Predicting the behavior of complex systems is critical in many scientific and engineering domains, and hinges on the model's ability to capture their underlying dynamics. Existing methods encode the intrinsic dynamics of high-dimensional observations through latent representations and predict autoregressively. However, these latent representations lose the inherent spatial structure of spatiotemporal dynamics, leading to the predictor's inability to effectively model spatial interactions and neglect emerging dynamics during long-term prediction. In this work, we propose SparseDiff, introducing a test-time adaptation strategy to dynamically update the encoding scheme to accommodate emergent spatiotemporal structures during the long-term evolution of the system.

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying systems. Recent efforts to evaluate the scientific capabilities of large language models (LLMs) fail to test these competencies because wet-lab experimentation is prohibitively expensive: in expertise, time and equipment. We introduce SciGym, a first-in-class benchmark that assesses LLMs' iterative experiment design and analysis abilities in open-ended scientific discovery tasks. SciGym overcomes the challenge of wet-lab costs by running a dry lab of biological systems. These models, encoded in Systems Biology Markup Language, are efficient for generating simulated data, making them ideal testbeds for experimentation on realistically complex systems.

What is the topic of the research in your paper? In our paper, we study how social structures emerge when the "individuals" in a network are artificial agents powered by large language models. To do so, we analyzed a platform called Moltbook - a social network entirely populated by AI agents, specifically LLM-based agents, that interact with each other through posts and comments. This social network creates a very unusual but powerful setting: instead of observing human behavior, we can study a brand new society made only of artificial entities and observe whether it organizes itself in similar ways. To understand the structure of interactions in this system, we modelled the platform as a network, where each agent is a node and each interaction is a connection between them.

Neural Information Processing Systems http://nips.cc/

Predicting critical transitions in complex systems, such as epileptic seizures in the brain, represents a major challenge in scientific research. The high-dimensional characteristics and hidden critical signals further complicate early-warning tasks. This study proposes a novel early-warning framework that integrates manifold learning with stochastic dynamical system modeling. Through systematic comparison, six methods including diffusion maps (DM) are selected to construct low-dimensional representations. Based on these, a data-driven stochastic differential equation model is established to robustly estimate the probability evolution scoring function of the system. Building on this, a new Score Function (SF) indicator is defined by incorporating Schrödinger bridge theory to quantify the likelihood of significant state transitions in the system. Experiments demonstrate that this indicator exhibits higher sensitivity and robustness in epilepsy prediction, enables earlier identification of critical points, and clearly captures dynamic features across various stages before and after seizure onset. This work provides a systematic theoretical framework and practical methodology for extracting early-warning signals from high-dimensional data.

This manuscript contributes a general and practical framework for casting a Markov process model of a system at equilibrium as a structural causal model, and carrying out counterfactual inference. Markov processes mathematically describe the mechanisms in the system, and predict the system's equilibrium behavior upon intervention, but do not support counterfactual inference. In contrast, structural causal models support counterfactual inference, but do not identify the mechanisms.

In this article, we present a framework for designing neural networks that remain consistent with the underlying principles of agent-based models. We begin by highlighting the limitations of standard neural differential equations in modeling complex systems, where physical invariants (like energy) are often absent but other constraints (like mass conservation, information locality, bounded rationality) must be enforced. To address this, we introduce Agent-Based-Model informed Neural Networks (ABM-NNs), which leverage restricted graph neural networks and hierarchical decomposition to learn interpretable, structure-preserving dynamics. We validate the framework across three case studies of increasing complexity: (i) a Generalized Lotka-Volterra system, where we recover ground-truth parameters from short trajectories in presence of interventions; (ii) a graph-based SIR contagion model, where our method outperforms state-of-the-art graph learning baselines (GCN, GraphSAGE, Graph Transformer) in out-of-sample forecasting and noise robustness; and (iii) a real-world macroeconomic model of the ten largest economies, where we learn coupled GDP dynamics from empirical data and demonstrate counterfactual analysis for policy interventions.

Agent-based modeling (ABM) is a principal approach for studying complex systems. By decomposing a system into simpler, interacting agents, agent-based modeling (ABM) allows researchers to observe the emergence of complex phenomena. High-performance array computing libraries like JAX can help scale such computational models to a large number of agents by using automatic vectorization and just-in-time (JIT) compilation. One of the caveats of using JAX to achieve such scaling is that the shapes of arrays used in the computational model should remain immutable throughout the simulation. In the context of agent-based modeling (ABM), this can pose constraints on certain agent manipulation operations that require flexible data structures. A subset of which is represented by the ability to update a dynamically selected number of agents by applying distinct changes to them during a simulation. To this effect, we introduce ABMax, an ABM framework based on JAX that implements multiple just-in-time (JIT) compilable algorithms to provide this functionality. On the canonical predation model benchmark, ABMax achieves runtime performance comparable to state-of-the-art implementations. Further, we show that this functionality can also be vectorized, making it possible to run many similar agent-based models in parallel. We also present two examples in the form of a traffic-flow model and a financial market model to show the use case of ABMax

The diversity of patterns that emerge from complex systems motivates their use for scientific or artistic purposes. When exploring these systems, the challenges faced are the size of the parameter space and the strongly non-linear mapping between parameters and emerging patterns. In addition, artists and scientists who explore complex systems do so with an expectation of particular patterns. Taking these expectations into account adds a new set of challenges, which the exploration process must address. We provide design choices and their implementation to address these challenges; enabling the maximization of the diversity of patterns discovered in the user's region of interest -- which we call the constrained diversity -- in a sample-efficient manner. The region of interest is expressed in the form of explicit constraints. These constraints are formulated by the user in a system-agnostic way, and their addition enables interactive system exploration leading to constrained diversity, while maintaining global diversity.

Describing and comparing complex systems requires principled, theoretically grounded tools. Built around the phenomenon of type turbulence, allotaxonographs provide map-and-list visual comparisons of pairs of heavy-tailed distributions. Allotaxonographs are designed to accommodate a wide range of instruments including rank- and probability-turbulence divergences, Jenson-Shannon divergence, and generalized entropy divergences. Here, we describe a suite of programmatic tools for rendering allotaxonographs for rank-turbulence divergence in Matlab, Javascript, and Python, all of which have different use cases.