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Hyukpyo Hong

Publications and source records attributed to Hyukpyo Hong.

5 recordsLinked to original sources

Finding Koopman Invariant Subspaces via Personalized PageRank

Selecting a finite dictionary of observables whose span is Koopman-invariant is a central challenge in data-driven Koopman operator approximation. We address this problem by exploiting zero-block structure in Extended Dynamic Mode Decomposition (EDMD) matrices. We show that any sub-dictionary whose span is Koopman-invariant induces an exact zero block in the EDMD matrix, even for finite data. We then show that such blocks can be detected by applying PageRank to a row-normalized EDMD matrix constructed from a large initial dictionary. The theory extends to approximately invariant subspaces and yields stronger guarantees for personalized PageRank (PPR) when the seed observables lie inside the target block and reach all observables in that block. Combining EDMD concentration bounds with PageRank perturbation theory gives end-to-end detection guarantees with $O(1/\sqrt{M})$ finite-sample scaling and explicit constants. More generally, without assuming an invariant subspace exists, high PPR mass on a sub-dictionary controls discounted multi-step leakage from the seed observables. Numerical experiments on the Duffing oscillator, Van der Pol oscillator, Lorenz system, and a three-well Ramachandran potential suggest that the method identifies compact, interpretable dictionaries with accurate predictions.

math.DS

Lean-GAP: A Dataset of Formalized Graduate Algebra Problems

We present Lean-GAP (Lean-Graduate Agebra Problems), 430 formalized graduate-level algebra problems from the textbook Abstract Algebra by Dummit and Foote. We develop a scalable pipeline consisting of PDF-to-LaTeX preprocessing, autoformalization into Lean 4, and verification of informal-formal correspondence. While the preprocessing and autoformalization stages can be largely automated, we find that verification remains the most subtle and labor-intensive component, requiring careful human oversight. Our contributions include (i) the construction of a structured dataset of formalized exercises, (ii) a systematic methodology for formalizing textbook mathematics, and (iii) an analysis of recurring challenges in the formalization process. We also compare the performance of different autoformalization models and highlight key bottlenecks in translating informal statements into formal language.

cs.LO

Asymptotic Robustness in Biochemical Systems

Living systems maintain stable internal states despite environmental fluctuations. Absolute concentration robustness (ACR) is a striking homeostatic phenomenon in which the steady-state concentration of a species remains invariant despite changes in total supply. Although experimental studies have reported approximate-but not exact-robustness in steady-state concentrations, such behavior has often been attributed to exact ACR motifs perturbed by measurement noise or minor reactions, rather than recognized as a structural property of a network itself. Here, we introduce a previously underappreciated phenomenon, namely asymptotic ACR (aACR): approximate robustness can emerge solely from the network structure, without requiring exact ACR motifs or negligible parameters. We find that aACR is more pervasive than classical ACR, as demonstrated in systems such as the Escherichia coli EnvZ-OmpR osmoregulation system and a futile cycle. Furthermore, we prove that such ubiquity stems solely from network structure without fine-tuning of kinetic parameters. The notion of aACR provides a rigorous and practical tool to analyze robust responses in broad biochemical systems.

math.DS

Robust Perfect Adaptation of Reaction Fluxes Ensured by Network Topology

Maintaining stability in an uncertain environment is essential for proper functioning of living systems. Robust perfect adaptation (RPA) is a property of a system that generates an output at a fixed level even after fluctuations in input stimulus without fine-tuning parameters, and it is important to understand how this feature is implemented through biochemical networks. The existing literature has mainly focused on RPA of the concentration of a chosen chemical species, and no generic analysis has been made on RPA of reaction fluxes, that play an equally important role. Here, we identify structural conditions on reaction networks under which all the reaction fluxes exhibit RPA against the perturbation of the parameters inside a subnetwork. Based on this understanding, we give a recipe for obtaining a simpler reaction network, from which we can fully recover the steady-state reaction fluxes of the original system. This helps us identify key parameters that determine the fluxes and study the properties of complex reaction networks using a smaller one without losing any information about steady-state reaction fluxes.

q-bio.MN

Computational translation framework identifies biochemical reaction networks with special topologies and their long-term dynamics

Long-term behaviors of biochemical systems are described by steady states in deterministic models and stationary distributions in stochastic models. Obtaining their analytic solutions can be done for limited cases, such as linear or finite-state systems, as it generally requires solving many coupled equations. Interestingly, analytic solutions can be easily obtained when underlying networks have special topologies, called weak reversibility (WR) and zero deficiency (ZD), and the kinetic law follows a generalized form of mass-action kinetics. However, such desired topological conditions do not hold for the majority of cases. Thus, translating networks to have WR and ZD while preserving the original dynamics was proposed. Yet, this approach is limited because manually obtaining the desired network translation among the large number of candidates is challenging. Here, we prove necessary conditions for having WR and ZD after translation, and based on these conditions, we develop a user-friendly computational package, TOWARDZ, that automatically and efficiently identifies translated networks with WR and ZD. This allows us to quantitatively examine how likely it is to obtain WR and ZD after translation depending on the number of species and reactions. Importantly, we also describe how our package can be used to analytically derive steady states of deterministic models and stationary distributions of stochastic models. TOWARDZ provides an effective tool to analyze biochemical systems.

q-bio.MN