[HTML][HTML] How to build the virtual cell with artificial intelligence: Priorities and opportunities
Cells are essential to understanding health and disease, yet traditional models fall short of
modeling and simulating their function and behavior. Advances in AI and omics offer …
modeling and simulating their function and behavior. Advances in AI and omics offer …
Masked Image Modeling: A Survey
In this work, we survey recent studies on masked image modeling (MIM), an approach that
emerged as a powerful self-supervised learning technique in computer vision. The MIM task …
emerged as a powerful self-supervised learning technique in computer vision. The MIM task …
ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy
K Kenyon-Dean, ZJ Wang, J Urbanik… - arxiv preprint arxiv …, 2024 - arxiv.org
Large-scale cell microscopy screens are used in drug discovery and molecular biology
research to study the effects of millions of chemical and genetic perturbations on cells. To …
research to study the effects of millions of chemical and genetic perturbations on cells. To …
[HTML][HTML] Insights into the Identification of iPSC-and Monocyte-Derived Macrophage-Polarizing Compounds by AI-Fueled Cell Painting Analysis Tools
JB Brüggenthies, J Dittmer, E Martin, I Zingman… - International Journal of …, 2024 - mdpi.com
Macrophage polarization critically contributes to a multitude of human pathologies. Hence,
modulating macrophage polarization is a promising approach with enormous therapeutic …
modulating macrophage polarization is a promising approach with enormous therapeutic …
Towards scientific discovery with dictionary learning: Extracting biological concepts from microscopy foundation models
Dictionary learning (DL) has emerged as a powerful interpretability tool for large language
models. By extracting known concepts (eg, Golden-Gate Bridge) from human-interpretable …
models. By extracting known concepts (eg, Golden-Gate Bridge) from human-interpretable …
SubCell: Vision foundation models for microscopy capture single-cell biology
Cells are the functional units of life, and the wide range of biological functions they perform
are orchestrated by myriad molecular interactions within an intricate subcellular architecture …
are orchestrated by myriad molecular interactions within an intricate subcellular architecture …
How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval
Predicting molecular impact on cellular function is a core challenge in therapeutic design.
Phenomic experiments, designed to capture cellular morphology, utilize microscopy based …
Phenomic experiments, designed to capture cellular morphology, utilize microscopy based …
Benchmarking Transcriptomics Foundation Models for Perturbation Analysis: one PCA still rules them all
I Bendidi, S Whitfield, K Kenyon-Dean… - arxiv preprint arxiv …, 2024 - arxiv.org
Understanding the relationships among genes, compounds, and their interactions in living
organisms remains limited due to technological constraints and the complexity of biological …
organisms remains limited due to technological constraints and the complexity of biological …
Exploring self-supervised learning biases for microscopy image representation
Self-supervised representation learning (SSRL) in computer vision relies heavily on simple
image transformations such as random rotation, crops, or illumination to learn meaningful …
image transformations such as random rotation, crops, or illumination to learn meaningful …
Spherical Phenotype Clustering
L Nightingale, J Tuersley, A Cairoli, J Howes, C Shand… - bioRxiv, 2024 - biorxiv.org
Phenotypic screening experiments comprise many images of the same cells perturbed in
different ways, with biologically significant variation often subtle or difficult to see by eye. The …
different ways, with biologically significant variation often subtle or difficult to see by eye. The …