The above title currently provides the best single label for the topics covered by my research group. Here I provide a brief summary of our current research and some of the research directions we intend to pursue. Systems biosciences study biological systems in a holistic manner, focusing on the interactions among system components rather than the components themselves. Large amounts of data of increasing complexity are generated in these sciences (which include systems ecology and systems biology): The use of machine learning to make sense of these data is thus a necessity. We discuss two machine learning tasks that appear in this context, predicting structured outputs and automated modeling of dynamic systems. We describe some techniques for solving these tasks and some example application of these techniques in systems ecology and systems biology.