify valid auxiliary functions for extreme value distributions and their max-domains of attraction.
problem Characterize valid auxiliary functions for extreme value distributions and their max-domains of attraction.
method Introduced 'universal' auxiliary functions valid for both VR and vMR representations, identified sets of valid auxiliary functions, and proposed a method for finding appropriate auxiliary functions.
result Characterized valid auxiliary functions for both VR and vMR representations for the entire MDA distribution families.
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.
Auxiliary Tuning adapts pre-trained models for novel tasks efficiently.
problem Adapting pre-trained models for new tasks efficiently.
method Supplementing pre-trained model with an auxiliary model that shifts output distribution.
result Achieved similar results to training from scratch with fewer resources.
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.
The paper improves high-dimensional linear regression prediction and estimation using auxiliary samples.
problem Estimating and predicting high-dimensional linear regression models with auxiliary samples.
method Proposes Trans-Lasso for data-driven transfer learning, establishing optimality for prediction and estimation.
result Knowledge from auxiliary samples can improve learning performance in target problems.
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.
New method classifies reticulocytes from red blood cells without labels.
problem Classifying reticulocytes from mature red blood cells without fluorescent labels.
method Unsupervised machine learning on morpho-rheological markers.
result Promising results in classifying reticulocytes from mature red blood cells.
For a finite family of 3-dimensional almost contact metric manifolds with closed the structure form η 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…
Method reweights auxiliary tasks to reduce data need for main task.
problem Limited labeled data for supervised learning.
method Formulates weighted likelihood function as surrogate prior, minimizing divergence to true prior.
result Effective use of limited labeled data with auxiliary tasks, improving performance.
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.
This paper reviews dMTL and methods for selecting auxiliary tasks.
problem Improving model performance for multiple tasks.
method Review of dMTL approaches and methods for selecting auxiliary tasks.
result Methods for selecting auxiliary tasks can improve dMTL performance.
Statistical inference is considered for variables of interest, called primary variables, when auxiliary variables are observed along with the primary variables. We consider the setting of incomplete data analysis, where some primary variables are not observed. Utilizing a parametric model of joint distribution of prima…
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…
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.
MFAI uses gradient boosted trees to leverage auxiliary info for scalable Bayesian matrix factorization.
problem Matrix factorization struggles with poor data quality, especially high sparsity and low SNR.
method Integrates gradient boosted trees into probabilistic matrix factorization framework.
result MFAI effectively leverages auxiliary information, improving model performance.
We construct a small regular cellular decomposition of the Fulton MacPherson operad FM2 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…
Multi-task learning (MTL) has achieved success over a wide range of problems, where the goal is to improve the performance of a primary task using a set of relevant auxiliary tasks. However, when the usefulness of the auxiliary tasks w.r.t. the primary task is not known a priori, the success of MTL models depends on th…
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 d-periodic graphs. 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…