Most real-world collectives, including animal groups, pedestrian crowds, active particles, and living cells, are heterogeneous. The differences among individuals in their intrinsic properties have emergent effects at the group level. It is often of interest to infer how the intrinsic properties differ among the individuals based on their observed movement patterns. However, the true individual properties may be masked by the nonlinear interactions in the collective. We investigate the inference problem in the context of a bidisperse collective with two types of agents, where the goal is to observe the motion of the collective and classify the agents according to their types. Since collective effects, such as jamming and clustering, affect individual motion, the information in an agent’s own movement is insufficient for accurate classification. A simple observer algorithm, based only on individual velocities, cannot accurately estimate the level of heterogeneity of the system and often misclassifies agents. We propose a novel approach to the classification problem, where collective effects on an agent’s motion are explicitly accounted for. We use insights about the phenomenology of collective motion to quantify the effect of the neighborhood on an agent’s motion using a neighborhood parameter. Such an approach can distinguish between agents of two types, even when their observed motion is identical. This approach estimates the level of heterogeneity much more accurately and achieves significant improvements in classification. Our results demonstrate that explicitly accounting for neighborhood effects is often necessary to correctly infer intrinsic properties of individuals.

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