Analyzing the motion of multiple biological agents, be it cells or individual animals, is pivotal for the understanding of complex collective behaviors. With the advent of advanced microscopy, detailed images of complex tissue formations involving multiple cell types have become more accessible in recent years. However, deciphering the underlying rules that govern cell movements is far from trivial.

Understanding the dynamic behavior of proteins is critical to elucidating their functional mechanisms, yet generating realistic, temporally coherent trajectories of protein ensembles remains a significant challenge. In this work, we introduce a novel hierarchical autoregressive framework for modeling protein dynamics that leverages the intrinsic multi-scale organization of molecular motions. Unlike existing methods that focus on generating static conformational ensembles or treat dynamic sampling as an independent process, our approach characterizes protein dynamics as a Markovian process. The framework employs a two-scale architecture: a low-resolution model captures slow, collective motions driving major conformational transitions, while a high-resolution model generates detailed local fluctuations conditioned on these large-scale movements. This hierarchical design ensures that the causal dependencies inherent in protein dynamics are preserved, enabling the generation of temporally coherent and physically realistic trajectories. By bridging high-level biophysical principles with state-of-the-art generative modeling, our approach provides an efficient framework for simulating protein dynamics that balances computational efficiency with physical accuracy.

Collective behaviors such as swarming and flocking emerge from simple, decentralized interactions in biological systems. Existing models, such as Vicsek and Cucker-Smale, lack collision avoidance, whereas the Olfati-Saber model imposes rigid formations, limiting their applicability in swarm robotics. To address these limitations, this paper proposes a minimal yet expressive model that governs agent dynamics using relative positions, velocities, and local density, modulated by two tunable parameters: the spatial offset and kinetic offset. The model achieves spatially flexible, collision-free behaviors that reflect naturalistic group dynamics. Furthermore, we extend the framework to cognitive autonomous systems, enabling energy-aware phase transitions between swarming and flocking through adaptive control parameter tuning. This cognitively inspired approach offers a robust foundation for real-world applications in multi-robot systems, particularly autonomous aerial swarms.

The synchronized flight of bird flocks, exemplified by starling murmurations, is perhaps the most striking example of collective behavior in natural systems, which fascinated scholars for quite a long time [1]. Evolutionary biologists, for instance, have long debated the advantages of living in groups [2], which should offer increased protection from predation by diluting the individual risk and 1 possibly confusing the attackers by the sheer size of the assembly. Flocking behavior involves a high degree of order in the individual directions of motion [3], and has been reproduced by minimal models of self-propelling particles (SPPs), such as Craig Reynolds Boids [4] or the celebrated Vicsek model [5] that has long captivated the attention of statistical physicists and played a pivotal role in the birth of the active matter research field. The essential ingredient of these models is the tendency of individual particles to align their direction of motion with those of their local neighbours, which is enough to promote long range order in systems with finite density (even in two spatial dimensions, due to the non-equilibrium nature of self-propelled particles) such as in toy models with periodic boundary conditions. In open systems, constituted by a finite number of individuals in an open, infinite space, purely alignment interactions are however not enough to maintain group cohesion.

Interacting individuals in complex systems often give rise to coherent motion exhibiting coordinated global structures. Such phenomena are ubiquitously observed in nature, from cell migration, bacterial swarms, animal and insect groups, and even human societies. Primary mechanisms responsible for the emergence of collective behavior have been extensively identified, including local alignments based on average or relative velocity, non-local pairwise repulsive-attractive interactions such as distance-based potentials, interplay between local and non-local interactions, and cognitive-based inhomogeneous interactions. However, discovering how to adapt these mechanisms to modulate emergent behaviours remains elusive. Here, we demonstrate that it is possible to generate coordinated structures in collective behavior at desired moments with intended global patterns by fine-tuning an inter-agent interaction rule. Our strategy employs deep neural networks, obeying the laws of dynamics, to find interaction rules that command desired collective structures. The decomposition of interaction rules into distancing and aligning forces, expressed by polynomial series, facilitates the training of neural networks to propose desired interaction models. Presented examples include altering the mean radius and size of clusters in vortical swarms, timing of transitions from random to ordered states, and continuously shifting between typical modes of collective motions. This strategy can even be leveraged to superimpose collective modes, resulting in hitherto unexplored but highly practical hybrid collective patterns, such as protective security formations. Our findings reveal innovative strategies for creating and controlling collective motion, paving the way for new applications in robotic swarm operations, active matter organisation, and for the uncovering of obscure interaction rules in biological systems.

