Permission systems are the main defense that mobile platforms, such as Android and iOS, offer to users to protect their private data from prying apps. However, due to the tension between usability and control, such systems have several limitations that often force users to overshare sensitive data. We address some of these limitations with SmarPer, an advanced permission mechanism for Android. To address the rigidity of current permission systems and their poor matching of users' privacy preferences, SmarPer relies on contextual information and machine learning methods to predict permission decisions at runtime. Note that the goal of SmarPer is to mimic the users' decisions, not to make privacy-preserving decisions per se. Using our SmarPer implementation, we collected 8,521 runtime permission decisions from 41 participants in real conditions. With this unique data set, we show that using an efficient Bayesian linear regression model results in a mean correct classification rate of 80% (±3%). This represents a mean relative reduction of approximately 50% in the number of incorrect decisions when compared with a user-defined static permission policy, i.e., the model used in current permission systems. SmarPer also focuses on the suboptimal trade-off between privacy and utility, instead of only "allow" or "deny" type of decisions, SmarPer also offers an "obfuscate" option where users can still obtain utility by revealing partial information to apps. We implemented obfuscation techniques in SmarPer for different data types and evaluated them during our data collection campaign. Our results show that 73% of the participants found obfuscation useful and it accounted for almost a third of the total number of decisions. In short, we are the first to show, using a large dataset of real in situ permission decisions, that it is possible to learn users' unique decision patterns at runtime using contextual information while supporting data obfuscation, this is an important step towards automating the management of permissions in smartphones.