The first paper I wrote in my PhD was about how we could use reinforcement learning to automatically find models that have trap space (attractor) behavior that matched experimental observations. A big bottle-neck in that process is figuring out what the actual attractor states of a model are. I resorted to just running simulations until the model reached a steady state, because its flexible and easy, but it's also prohibitively slow for models that are reasonably large. So, hopefully this paper will let us find the attractors of much larger Boolean models without having to run full simulations.<p>That said, the whole experience convinced me that modeling biology with Boolean logic is a bad idea. First, you have to force biological data, which is weird and long-tailed and multi-modal into two logical buckets, on or off, zero or one. Biology just doesn't work like that, lots of genes have graded, gradual differences in expression, not just zero/one. Then, you have to actually build a Boolean model, but you never have enough data to properly constrain the model. There are probably hundreds of wildly different model configurations that all give you equivalent behavior. Which one is right? Who knows. Finally you run the simulations and you get the attractors or trap spaces, and you show your results to a wet lab biologist and they don't believe the results because the model is way too simple. Genes aren't just on or off, and interactions between genes don't work like Boolean logic.<p>It's way better to just write down differential equations that describe the actual biophysical processes happening. With modern computers and solvers, ODE's are basically just as easy to simulate as a Boolean model, and they're much better representations of biology than Boolean logic.
Always depressing to see a paper like this. I can almost guarantee one could make this whole thing into a two-page document with a clearer vision and followable to, well, anyone else.<p>The purpose of academic papers is to file a claim to ownership of ideas / progress. But it would be cool if in another place they published the intuitions they used to come up with the claim in the first place.