Cover Image

CellForge: Agentic Design of Virtual Cell Models

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Tang, Xiangru, Yu, Zhuoyun, Chen, Jiapeng, Cui, Yan, Shao, Daniel, Wang, Weixu, Wu, Fang, Zhuang, Yuchen, Shi, Wenqi, Huang, Zhi, Cohan, Arman, Lin, Xihong, Theis, Fabian, Krishnaswamy, Smita, Gerstein, Mark
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Artificial Intelligence Computation and Language Quantitative Methods
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Linearized Optimal Transport for Analysis of High-Dimensional Point-Cloud and Single-Cell Data
by: Wang, Tianxiang, et al.
Published: (2025)

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics
by: Rocha, Joao F., et al.
Published: (2025)

Enforcing Latent Euclidean Geometry in Single-Cell VAEs for Manifold Interpolation
by: Palma, Alessandro, et al.
Published: (2025)

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

Virtual Cells: From Conceptual Frameworks to Biomedical Applications
by: Bhardwaj, Saurabh, et al.
Published: (2025)

Improved prediction of ligand-protein binding affinities by meta-modeling
by: Lee, Ho-Joon, et al.
Published: (2023)

Virtual Cells: Predict, Explain, Discover
by: Noutahi, Emmanuel, et al.
Published: (2025)

CellFluxRL: Biologically-Constrained Virtual Cell Modeling via Reinforcement Learning
by: Wu, Dongxia, et al.
Published: (2026)

Investigating Data Contamination in Modern Benchmarks for Large Language Models
by: Deng, Chunyuan, et al.
Published: (2023)

Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow
by: Sakalyan, Kristiyan, et al.
Published: (2025)

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities
by: Bunne, Charlotte, et al.
Published: (2024)

Deciphering Cell Systems: Machine Learning Perspectives And Approaches For The Analysis Of Single-Cell Data
by: Yang, Yongjian
Published: (2024)

scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data
by: Smits, Thomas C., et al.
Published: (2025)

AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
by: De Brouwer, Edward, et al.
Published: (2026)

scPPDM: A Diffusion Model for Single-Cell Drug-Response Prediction
by: Liang, Zhaokang, et al.
Published: (2025)

Reinventing Clinical Dialogue: Agentic Paradigms for LLM Enabled Healthcare Communication
by: Zhi, Xiaoquan, et al.
Published: (2025)

Uncertainty quantification in flow cytometry using a cell sorter
by: Krishnaswamy-Usha, Amudhan, et al.
Published: (2024)

Flat Cell Imaging
by: Nasirimarekani, Vahid, et al.
Published: (2024)

Multiscale Cross-Modal Mapping of Molecular, Pathologic, and Radiologic Phenotypes in Lipid-Deficient Clear Cell Renal CellCarcinoma
by: Cui, Ying, et al.
Published: (2025)

Neurosymbolic Learning for Predicting Cell Fate Decisions from Longitudinal Single Cell Transcriptomics in Paediatric Acute Myeloid Leukemia
by: Uthamacumaran, Abicumaran, et al.
Published: (2025)

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models
by: Xu, Ran, et al.
Published: (2023)

SynCell: Contextualized Drug Synergy Prediction
by: Peng, Keqin, et al.
Published: (2025)

Dynamical Inference of Cell Size Regulation Parameters
by: Nieto, Cesar, et al.
Published: (2025)

Deep Clustering for Blood Cell Classification and Quantification
by: Macarie-Ancau, Mihaela, et al.
Published: (2025)

Cell lineage tracing: Methods, applications, and challenges
by: Shanjun Mao, et al.
Published: (2025)

CellProfiler plugins -- an easy image analysis platform integration for containers and Python tools
by: Weisbart, Erin, et al.
Published: (2023)

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

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics
by: Sun, Xingzhi, et al.
Published: (2024)

Leveraging Transformer Models to Capture Multi-Scale Dynamics in Biomolecules by nano-GPT
by: Zeng, Wenqi, et al.
Published: (2025)

AROMA: Augmented Reasoning Over a Multimodal Architecture for Virtual Cell Genetic Perturbation Modeling
by: Wang, Zhenyu, et al.
Published: (2026)

Robust Approximate Characterization of Single-Cell Heterogeneity in Microbial Growth
by: Paul, Richard D., et al.
Published: (2024)

Information-Theoretical Measures for Developmental Cell-Fate Proportioning Processes
by: Ramirez-Sierra, Michael A., et al.
Published: (2025)

Cell Painting Gallery: an open resource for image-based profiling
by: Weisbart, Erin, et al.
Published: (2024)

Infrared Microscopy of Biochemistry and Metabolism in Single Living Eukaryotic Cells
by: Quaroni, Luca
Published: (2025)

RNAGenScape: Property-Guided, Optimized Generation of mRNA Sequences with Manifold Langevin Dynamics
by: Liao, Danqi, et al.
Published: (2025)

A model of tuberculosis progression using CompuCell3D
by: Doran, James W. G., et al.
Published: (2026)

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

A Part-to-Whole Circular Cell Explorer
by: Zhao, Siyuan, et al.
Published: (2024)

Single-Cell Proteomics Using Mass Spectrometry
by: Momenzadeh, Amanda, et al.
Published: (2025)

Deep Learning for Blood-Brain Barrier Permeability Prediction: From Discriminative Models to Mechanism-Aware Design
by: Yang, Zihan, et al.
Published: (2025)