When Good Equations Get Bad Scores: Improving Symbolic Regression Through Better Parameter Optimization

A fundamental challenge in symbolic regression (SR) is efficiently recovering complex mathematical expressions from observational data. Although this problem is NP-hard, many expressions of practical interest decompose naturally into combinations of nonlinear feature modules, concentrating structural complexity into a small number of reusable components. Here, we introduce FePySR, a two-stage framework that reduces the SR search space by extracting valid features prior to equation search. FePySR first employs a heterogeneous neural network to constrain observational data to a set of candidate expressions, then performs structural optimization within this refined expression space using PySR. Across five standard benchmarks, FePySR outperforms state-of-the-art methods by achieving higher equation recovery rates. On a set of 75 highly complex synthesized equations, FePySR recovers 36 equations, while producing substantially smaller mean squared errors on the remaining unrecovered cases, with reduced computation time compared to PySR. FePySR's first stage also maintains consistent performance under varying numbers of selected top features and increasing levels of noise in the observational data. Applied to ordinary differential equations governing biological systems, FePySR successfully identifies governing equations in 24 out of 100 tests where PySR recovers none. Taken together, FePySR is a generalizable framework that can enhance the SR solvers, enabling the efficient and reliable recovery of symbolic expressions across scientific domains.

Symbolic regression (SR) seeks closed-form mathematical expressions that fit observed data. Neural SR methods amortize the search by training an encoder to map observations directly to expressions in a single pass, but this amortized inference leaves a residual amortization gap between its one-shot prediction and the true posterior. We propose Latent Equation Embedding (LEE), a framework that closes this gap through iterative amortized inference in a functionally grounded latent space. LEE learns a shared latent space Z equipped with three components: an encoder f_theta that jointly embeds symbolic tokens and numerical observations into a single latent vector z; an expression decoder g_expr that reconstructs formulas from z; and an evaluation decoder g_eval that predicts function values from z, explicitly grounding the latent space in functional behavior. At inference, LEE performs iterative refinement by re-encoding decoded expressions jointly with observations, progressively improving the latent estimate. LEE uses the encoder itself as a learned inference optimizer: each re-encoding step implicitly computes the mismatch between the candidate and the data. Because g_eval is differentiable in z, we additionally interleave continuous gradient descent with discrete re-encoding, yielding a hybrid iterative and gradient refinement procedure. On SRBench across three noise levels, against 19 baselines spanning genetic programming, symbolic-neural hybrids, and pre-trained Transformers, LEE produces expressions 2--10x simpler than the strongest accuracy-oriented baselines, including Operon, GP-GOMEA, TPSR, RAG-SR, and GenSR, with complexity 8--11 versus 20--90. These results advance the low-complexity region of the accuracy-complexity Pareto frontier and show graceful degradation as noise increases.

Many equations arising in science currently cannot be solved by available analytical techniques and are therefore solved numerically, without yielding explicit symbolic expressions. Existing symbolic regression approaches can recover symbolic expressions, but require training data obtained from the underlying process, rather than the governing equation alone. We propose the Symbolic Equation Solver (SES), a framework that formulates equation solving as an optimization problem over differentiable symbolic models. SES constructs its objective from the equation together with initial or boundary conditions, eliminating the need for paired input-output data. The learned model is expressed in explicit symbolic form, enabling further analysis. We evaluate SES on representative algebraic and differential equations, including a system of algebraic equations, an equation with transcendental terms, an ordinary differential equation, and partial differential equations with different initial or boundary conditions. Across these settings, SES recovers compact symbolic expressions that match the corresponding analytical solutions.