Deep Representation Learning FOR Morphological Profiling

Morphological Profiling

CellProfiler extracts ~ 100 - 1000 cell level features

We perform feature / dimensional reduction and calculate the mean for each perturbation

Example Use Case: Classifying Mechanism of ACTIONS

Deep learning can learn Meaningful Representations

Word2Vec

DCGANs

maybe for Profiles ?

+

=

Cells treated with A

Cells treated with B

Cells treated with A and B ?

or not?

Deep Profiles

Can we learn a robust representation from unlabeled data ? 

1000-dim CP feature vector
https://swarbrickjones.files.wordpress.com
cropped cell images
1000-dim CP feature vector
cropped cell images

latent space

LEarning A Meaningful Latent Space

subpopulation Profiles

unsupervised clustering in latent space

(semi) supervised training using hand-labeled data

NOISY LABELS: From Cell level to whole image level

Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning, Arxiv 2015, O Kraus, LJ Ba, B Frey 

Unguided SUBPOPULATION DETECTION USING ATTENTION?

Spatial Transformer Networks NIPS 2015 Max Jaderberg, Karen Simonyan, Andrew Zisserman, Koray Kavukcuoglu

Learning Representations for Cell Profiling

By David Dao

Learning Representations for Cell Profiling

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