Inferring a Continuous Distribution of Atom Coordinates from Cryo-EM Images using VAEs

Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied macromolecule, or a relatively small number of its conformations. This reduces the effectiveness of the technique for proteins with flexible regions, which are known to play a key role in protein function. Recent methods for capturing conformational heterogeneity in cryo-EM data model it in volume space, making recovery of continuous atomic structures challenging. Here we present a fully deep-learning-based approach using variational auto-encoders (VAEs) to recover a continuous distribution of atomic protein structures and poses directly from picked particle images and demonstrate its efficacy on realistic simulated data. We hope that methods built on this work will allow incorporation of stronger prior information about protein structure and enable better understanding of non-rigid protein structures.

Deep reinforcement learning models the emergent dynamics of human cooperation

Collective action demands that individuals efficiently coordinate how much, where, and when to cooperate. Laboratory experiments have extensively explored the first part of this process, demonstrating that a variety of social-cognitive mechanisms influence how much individuals choose to invest in group efforts. However, experimental research has been unable to shed light on how social cognitive mechanisms contribute to the where and when of collective action. We leverage multi-agent deep reinforcement learning to model how a social-cognitive mechanism--specifically, the intrinsic motivation to achieve a good reputation--steers group behavior toward specific spatial and temporal strategies for collective action in a social dilemma. We also collect behavioral data from groups of human participants challenged with the same dilemma. The model accurately predicts spatial and temporal patterns of group behavior: in this public goods dilemma, the intrinsic motivation for reputation catalyzes the development of a non-territorial, turn-taking strategy to coordinate collective action.

Quantifying environment and population diversity in multi-agent reinforcement learning

Generalization is a major challenge for multi-agent reinforcement learning. How well does an agent perform when placed in novel environments and in interactions with new co-players? In this paper, we investigate and quantify the relationship between generalization and diversity in the multi-agent domain. Across the range of multi-agent environments considered here, procedurally generating training levels significantly improves agent performance on held-out levels. However, agent performance on the specific levels used in training sometimes declines as a result. To better understand the effects of co-player variation, our experiments introduce a new environment-agnostic measure of behavioral diversity. Results demonstrate that population size and intrinsic motivation are both effective methods of generating greater population diversity. In turn, training with a diverse set of co-players strengthens agent performance in some (but not all) cases.