Analyzing the motion of multiple biological agents, be it cells or individual animals, is pivotal for the understanding of complex collective behaviors. With the advent of advanced microscopy, detailed images of complex tissue formations involving multiple cell types have become more accessible in recent years. However, deciphering the underlying rules that govern cell movements is far from trivial. Here, we present a novel deep learning framework to estimate the underlying equations of motion from observed trajectories, a pivotal step in decoding such complex dynamics. Our framework integrates graph neural networks with neural differential equations, enabling effective prediction of two-body interactions based on the states of the interacting entities. We demonstrate the efficacy of our approach through two numerical experiments. First, we used a simulated data from a toy model to tune the hyperparameters. Based on the obtained hyperparameters, we then applied this approach to a more complex model that describes interacting cells of cellular slime molds. Our results show that the proposed method can accurately estimate the function of two-body interactions, thereby precisely replicating both individual and collective behaviors within these systems.

Collective motion is ubiquitous in nature; groups of animals, such as fish, birds, and ungulates appear to move as a whole, exhibiting a rich behavioral repertoire that ranges from directed movement to milling to disordered swarming. Typically, such macroscopic patterns arise from decentralized, local interactions among constituent components (e.g., individual fish in a school). Preeminent models of this process describe individuals as self-propelled particles, subject to self-generated motion and 'social forces' such as short-range repulsion and long-range attraction or alignment. However, organisms are not particles; they are probabilistic decision-makers. Here, we introduce an approach to modelling collective behavior based on active inference. This cognitive framework casts behavior as the consequence of a single imperative: to minimize surprise. We demonstrate that many empirically-observed collective phenomena, including cohesion, milling and directed motion, emerge naturally when considering behavior as driven by active Bayesian inference -- without explicitly building behavioral rules or goals into individual agents. Furthermore, we show that active inference can recover and generalize the classical notion of social forces as agents attempt to suppress prediction errors that conflict with their expectations. By exploring the parameter space of the belief-based model, we reveal non-trivial relationships between the individual beliefs and group properties like polarization and the tendency to visit different collective states. We also explore how individual beliefs about uncertainty determine collective decision-making accuracy. Finally, we show how agents can update their generative model over time, resulting in groups that are collectively more sensitive to external fluctuations and encode information more robustly.

Inspired by the swarming or flocking of animal systems we study groups of agents moving in unbounded 2D space. Individual trajectories derive from a ``bottom-up'' principle: individuals reorient to maximise their future path entropy over environmental states. This can be seen as a proxy for keeping options open, a principle that may confer evolutionary fitness in an uncertain world. We find an ordered (co-aligned) state naturally emerges, as well as disordered states or rotating clusters; similar phenotypes are observed in birds, insects and fish, respectively. The ordered state exhibits an order-disorder transition under two forms of noise: (i) standard additive orientational noise, applied to the post-decision orientations (ii) ``cognitive'' noise, overlaid onto each individual's model of the future paths of other agents. Unusually, the order increases at low noise, before later decreasing through the order-disorder transition as the noise increases further.

During the last two decades, various models have been proposed for fish collective motion. These models are mainly developed to decipher the biological mechanisms of social interaction between animals. They consider very simple homogeneous unbounded environments and it is not clear that they can simulate accurately the collective trajectories. Moreover when the models are more accurate, the question of their scalability to either larger groups or more elaborate environments remains open. This study deals with learning how to simulate realistic collective motion of collective of zebrafish, using real-world tracking data. The objective is to devise an agent-based model that can be implemented on an artificial robotic fish that can blend into a collective of real fish. We present a novel approach that uses Quality Diversity algorithms, a class of algorithms that emphasise exploration over pure optimisation. In particular, we use CVT-MAP-Elites, a variant of the state-of-the-art MAP-Elites algorithm for high dimensional search space. Results show that Quality Diversity algorithms not only outperform classic evolutionary reinforcement learning methods at the macroscopic level (i.e. group behaviour), but are also able to generate more realistic biomimetic behaviours at the microscopic level (i.e. individual behaviour).