Biological systems are non-linear, include unobserved variables and the physical principles that govern their dynamics are partly unknown. This makes the characterization of their behavior very challenging. Notably, their activity occurs on multiple interdependent spatial and temporal scales that require linking mechanisms across scales. To address the challenge of bridging gaps between scales, we leverage partial differential equations (PDE) discovery. PDE discovery suggests meso-scale dynamics characteristics from micro-scale data. In this article, we present our framework combining particle-based simulations and PDE discovery and conduct preliminary experiments to assess equation discovery in controlled settings. We evaluate five state-of-the-art PDE discovery methods on particle-based simulations of calcium diffusion in astrocytes. The performances of the methods are evaluated on both the form of the discovered equation and the forecasted temporal variations of calcium concentration. Our results show that several methods accurately recover the diffusion term, highlighting the potential of PDE discovery for capturing macroscopic dynamics in biological systems from microscopic data.
Symbolic regression is a fundamental tool for discovering interpretable mathematical expressions from data, with broad applications across scientific and engineering domains. Recently, large language models (LLMs) have demonstrated strong performance in this task, leveraging embedded scientific priors and reasoning capabilities to surpass traditional methods. However, existing LLM-based approaches, such as LLM-SR, often over-rely on internal priors, lacking explicit data understanding and systematic reflection during equation generation. To address these limitations, we propose DrSR (Dual Reasoning Symbolic Regression), a framework that combines data-driven insight with reflective learning to enhance both robustness and discovery capability. Specifically, DrSR guides LLMs to analyze structural relationships (e.g., monotonicity, nonlinearity, and correlation) within the data to generate structured descriptions. Simultaneously, it monitors equation performance and establishes a feedback loop to refine subsequent generations. By integrating data understanding and generation reflection in a closed loop, DrSR enables more efficient exploration of the symbolic expression space. Experiments across interdisciplinary datasets in physics, chemistry, biology, and materials science demonstrate that DrSR substantially improves the valid equation rate and consistently outperforms both classical and recent LLM-based methods in terms of accuracy, generalization, and search efficiency. These results underscore its potential for scientific equation discovery.
The explicit governing equation is one of the simplest and most intuitive forms for characterizing physical laws. However, directly discovering partial differential equations (PDEs) from data poses significant challenges, primarily in determining relevant terms from a vast search space. Symmetry, as a crucial prior knowledge in scientific fields, has been widely applied in tasks such as designing equivariant networks and guiding neural PDE solvers. In this paper, we propose a pipeline for governing equation discovery based on differential invariants, which can losslessly reduce the search space of existing equation discovery methods while strictly adhering to symmetry. Specifically, we compute the set of differential invariants corresponding to the infinitesimal generators of the symmetry group and select them as the relevant terms for equation discovery. Taking DI-SINDy (SINDy based on Differential Invariants) as an example, we demonstrate that its success rate and accuracy in PDE discovery surpass those of other symmetry-informed governing equation discovery methods across a series of PDEs.
Though neural networks trained on large datasets have been successfully used to describe and predict many physical phenomena, there is a sense among scientists that, unlike traditional scientific models comprising simple mathematical expressions, their findings cannot be integrated into the body of scientific knowledge. Critics of machine learning's inability to produce human-understandable relationships have converged on the concept of "interpretability" as its point of departure from more traditional forms of science. As the growing interest in interpretability has shown, researchers in the physical sciences seek not just predictive models, but also to uncover the fundamental principles that govern a system of interest. However, clarity around a definition of interpretability and the precise role that it plays in science is lacking in the literature. In this work, we argue that researchers in equation discovery and symbolic regression tend to conflate the concept of sparsity with interpretability. We review key papers on interpretable machine learning from outside the scientific community and argue that, though the definitions and methods they propose can inform questions of interpretability for scientific machine learning (SciML), they are inadequate for this new purpose. Noting these deficiencies, we propose an operational definition of interpretability for the physical sciences. Our notion of interpretability emphasizes understanding of the mechanism over mathematical sparsity. Innocuous though it may seem, this emphasis on mechanism shows that sparsity is often unnecessary. It also questions the possibility of interpretable scientific discovery when prior knowledge is lacking. We believe a precise and philosophically informed definition of interpretability in SciML will help focus research efforts toward the most significant obstacles to realizing a data-driven scientific future.
