We have a limited understanding of the mechanisms that underlie complex learning in emotional situations, and how these processes can go awry and result in maladaptive behaviors and in extreme cases, underlie psychopathologies. In this project, we developed models of complex behaviors motivated by either positive or negative reinforcers and examined how they are governed and coded in neural networks. We focus on the pathway between the Amygdala and the prefrontal-cortex, as it is the main network that underlies learning and memory formation in emotional contexts. It is also a network that is implicated in almost all psychiatric conditions, mainly in anxiety and post-trauma disorders. We record neural activity using deep multi-contact arrays to unveil the coding schemes embedded in these networks, and develop models of learning that are highly evolved in primates, such as rule learning, generalization (the ability to abstract) and social interactions. The development of more complex models of behavior is crucial and is the next logical and required step in achieving the translation of models for mood disorders, as well as in understanding the basic mechanisms behind the rich repertoire of primates’ emotional behaviors. We found that neural activity in the Amygdala responds differently to punishments and rewards in a way that can explain the differential behavior, and showed that wide networks in the primate brain use precise coding mechanisms to store emotional memories, as well as underlie changes in learning during uncertainty. We also extended these findings to social situations; and showed that the same brain circuit codes for the valence of social interaction and the processing of primary sensory stimuli, indicating a shared origin that allows rapid responses in the face of danger. This was strengthened by a cross-species comparison demonstrating a neural tradeoff between primate species and brain networks. Finally, we developed a rule-learning scheme and described the dynamics in these valence-based neural networks. Our future studies continue to elaborate on this path and investigate the neural codes and interactions between brain regions that underlie complex learning and its abstraction in aversive and positive environments. This work might lead to a better understanding of maladaptive behaviors and psychopathologies.