The philosophical debate around the impact of machine learning in science is often framed in terms of a choice between AI and classical methods as mutually exclusive alternatives involving difficult epistemological trade-offs. A common worry regarding machine learning methods specifically is that they lead to opaque models that make predictions but do not lead to explanation or understanding. Focusing on the field of molecular biology, I argue that in practice machine learning is often used with explanatory aims. More specifically, I (...) argue that machine learning can be tightly integrated with other, more traditional, research methods and in a clear sense can contribute to insight into the causal processes underlying phenomena of interest to biologists. One could even say that machine learning is not the end of theory in important areas of biology, as has been argued, but rather a new beginning. I support these claims with a detailed discussion of a case study involving gene regulation by microRNAs. (shrink)

It has been argued that our currently most satisfactory social epistemology of science can’t account for science that is based on artificial intelligence (AI) because this social epistemology requires trust between scientists that can take full responsibility for the research tools they use, and scientists can’t take full responsibility for the AI tools they use since these systems are epistemically opaque. I think this argument overlooks that much AI-based science can be done without opaque models, and that agents can take (...) full responsibility for the systems they use even if these systems are opaque. Requiring that an agent fully understand how a system works is an untenably strong condition for that agent to take full responsibility for the system and risks absolving AI developers from responsibility for their products. AI-based science need not create trust-related social epistemological problems if we keep in mind that what makes both individual scientists and their use of AI systems trustworthy isn’t full transparency of the internal processing but their adherence to social and institutional norms that ensure that scientific claims can be trusted. (shrink)

I argue that ML models used in science function as highly idealized toy models. If we treat ML models as a type of highly idealized toy model, then we can deploy standard representational and epistemic strategies from the toy model literature to explain why ML models can still provide epistemic success despite their lack of similarity to their targets.