Deep Symbolic Optimization (DSO) is a novel computational framework that enables symbolic optimization for scientific discovery, particularly in applications involving the search for intricate symbolic structures. One notable example is equation discovery, which aims to automatically derive mathematical models expressed in symbolic form. In DSO, the discovery process is formulated as a sequential decision-making task. A generative neural network learns a probabilistic model over a vast space of candidate symbolic expressions, while reinforcement learning strategies guide the search toward the most promising regions. This approach integrates gradient-based optimization with evolutionary and local search techniques, and it incorporates in-situ constraints, domain-specific priors, and advanced policy optimization methods. The result is a robust framework capable of efficiently exploring extensive search spaces to identify interpretable and physically meaningful models. Extensive evaluations on benchmark problems have demonstrated that DSO achieves state-of-the-art performance in both accuracy and interpretability. In this chapter, we provide a comprehensive overview of the DSO framework and illustrate its transformative potential for automating symbolic optimization in scientific discovery.
Scientific equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorized forms, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy. These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.
The understanding and modeling of complex physical phenomena through dynamical systems has historically driven scientific progress, as it provides the tools for predicting the behavior of different systems under diverse conditions through time. The discovery of dynamical systems has been indispensable in engineering, as it allows for the analysis and prediction of complex behaviors for computational modeling, diagnostics, prognostics, and control of engineered systems. Joining recent efforts that harness the power of symbolic regression in this domain, we propose a novel framework for the end-to-end discovery of ordinary differential equations (ODEs), termed Grammar-based ODE Discovery Engine (GODE). The proposed methodology combines formal grammars with dimensionality reduction and stochastic search for efficiently navigating high-dimensional combinatorial spaces. Grammars allow us to seed domain knowledge and structure for both constraining, as well as, exploring the space of candidate expressions. GODE proves to be more sample- and parameter-efficient than state-of-the-art transformer-based models and to discover more accurate and parsimonious ODE expressions than both genetic programming- and other grammar-based methods for more complex inference tasks, such as the discovery of structural dynamics. Thus, we introduce a tool that could play a catalytic role in dynamics discovery tasks, including modeling, system identification, and monitoring tasks.
The ability to discover meaningful, accurate, and concise mathematical equations that describe datasets is valuable across various domains. Equations offer explicit relationships between variables, enabling deeper insights into underlying data patterns. Most existing equation discovery methods rely on genetic programming, which iteratively searches the equation space but is often slow and prone to overfitting. By representing equations as directed acyclic graphs, we leverage the use of graph neural networks to learn the underlying semantics of equations, and generate new, previously unseen equations. Although graph generative models have been shown to be successful in discovering new types of graphs in many fields, there application in discovering equations remains largely unexplored. In this work, we propose Graph-EQ, a deep graph generative model designed for efficient equation discovery. Graph-EQ uses a conditional variational autoencoder (CVAE) to learn a rich latent representation of the equation space by training it on a large corpus of equations in an unsupervised manner. Instead of directly searching the equation space, we employ Bayesian optimization to efficiently explore this learned latent space. We show that the encoder-decoder architecture of Graph-Eq is able to accurately reconstruct input equations. Moreover, we show that the learned latent representation can be sampled and decoded into valid equations, including new and previously unseen equations in the training data. Finally, we assess Graph-Eq's ability to discover equations that best fit a dataset by exploring the latent space using Bayesian optimization. Latent space exploration is done on 20 dataset with known ground-truth equations, and Graph-Eq is shown to successfully discover the grountruth equation in the majority of datasets.
