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Now that does not mean that one could not think about automated ways of finding vaccine candidates, but instead of modelling (implicitly or explicitly) viruses and vaccines, you would need to model virus-derived particles and human immune responses (plus the effect of adjuvants, etc.).

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Good information, so we would have a Neural Net that takes a vaccine input and predicts the human (or animal) immune response, and another neural net that generates the vaccine inputs. I suppose the problem would be lack of labeled training data, which is why I was thinking about the chess example which works by simply knowing the rules of the game.

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