Phenotypic Profiling of High Throughput Imaging Screens with Generic Deep Convolutional Features
| Autor: | Yinhai Wang, Martin R. Brown, Hongming Chen, Thierry Dorval, Boguslaw Obara, Philip T. Jackson, Sinead Knight, Claus Bendtsen |
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| Rok vydání: | 2019 |
| Předmět: |
Profiling (computer programming)
FOS: Computer and information sciences business.industry Drug discovery Computer science Deep learning Computer Vision and Pattern Recognition (cs.CV) Computer Science - Computer Vision and Pattern Recognition Pattern recognition 02 engineering and technology Set (abstract data type) 03 medical and health sciences 0302 clinical medicine 030221 ophthalmology & optometry 0202 electrical engineering electronic engineering information engineering Embedding 020201 artificial intelligence & image processing Artificial intelligence Cluster analysis business Throughput (business) Curse of dimensionality |
| Zdroj: | MVA |
| DOI: | 10.48550/arxiv.1903.06516 |
| Popis: | While deep learning has seen many recent applications to drug discovery, most have focused on predicting activity or toxicity directly from chemical structure. Phenotypic changes exhibited in cellular images are also indications of the mechanism of action (MoA) of chemical compounds. In this paper, we show how pre-trained convolutional image features can be used to assist scientists in discovering interesting chemical clusters for further investigation. Our method reduces the dimensionality of raw fluorescent stained images from a high throughput imaging (HTI) screen, producing an embedding space that groups together images with similar cellular phenotypes. Running standard unsupervised clustering on this embedding space yields a set of distinct phenotypic clusters. This allows scientists to further select and focus on interesting clusters for downstream analyses. We validate the consistency of our embedding space qualitatively with t-sne visualizations, and quantitatively by measuring embedding variance among images that are known to be similar. Results suggested the usefulness of our proposed workflow using deep learning and clustering and it can lead to robust HTI screening and compound triage. |
| Databáze: | OpenAIRE |
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