Deep learning approaches are becoming increasingly attractive for equation discovery. We show the advantages and disadvantages of using neural-guided equation discovery by giving an overview of recent papers and the results of experiments using our modular equation discovery system MGMT ($\textbf{M}$ulti-Task $\textbf{G}$rammar-Guided $\textbf{M}$onte-Carlo $\textbf{T}$ree Search for Equation Discovery). The system uses neural-guided Monte-Carlo Tree Search (MCTS) and supports both supervised and reinforcement learning, with a search space defined by a context-free grammar. We summarize seven desirable properties of equation discovery systems, emphasizing the importance of embedding tabular data sets for such learning approaches. Using the modular structure of MGMT, we compare seven architectures (among them, RNNs, CNNs, and Transformers) for embedding tabular datasets on the auxiliary task of contrastive learning for tabular data sets on an equation discovery task. For almost all combinations of modules, supervised learning outperforms reinforcement learning. Moreover, our experiments indicate an advantage of using grammar rules as action space instead of tokens. Two adaptations of MCTS -- risk-seeking MCTS and AmEx-MCTS -- can improve equation discovery with that kind of search.
Symbolic Regression (SR) holds great potential for uncovering underlying mathematical and physical relationships from observed data. However, the vast combinatorial space of possible expressions poses significant challenges for both online search methods and pre-trained transformer models. Additionally, current state-of-the-art approaches typically do not consider the integration of domain experts' prior knowledge and do not support iterative interactions with the model during the equation discovery process. To address these challenges, we propose the Symbolic Q-network (Sym-Q), an advanced interactive framework for large-scale symbolic regression. Unlike previous large-scale transformer-based SR approaches, Sym-Q leverages reinforcement learning without relying on a transformer-based decoder. This formulation allows the agent to learn through offline reinforcement learning using any type of tree encoder, enabling more efficient training and inference. Furthermore, we propose a co-design mechanism, where the reinforcement learning-based Sym-Q facilitates effective interaction with domain experts at any stage of the equation discovery process. Users can dynamically modify generated nodes of the expression, collaborating with the agent to tailor the mathematical expression to best fit the problem and align with the assumed physical laws, particularly when there is prior partial knowledge of the expected behavior. Our experiments demonstrate that the pre-trained Sym-Q surpasses existing SR algorithms on the challenging SSDNC benchmark. Moreover, we experimentally show on real-world cases that its performance can be further enhanced by the interactive co-design mechanism, with Sym-Q achieving greater performance gains than other state-of-the-art models. Our reproducible code is available at https://github.com/EPFL-IMOS/Sym-Q.
Equation discovery methods hold promise for extracting knowledge from physics-related data. However, existing approaches often require substantial prior information that significantly reduces the amount of knowledge extracted. In this paper, we enhance the EPDE algorithm -- an evolutionary optimization-based discovery framework. In contrast to methods like SINDy, which rely on pre-defined libraries of terms and linearities, our approach generates terms using fundamental building blocks such as elementary functions and individual differentials. Within evolutionary optimization, we may improve the computation of the fitness function as is done in gradient methods and enhance the optimization algorithm itself. By incorporating multi-objective optimization, we effectively explore the search space, yielding more robust equation extraction, even when dealing with complex experimental data. We validate our algorithm's noise resilience and overall performance by comparing its results with those from the state-of-the-art equation discovery framework SINDy.
Time-delayed differential equations (TDDEs) are widely used to model complex dynamic systems where future states depend on past states with a delay. However, inferring the underlying TDDEs from observed data remains a challenging problem due to the inherent nonlinearity, uncertainty, and noise in real-world systems. Conventional equation discovery methods often exhibit limitations when dealing with large time delays, relying on deterministic techniques or optimization-based approaches that may struggle with scalability and robustness. In this paper, we present BayTiDe - Bayesian Approach for Discovering Time-Delayed Differential Equations from Data, that is capable of identifying arbitrarily large values of time delay to an accuracy that is directly proportional to the resolution of the data input to it. BayTiDe leverages Bayesian inference combined with a sparsity-promoting discontinuous spike-and-slab prior to accurately identify time-delayed differential equations. The approach accommodates arbitrarily large time delays with accuracy proportional to the input data resolution, while efficiently narrowing the search space to achieve significant computational savings. We demonstrate the efficiency and robustness of BayTiDe through a range of numerical examples, validating its ability to recover delayed differential equations from noisy data.
