Mixed Models with Multiple Instance Learning
- URL: http://arxiv.org/abs/2311.02455v2
- Date: Fri, 8 Mar 2024 11:04:49 GMT
- Title: Mixed Models with Multiple Instance Learning
- Authors: Jan P. Engelmann, Alessandro Palma, Jakub M. Tomczak, Fabian J. Theis,
Francesco Paolo Casale
- Abstract summary: We introduce MixMIL, a framework integrating Generalized Linear Mixed Models (GLMM) and Multiple Instance Learning (MIL)
Our empirical results reveal that MixMIL outperforms existing MIL models in single-cell datasets.
- Score: 51.440557223100164
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Predicting patient features from single-cell data can help identify cellular
states implicated in health and disease. Linear models and average cell type
expressions are typically favored for this task for their efficiency and
robustness, but they overlook the rich cell heterogeneity inherent in
single-cell data. To address this gap, we introduce MixMIL, a framework
integrating Generalized Linear Mixed Models (GLMM) and Multiple Instance
Learning (MIL), upholding the advantages of linear models while modeling cell
state heterogeneity. By leveraging predefined cell embeddings, MixMIL enhances
computational efficiency and aligns with recent advancements in single-cell
representation learning. Our empirical results reveal that MixMIL outperforms
existing MIL models in single-cell datasets, uncovering new associations and
elucidating biological mechanisms across different domains.
Related papers
- scReader: Prompting Large Language Models to Interpret scRNA-seq Data [12.767105992391555]
We propose an innovative hybrid approach that integrates the general knowledge capabilities of large language models with domain-specific representation models for single-cell omics data interpretation.
By inputting single-cell gene-level expression data with prompts, we effectively model cellular representations based on the differential expression levels of genes across various species and cell types.
arXiv Detail & Related papers (2024-12-24T04:28:42Z) - Generating Multi-Modal and Multi-Attribute Single-Cell Counts with CFGen [76.02070962797794]
We present Cell Flow for Generation, a flow-based conditional generative model for multi-modal single-cell counts.
Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks.
arXiv Detail & Related papers (2024-07-16T14:05:03Z) - MMIL: A novel algorithm for disease associated cell type discovery [58.044870442206914]
Single-cell datasets often lack individual cell labels, making it challenging to identify cells associated with disease.
We introduce Mixture Modeling for Multiple Learning Instance (MMIL), an expectation method that enables the training and calibration of cell-level classifiers.
arXiv Detail & Related papers (2024-06-12T15:22:56Z) - Scalable Amortized GPLVMs for Single Cell Transcriptomics Data [9.010523724015398]
Dimensionality reduction is crucial for analyzing large-scale single-cell RNA-seq data.
We introduce an improved model, the amortized variational model (BGPLVM)
BGPLVM is tailored for single-cell RNA-seq with specialized encoder, kernel, and likelihood designs.
arXiv Detail & Related papers (2024-05-06T21:54:38Z) - UniCell: Universal Cell Nucleus Classification via Prompt Learning [76.11864242047074]
We propose a universal cell nucleus classification framework (UniCell)
It employs a novel prompt learning mechanism to uniformly predict the corresponding categories of pathological images from different dataset domains.
In particular, our framework adopts an end-to-end architecture for nuclei detection and classification, and utilizes flexible prediction heads for adapting various datasets.
arXiv Detail & Related papers (2024-02-20T11:50:27Z) - Single-Cell Deep Clustering Method Assisted by Exogenous Gene
Information: A Novel Approach to Identifying Cell Types [50.55583697209676]
We develop an attention-enhanced graph autoencoder, which is designed to efficiently capture the topological features between cells.
During the clustering process, we integrated both sets of information and reconstructed the features of both cells and genes to generate a discriminative representation.
This research offers enhanced insights into the characteristics and distribution of cells, thereby laying the groundwork for early diagnosis and treatment of diseases.
arXiv Detail & Related papers (2023-11-28T09:14:55Z) - Single-cell Multi-view Clustering via Community Detection with Unknown
Number of Clusters [64.31109141089598]
We introduce scUNC, an innovative multi-view clustering approach tailored for single-cell data.
scUNC seamlessly integrates information from different views without the need for a predefined number of clusters.
We conducted a comprehensive evaluation of scUNC using three distinct single-cell datasets.
arXiv Detail & Related papers (2023-11-28T08:34:58Z) - Learning Causal Representations of Single Cells via Sparse Mechanism
Shift Modeling [3.2435888122704037]
We propose a deep generative model of single-cell gene expression data for which each perturbation is treated as an intervention targeting an unknown, but sparse, subset of latent variables.
We benchmark these methods on simulated single-cell data to evaluate their performance at latent units recovery, causal target identification and out-of-domain generalization.
arXiv Detail & Related papers (2022-11-07T15:47:40Z) - Learning Anisotropic Interaction Rules from Individual Trajectories in a
Heterogeneous Cellular Population [0.0]
We develop WSINDy for second order IPSs to model the movement of communities of cells.
Our approach learns the interaction rules that govern the dynamics of a heterogeneous population of migrating cells.
We demonstrate the efficiency and proficiency of the method on several test scenarios, motivated by common cell migration experiments.
arXiv Detail & Related papers (2022-04-29T15:00:21Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.