Cover Image

Engineering morphogenesis of cell clusters with differentiable programming

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Deshpande, Ramya, Mottes, Francesco, Vlad, Ariana-Dalia, Brenner, Michael P., Co, Alma dal
Format:	Preprint
Published:	2024
Subjects:	Cell Behavior Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Towards generalizable single-cell perturbation modeling via the Conditional Monge Gap
by: Driessen, Alice, et al.
Published: (2025)

Spatial dynamic modelling to understand how dendritic cell clustering affects T cell activation
by: Germano, Domenic P. J., et al.
Published: (2026)

Modeling the extracellular matrix in cell migration and morphogenesis: A guide for the curious biologist
by: Crossley, Rebecca M., et al.
Published: (2023)

Sparse autoencoders reveal organized biological knowledge but minimal regulatory logic in single-cell foundation models: a comparative atlas of Geneformer and scGPT
by: Kendiukhov, Ihor
Published: (2026)

Transfer Learning for T-Cell Response Prediction
by: Stadelmaier, Josua, et al.
Published: (2024)

Why Attention Graphs Are All We Need: Pioneering Hierarchical Classification of Hematologic Cell Populations with LeukoGraph
by: Mojarrad, Fatemeh Nassajian, et al.
Published: (2024)

Embedding-based Multimodal Learning on Pan-Squamous Cell Carcinomas for Improved Survival Outcomes
by: Waqas, Asim, et al.
Published: (2024)

Deep-Ace: LSTM-based Prokaryotic Lysine Acetylation Site Predictor
by: Ilyas, Maham, et al.
Published: (2024)

Learning Model Parameter Dynamics in a Combination Therapy for Bladder Cancer from Sparse Biological Data
by: Olumoyin, Kayode, et al.
Published: (2025)

scMamba: A Scalable Foundation Model for Single-Cell Multi-Omics Integration Beyond Highly Variable Feature Selection
by: Yuan, Zhen, et al.
Published: (2025)

Modeling non-genetic information dynamics in cells using reservoir computing
by: Niraula, Dipesh, et al.
Published: (2023)

Cell differentiation can underpin the reproducibility of morphogenesis
by: Devlin, Dominic K, et al.
Published: (2025)

Season combinatorial intervention predictions with Salt & Peper
by: Gaudelet, Thomas, et al.
Published: (2024)

Long-range gene expression prediction with token alignment of large language model
by: Honig, Edouardo, et al.
Published: (2024)

Causal Circuit Tracing Reveals Distinct Computational Architectures in Single-Cell Foundation Models: Inhibitory Dominance, Biological Coherence, and Cross-Model Convergence
by: Kendiukhov, Ihor
Published: (2026)

HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data
by: Madhu, Hiren, et al.
Published: (2025)

STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations
by: Fu, Boyang, et al.
Published: (2026)

Discovery of a Hematopoietic Manifold in scGPT Yields a Method for Extracting Performant Algorithms from Biological Foundation Model Internals
by: Kendiukhov, Ihor
Published: (2026)

scI2CL: Effectively Integrating Single-cell Multi-omics by Intra- and Inter-omics Contrastive Learning
by: Liu, Wuchao, et al.
Published: (2025)

Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells
by: Kinnunen, Patrick C., et al.
Published: (2023)

3D mechano-geometric multicellular model of apical stem cell-driven plant morphogenesis
by: Kamamoto, Naoya, et al.
Published: (2026)

Mapping, modeling, and reprogramming cell-fate decision making systems
by: Ham, Lucy, et al.
Published: (2024)

A mathematical model for smooth muscle cell phenotype switching in atherosclerotic plaque
by: Ndenda, Joseph P., et al.
Published: (2024)

HemaGraph: Breaking Barriers in Hematologic Single Cell Classification with Graph Attention
by: Bini, Lorenzo, et al.
Published: (2024)

Persistent pseudopod splitting is an effective chemotaxis strategy in shallow gradients
by: Alonso, Albert, et al.
Published: (2024)

Scientific Hypothesis Generation by a Large Language Model: Laboratory Validation in Breast Cancer Treatment
by: Abdel-Rehim, Abbi, et al.
Published: (2024)

Modeling Adoptive Cell Therapy in Bladder Cancer from Sparse Biological Data using PINNs
by: Olumoyin, Kayode, et al.
Published: (2025)

Run-and-tumble chemotaxis using reinforcement learning
by: Pramanik, Ramesh, et al.
Published: (2025)

VCWorld: A Biological World Model for Virtual Cell Simulation
by: Wei, Zhijian, et al.
Published: (2025)

SSRCA: a novel machine learning pipeline to perform sensitivity analysis for agent-based models
by: Rohr, Edward H., et al.
Published: (2025)

RxRx3-core: Benchmarking drug-target interactions in High-Content Microscopy
by: Kraus, Oren, et al.
Published: (2025)

Non-invasive maturity assessment of iPSC-CMs based on optical maturity characteristics using interpretable AI
by: Scheurer, Fabian, et al.
Published: (2025)

Unraveling cell-cell communication with NicheNet by inferring active ligands from transcriptomics data
by: Sang-aram, Chananchida, et al.
Published: (2024)

Quantifying the effect of phenotype on clustering behaviour in melanoma: from monoculture to co-culture
by: Schofield, Nathan, et al.
Published: (2026)

Information bounds on the accuracy of cell polarization
by: Yi, Tau-Mu
Published: (2025)

Topological constraints on self-organisation in locally interacting systems
by: Sacco, Francesco, et al.
Published: (2025)

The morphology of cell spheroids in simple shear flow
by: Ferraro, Rosalia, et al.
Published: (2024)

Ignition criteria for trigger waves in cell signaling
by: Schlomann, Brandon H., et al.
Published: (2025)

SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction
by: Phillips, Lawrence, et al.
Published: (2025)

Benchmarking virtual cell models for in-the-wild perturbation response
by: Mao, Xinjie, et al.
Published: (2026)