In differential equation discovery algorithms, a priori expert knowledge is mainly used implicitly to constrain the form of the expected equation, making it impossible for the algorithm to truly discover equations. Instead, most differential equation discovery algorithms try to recover the coefficients for a known structure. In this paper, we describe an algorithm that allows the discovery of unknown equations using automatically or manually extracted background knowledge. Instead of imposing rigid constraints, we modify the structure space so that certain terms are likely to appear within the crossover and mutation operators. In this way, we mimic expertly chosen terms while preserving the possibility of obtaining any equation form. The paper shows that the extraction and use of knowledge allows it to outperform the SINDy algorithm in terms of search stability and robustness. Synthetic examples are given for Burgers, wave, and Korteweg--De Vries equations.
Machine learning for scientific discovery is increasingly becoming popular because of its ability to extract and recognize the nonlinear characteristics from the data. The black-box nature of deep learning methods poses difficulties in interpreting the identified model. There is a dire need to interpret the machine learning models to develop a physical understanding of dynamic systems. An interpretable form of neural network called Kolmogorov-Arnold networks (KAN) or Multiplicative KAN (MultKAN) offers critical features that help recognize the nonlinearities in the governing ordinary/partial differential equations (ODE/PDE) of various dynamic systems and find their equation structures. In this study, an equation discovery framework is proposed that includes i) sequentially regularized derivatives for denoising (SRDD) algorithm to denoise the measure data to obtain accurate derivatives, ii) KAN to identify the equation structure and suggest relevant nonlinear functions that are used to create a small overcomplete library of functions, and iii) physics-informed spline fitting (PISF) algorithm to filter the excess functions from the library and converge to the correct equation. The framework was tested on the forced Duffing oscillator, Van der Pol oscillator (stiff ODE), Burger's equation, and Bouc-Wen model (coupled ODE). The proposed method converged to the true equation for the first three systems. It provided an approximate model for the Bouc-Wen model that could acceptably capture the hysteresis response. Using KAN maintains low complexity, which helps the user interpret the results throughout the process and avoid the black-box-type nature of machine learning methods.
Complex systems in physics, chemistry, and biology that evolve over time with inherent randomness are typically described by stochastic differential equations (SDEs). A fundamental challenge in science and engineering is to determine the governing equations of a complex system from snapshot data. Traditional equation discovery methods often rely on stringent assumptions, such as the availability of the trajectory information or time-series data, and the presumption that the underlying system is deterministic. In this work, we introduce a data-driven, simulation-free framework, called Sparse Identification of Differential Equations from Snapshots (SpIDES), that discovers the governing equations of a complex system from snapshots by utilizing the advanced machine learning techniques to perform three essential steps: probability flow reconstruction, probability density estimation, and Bayesian sparse identification. We validate the effectiveness and robustness of SpIDES by successfully identifying the governing equation of an over-damped Langevin system confined within two potential wells. By extracting interpretable drift and diffusion terms from the SDEs, our framework provides deeper insights into system dynamics, enhances predictive accuracy, and facilitates more effective strategies for managing and simulating stochastic systems.
Sparse system identification of nonlinear dynamic systems is still challenging, especially for stiff and high-order differential equations for noisy measurement data. The use of highly correlated functions makes distinguishing between true and false functions difficult, which limits the choice of functions. In this study, an equation discovery method has been proposed to tackle these problems. The key elements include a) use of B-splines for data fitting to get analytical derivatives superior to numerical derivatives, b) sequentially regularized derivatives for denoising (SRDD) algorithm, highly effective in removing noise from signal without system information loss, c) uncorrelated component analysis (UCA) algorithm that identifies and eliminates highly correlated functions while retaining the true functions, and d) physics-informed spline fitting (PISF) where the spline fitting is updated gradually while satisfying the governing equation with a dictionary of candidate functions to converge to the correct equation sequentially. The complete framework is built on a unified deep-learning architecture that eases the optimization process. The proposed method is demonstrated to discover various differential equations at various noise levels, including three-dimensional, fourth-order, and stiff equations. The parameter estimation converges accurately to the true values with a small coefficient of variation, suggesting robustness to the noise.
