This article extends the preprint "Characterizing Agent-Based Model Dynamics via $ε$-Machines and Kolmogorov-Style Complexity" by introducing diffusion models as orthogonal and complementary tools for characterizing the output of agent-based models (ABMs). Where $ε$-machines capture the predictive temporal structure and intrinsic computation of ABM-generated time series, diffusion models characterize high-dimensional cross-sectional distributions, learn underlying data manifolds, and enable synthetic generation of plausible population-level outcomes. We provide a formal analysis demonstrating that the two approaches operate on distinct mathematical domains -- processes vs. distributions -- and show that their combination yields a two-axis representation of ABM behavior based on temporal organization and distributional geometry. To our knowledge, this is the first framework to integrate computational mechanics with score-based generative modeling for the structural analysis of ABM outputs, thereby situating ABM characterization within the broader landscape of modern machine-learning methods for density estimation and intrinsic computation. The framework is validated using the same elder-caregiver ABM dataset introduced in the companion paper, and we provide precise definitions and propositions formalizing the mathematical complementarity between $ε$-machines and diffusion models. This establishes a principled methodology for jointly analyzing temporal predictability and high-dimensional distributional structure in complex simulation models.

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

Neural surrogates and operator networks for solving partial differential equation (PDE) problems have attracted significant research interest in recent years. However, most existing approaches are limited in their ability to generalize solutions across varying non-parametric geometric domains. In this work, we address this challenge in the context of Polyethylene Terephthalate (PET) bottle buckling analysis, a representative packaging design problem conventionally solved using computationally expensive finite element analysis (FEA). We introduce a hybrid DeepONet-Transolver framework that simultaneously predicts nodal displacement fields and the time evolution of reaction forces during top load compression. Our methodology is evaluated on two families of bottle geometries parameterized by two and four design variables. Training data is generated using nonlinear FEA simulations in Abaqus for 254 unique designs per family. The proposed framework achieves mean relative $L^{2}$ errors of 2.5-13% for displacement fields and approximately 2.4% for time-dependent reaction forces for the four-parameter bottle family. Point-wise error analyses further show absolute displacement errors on the order of $10^{-4}$-$10^{-3}$, with the largest discrepancies confined to localized geometric regions. Importantly, the model accurately captures key physical phenomena, such as buckling behavior, across diverse bottle geometries. These results highlight the potential of our framework as a scalable and computationally efficient surrogate, particularly for multi-task predictions in computational mechanics and applications requiring rapid design evaluation.

In recent years, Artificial intelligence (AI) has become ubiquitous, empowering various fields, especially integrating artificial intelligence and traditional science (AI for Science: Artificial intelligence for science), which has attracted widespread attention. In AI for Science, using artificial intelligence algorithms to solve partial differential equations (AI for PDEs: Artificial intelligence for partial differential equations) has become a focal point in computational mechanics. The core of AI for PDEs is the fusion of data and partial differential equations (PDEs), which can solve almost any PDEs. Therefore, this article provides a comprehensive review of the research on AI for PDEs, summarizing the existing algorithms and theories. The article discusses the applications of AI for PDEs in computational mechanics, including solid mechanics, fluid mechanics, and biomechanics. The existing AI for PDEs algorithms include those based on Physics-Informed Neural Networks (PINNs), Deep Energy Methods (DEM), Operator Learning, and Physics-Informed Neural Operator (PINO). AI for PDEs represents a new method of scientific simulation that provides approximate solutions to specific problems using large amounts of data, then fine-tuning according to specific physical laws, avoiding the need to compute from scratch like traditional algorithms. Thus, AI for PDEs is the prototype for future foundation models in computational mechanics, capable of significantly accelerating traditional numerical algorithms.

