The ability to design and optimize biological sequences with specific functionalities would unlock enormous value in technology and healthcare.
In this work, we implement an open-source Fitness Landscape EXploration Sandbox (FLEXS: github. com/samsinai/FLEXS) environment to test and evaluate these algorithms based on their optimality, consistency, and robustness.
This primer can serve as a starting point for researchers from different domains that are interested in the problem of searching a sequence space with a model, but are perhaps unaware of approaches that originate outside their field.
Here we present an embedding of natural protein sequences using a Variational Auto-Encoder and use it to predict how mutations affect protein function.