Data-driven discovery of partial differential equations (PDEs) has emerged as a promising approach for deriving governing physics when domain knowledge about observed data is limited. Despite recent progress, the identification of governing equations and their parametric dependencies using conventional information criteria remains challenging in noisy situations, as the criteria tend to select overly complex PDEs. In this paper, we introduce an extension of the uncertainty-penalized Bayesian information criterion (UBIC), which is adapted to solve parametric PDE discovery problems efficiently without requiring computationally expensive PDE simulations. This extended UBIC uses quantified PDE uncertainty over different temporal or spatial points to prevent overfitting in model selection. The UBIC is computed with data transformation based on power spectral densities to discover the governing parametric PDE that truly captures qualitative features in frequency space with a few significant terms and their parametric dependencies (i.e., the varying PDE coefficients), evaluated with confidence intervals. Numerical experiments on canonical PDEs demonstrate that our extended UBIC can identify the true number of terms and their varying coefficients accurately, even in the presence of noise. The code is available at \url{https://github.com/Pongpisit-Thanasutives/parametric-discovery}.
Over the past few years, equation discovery has gained popularity in different fields of science and engineering. However, existing equation discovery algorithms rely on the availability of noisy measurements of the state variables (i.e., displacement {and velocity}). This is a major bottleneck in structural dynamics, where we often only have access to acceleration measurements. To that end, this paper introduces a novel equation discovery algorithm for discovering governing equations of dynamical systems from acceleration-only measurements. The proposed algorithm employs a library-based approach for equation discovery. To enable equation discovery from acceleration-only measurements, we propose a novel Approximate Bayesian Computation (ABC) model that prioritizes parsimonious models. The efficacy of the proposed algorithm is illustrated using {four} structural dynamics examples that include both linear and nonlinear dynamical systems. The case studies presented illustrate the possible application of the proposed approach for equation discovery of dynamical systems from acceleration-only measurements.
Symbolic regression plays a crucial role in modern scientific research thanks to its capability of discovering concise and interpretable mathematical expressions from data. A grand challenge lies in the arduous search for parsimonious and generalizable mathematical formulas, in an infinite search space, while intending to fit the training data. Existing algorithms have faced a critical bottleneck of accuracy and efficiency over a decade when handling problems of complexity, which essentially hinders the pace of applying symbolic regression for scientific exploration across interdisciplinary domains. To this end, we introduce a parallelized tree search (PTS) model to efficiently distill generic mathematical expressions from limited data. Through a series of extensive experiments, we demonstrate the superior accuracy and efficiency of PTS for equation discovery, which greatly outperforms the state-of-the-art baseline models on over 80 synthetic and experimental datasets (e.g., lifting its performance by up to 99% accuracy improvement and one-order of magnitude speed up). PTS represents a key advance in accurate and efficient data-driven discovery of symbolic, interpretable models (e.g., underlying physical laws) and marks a pivotal transition towards scalable symbolic learning.
Hybrid dynamical systems are prevalent in science and engineering to express complex systems with continuous and discrete states. To learn the laws of systems, all previous methods for equation discovery in hybrid systems follow a two-stage paradigm, i.e. they first group time series into small cluster fragments and then discover equations in each fragment separately through methods in non-hybrid systems. Although effective, these methods do not fully take advantage of the commonalities in the shared dynamics of multiple fragments that are driven by the same equations. Besides, the two-stage paradigm breaks the interdependence between categorizing and representing dynamics that jointly form hybrid systems. In this paper, we reformulate the problem and propose an end-to-end learning framework, i.e. Amortized Equation Discovery (AMORE), to jointly categorize modes and discover equations characterizing the dynamics of each mode by all segments of the mode. Experiments on four hybrid and six non-hybrid systems show that our method outperforms previous methods on equation discovery, segmentation, and forecasting.