Imagen de Portada

Parameter-free representations outperform single-cell foundation models on downstream benchmarks

Fuente: arXiv

Guardado en:

Detalles Bibliográficos
Autores principales:	Souza, Huan, Mehta, Pankaj
Formato:	Preprint
Publicado:	2026
Materias:	Genomics Machine Learning Quantitative Methods
Acceso en línea:	Acceder al recurso
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

Ejemplares similares

SAGE-FM: A lightweight and interpretable spatial transcriptomics foundation model
por: Zhan, Xianghao, et al.
Publicado: (2026)

scDiffusion: conditional generation of high-quality single-cell data using diffusion model
por: Luo, Erpai, et al.
Publicado: (2024)

Hierarchical novel class discovery for single-cell transcriptomic profiles
por: Senoussi, Malek, et al.
Publicado: (2024)

scMRDR: A scalable and flexible framework for unpaired single-cell multi-omics data integration
por: Sun, Jianle, et al.
Publicado: (2025)

A Bayesian approach to model uncertainty in single-cell genomic data
por: Ren, Shanshan, et al.
Publicado: (2025)

Evaluating DNA function understanding in genomic language models using evolutionarily implausible sequences
por: Jiang, Shiyu, et al.
Publicado: (2025)

What Topological and Geometric Structure Do Biological Foundation Models Learn? Evidence from 141 Hypotheses
por: Kendiukhov, Ihor
Publicado: (2026)

CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models
por: Ambrozak, Simon, et al.
Publicado: (2026)

Integrate Any Omics: Towards genome-wide data integration for patient stratification
por: Ma, Shihao, et al.
Publicado: (2024)

A novel application of Shapley values for large multidimensional time-series data: Applying explainable AI to a DNA profile classification neural network
por: Elborough, Lauren, et al.
Publicado: (2024)

Data Valuation with Gradient Similarity
por: Evans, Nathaniel J., et al.
Publicado: (2024)

Learning Genomic Structure from $k$-mers
por: Thor, Filip, et al.
Publicado: (2025)

Multi-Modal and Multi-Attribute Generation of Single Cells with CFGen
por: Palma, Alessandro, et al.
Publicado: (2024)

BarcodeMamba: State Space Models for Biodiversity Analysis
por: Gao, Tiancheng, et al.
Publicado: (2024)

Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+
por: Weinberger, Ethan, et al.
Publicado: (2024)

Quantum Ensembling Methods for Healthcare and Life Science
por: Rhrissorrakrai, Kahn, et al.
Publicado: (2025)

GCBLANE: A graph-enhanced convolutional BiLSTM attention network for improved transcription factor binding site prediction
por: Ferrao, Jonas Chris, et al.
Publicado: (2025)

Deciphering regulatory architectures from synthetic single-cell expression patterns
por: Pan, Rosalind Wenshan, et al.
Publicado: (2024)

BMFM-RNA: whole-cell expression decoding improves transcriptomic foundation models
por: Danziger, Michael M., et al.
Publicado: (2025)

Beyond Continuity: Simulation-free Reconstruction of Discrete Branching Dynamics from Single-cell Snapshots
por: Ying, Junda, et al.
Publicado: (2026)

MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning
por: Cho, Seungik
Publicado: (2026)

Optimizing Prognostic Biomarker Discovery in Pancreatic Cancer Through Hybrid Ensemble Feature Selection and Multi-Omics Data
por: Zobolas, John, et al.
Publicado: (2025)

Hypergraph Representations of scRNA-seq Data for Improved Clustering with Random Walks
por: He, Wan, et al.
Publicado: (2025)

Mixed Models with Multiple Instance Learning
por: Engelmann, Jan P., et al.
Publicado: (2023)

Is your data alignable? Principled and interpretable alignability testing and integration of single-cell data
por: Ma, Rong, et al.
Publicado: (2023)

CEP-IP: An Explainable Framework for Cell Subpopulation Identification in Single-cell Transcriptomics
por: Wong, Kah Keng
Publicado: (2025)

High-dimensional Many-to-many-to-many Mediation Analysis
por: Nguyen, Tien Dat, et al.
Publicado: (2026)

Revolutionizing Genomics with Reinforcement Learning Techniques
por: Karami, Mohsen, et al.
Publicado: (2023)

Fusing Sequence Motifs and Pan-Genomic Features: Antimicrobial Resistance Prediction using an Explainable Lightweight 1D CNN-XGBoost Ensemble
por: Siddiqui, Md. Saiful Bari, et al.
Publicado: (2025)

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype
por: Chi, Changxi, et al.
Publicado: (2025)

CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement
por: Baek, Seungheun, et al.
Publicado: (2024)

OmicsCL: Unsupervised Contrastive Learning for Cancer Subtype Discovery and Survival Stratification
por: Karagoz, Atahan
Publicado: (2025)

Fine-tuning the ESM2 protein language model to understand the functional impact of missense variants
por: Saadat, Ali, et al.
Publicado: (2024)

Lingshu-Cell: A generative cellular world model for transcriptome modeling toward virtual cells
por: Zhang, Han, et al.
Publicado: (2026)

Penalized Principal Component Analysis Using Smoothing
por: Hurwitz, Rebecca M., et al.
Publicado: (2023)

Geometric coherence of single-cell CRISPR perturbations reveals regulatory architecture and predicts cellular stress
por: Raju, Prashant C.
Publicado: (2026)

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction
por: Shi, Peiting, et al.
Publicado: (2026)

pHapCompass: Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase
por: Hosseini, Marjan, et al.
Publicado: (2025)

MotifbreakR v2: extended capability and database integration
por: Coetzee, Simon G., et al.
Publicado: (2024)

DNA Language Model and Interpretable Graph Neural Network Identify Genes and Pathways Involved in Rare Diseases
por: Saadat, Ali, et al.
Publicado: (2024)