What computational structure are we building into large language models when we train them on next-token prediction? Here, we present evidence that this structure is given by the meta-dynamics of belief updating over hidden states of the data-generating process. Leveraging the theory of optimal prediction, we anticipate and then find that belief states are linearly represented in the residual stream of transformers, even in cases where the predicted belief state geometry has highly nontrivial fractal structure. We investigate cases where the belief state geometry is represented in the final residual stream or distributed across the residual streams of multiple layers, providing a framework to explain these observations. Furthermore we demonstrate that the inferred belief states contain information about the entire future, beyond the local next-token prediction that the transformers are explicitly trained on. Our work provides a framework connecting the structure of training data to the computational structure and representations that transformers use to carry out their behavior.

This review article highlights state-of-the-art data-driven techniques to discover, encode, surrogate, or emulate constitutive laws that describe the path-independent and path-dependent response of solids. Our objective is to provide an organized taxonomy to a large spectrum of methodologies developed in the past decades and to discuss the benefits and drawbacks of the various techniques for interpreting and forecasting mechanics behavior across different scales. Distinguishing between machine-learning-based and model-free methods, we further categorize approaches based on their interpretability and on their learning process/type of required data, while discussing the key problems of generalization and trustworthiness. We attempt to provide a road map of how these can be reconciled in a data-availability-aware context. We also touch upon relevant aspects such as data sampling techniques, design of experiments, verification, and validation.

In this thesis, we explore the use of complex systems to study learning and adaptation in natural and artificial systems. The goal is to develop autonomous systems that can learn without supervision, develop on their own, and become increasingly complex over time. Complex systems are identified as a suitable framework for understanding these phenomena due to their ability to exhibit growth of complexity. Being able to build learning algorithms that require limited to no supervision would enable greater flexibility and adaptability in various applications. By understanding the fundamental principles of learning in complex systems, we hope to advance our ability to design and implement practical learning algorithms in the future. This thesis makes the following key contributions: the development of a general complexity metric that we apply to search for complex systems that exhibit growth of complexity, the introduction of a coarse-graining method to study computations in large-scale complex systems, and the development of a metric for learning efficiency as well as a benchmark dataset for evaluating the speed of learning algorithms. Our findings add substantially to our understanding of learning and adaptation in natural and artificial systems. Moreover, our approach contributes to a promising new direction for research in this area. We hope these findings will inspire the development of more effective and efficient learning algorithms in the future.

We merge computational mechanics' definition of causal states (predictively-equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely-applicable method that infers causal structure directly from observations of a system's behaviors whether they are over discrete or continuous events or time. A structural representation -- a finite- or infinite-state kernel $\epsilon$-machine -- is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker-Plank equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably-infinite causal states and (iii) a continuous-time, continuous-value process generated by a thermally-driven chaotic flow. The method robustly estimates causal structure in the presence of varying external and measurement noise levels.

There are more than a trillion sensors in the world today and according to some estimates there will be about 50 trillion cameras worldwide within the next 5 years, all collecting data either sporadically or around the clock. With such explosive growth of available data and computing resources, recent advances in machine learning and data analytics have yielded transformative results across diverse scientific disciplines, including image recognition, natural language processing, cognitive science, and genomics. However, in many engineering applications, quality and error-free data is not easy to obtain, e.g., for system dynamics characterized by bifurcations and instabilities, hysteresis, delayed responses, and often irreversible responses. Admittedly, as in all everyday applications, in engineering problems, the volume of data has increased substantially compared to even a decade ago but analyzing big data is expensive and time-consuming. Data-driven methods, which have been enabled in the past decade by the availability of sensors, data storage, and computational resources, are taking center stage across many disciplines (physical and information) of science.

Building compact models of nonlinear processes goes to the heart of our understanding the complex world around us--a world replete with unanticipated, emergent patterns. Via discovery mechanisms that we do not yet understand well, we eventually do come to know many of these patterns, even if we have never seen them before. Such discoveries can be substantial. At a minimum, compact models that capture such emergent "macrostates" are essential tools in harnessing complex processes to useful ends. Most ambitiously, one would hope to automate the discovery process itself, providing an especially useful tool for the era of Big Data. One key problem in the larger endeavor of pattern discovery is dimension reduction: reduce the high-dimensional state space of a stochastic dynamical system into smaller, more manageable models that nonetheless still capture the relevant dynamics. The study of complex systems always requires this.