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Applying deep learning in the life sciences
Deep-learning algorithms have proven to be powerful across many aspects of the life sciences and healthcare. Here are eight examples of how they’re being applied throughout the pipeline:

1. Deep-learning-powered lead optimization: Lead optimization is a key problem. Once you’ve gotten your lead, how do you explore a 10⁸⁰ space to find a better molecule based on your lead? According to a recent publication, a type of deep-learning engine called an “encoder” can encode structures with a discrete library into a continuous gradient space. That allows you to explore a much larger area of compound space than you have in your discrete library. You can then drop novel molecules out of the gradient space, design small compounds and test them to see how they perform, compared with all of the molecules in your existing library.
2. Predicting compound activity: One variant of deep learning is known as “one-shot deep learning,” in which you train the algorithm to identify differences, rather than similarities, in data. That requires a lot less training data, which is a critical advantage. A recent paper shows that one-shot deep-learning approaches excel in predicting compound bioactivity based on training with a small set of data. So, if you’re in a new space and don’t know much about the activity of the compounds you’re using, you can still apply these approaches to get a reading of a novel molecule.
3. Cell assay imaging analytics: Applying deep learning to cell assay imaging is an obvious path to pursue. All of the papers that have been published in this space so far have shown that deep-learning algorithms can do as well as or better than humans in detecting things like phenotypes. Better yet, they’re more efficient. You still need a human who has to be trained initially and can understand the outcomes. But overall, people are freed up to think about higher-level matters, rather than sitting there looking at images.
4. Toxicity prediction: Deep learning has been shown to be significantly more effective than existing methods in predicting the toxicity of any given molecule. Over time, it learns to look for the specific elements or substructures that are causing the toxicity.
5. Counterfeit scanning: Deep-learning systems can be trained to detect counterfeit drugs on the web and other sources by examining the package labeling or the pills themselves. They can pick up on little differences between real and counterfeit with a pretty high degree of accuracy. For example, logos or lettering printed on packaging can be slightly off because the presses aren’t exactly the same as the original.
6. Electronic health record (EHR) analysis: Deep-learning approaches have been shown to significantly outperform traditional methods in doing things like patient cohort identification, readmissions analysis, clinical trial recruitment and clinical predictive modeling from EHR data stores.
7. Language translation: Clinical trial protocol translation is a critical issue. If you provide a protocol in one language and then have someone translate it into another language, how do you know if they have translated all of the important phrases accurately? You can use deep learning to translate back into the original language and figure out how to normalize all those key criteria in your clinical trial.
8. Electronic laboratory notebook (ELN) analysis: Many life sciences companies know they have a huge amount of information in their ELNs, but no good way of getting it out. You can have deep-learning systems go in and pull out this information; they can literally read the text in an ELN and figure out what it means.

How deep learning is poised to transform the life sciences and healthcare