arXiv subjects

Kashvi Srivastava

Publications and source records attributed to Kashvi Srivastava.

3 recordsLinked to original sources

arXiv2025

Accuracy versus Predominance: Reassessing the validity of the quasi-steady-state approximation

The application of the standard quasi-steady-state approximation to the Michaelis--Menten reaction mechanism is a textbook example of biochemical model reduction, derived using singular perturbation theory. However, determining the specific biochemical conditions that dictate the validity of the standard quasi-steady-state approximation remains a challenging endeavor. Emerging research suggests that the accuracy of the standard quasi-steady-state approximation improves as the ratio of the initial enzyme concentration, $e_0$, to the Michaelis constant, $K_M$, decreases. In this work, we examine this ratio and its implications for the accuracy and validity of the standard quasi-steady-state approximation as compared to other quasi-steady-state reductions in its proximity. Using standard tools from the analysis of ordinary differential equations, we show that while $e_0/K_M$ provides an indication of the standard quasi-steady-state approximation's asymptotic accuracy, the standard quasi-steady-state approximation's predominance relies on a small ratio of $e_0$ to the Van Slyke-Cullen constant, $K$. Here, we define the predominance of a quasi-steady-state reduction when it offers the highest approximation accuracy among other well-known reductions with overlapping validity conditions. We conclude that the magnitude of $e_0/K$ offers the most accurate measure of the validity of the standard quasi-steady-state approximation.

physics.chem-ph↗

arXiv2024

Double Descent and Overfitting under Noisy Inputs and Distribution Shift for Linear Denoisers

Despite the importance of denoising in modern machine learning and ample empirical work on supervised denoising, its theoretical understanding is still relatively scarce. One concern about studying supervised denoising is that one might not always have noiseless training data from the test distribution. It is more reasonable to have access to noiseless training data from a different dataset than the test dataset. Motivated by this, we study supervised denoising and noisy-input regression under distribution shift. We add three considerations to increase the applicability of our theoretical insights to real-life data and modern machine learning. First, while most past theoretical work assumes that the data covariance matrix is full-rank and well-conditioned, empirical studies have shown that real-life data is approximately low-rank. Thus, we assume that our data matrices are low-rank. Second, we drop independence assumptions on our data. Third, the rise in computational power and dimensionality of data have made it important to study non-classical regimes of learning. Thus, we work in the non-classical proportional regime, where data dimension $d$ and number of samples $N$ grow as $d/N = c + o(1)$. For this setting, we derive data-dependent, instance specific expressions for the test error for both denoising and noisy-input regression, and study when overfitting the noise is benign, tempered or catastrophic. We show that the test error exhibits double descent under general distribution shift, providing insights for data augmentation and the role of noise as an implicit regularizer. We also perform experiments using real-life data, where we match the theoretical predictions with under 1\% MSE error for low-rank data.

cs.LG↗

arXiv2022

Stochastic enzyme kinetics and the quasi-steady-state reductions: Application of the slow scale linear noise approximation à la Fenichel

The linear noise approximation models the random fluctuations from the mean-field model of a chemical reaction that unfolds near the thermodynamic limit. Specifically, the fluctuations obey a linear Langevin equation up to order $Ω^{-1/2}$, where $Ω$ is the size of the chemical system (usually the volume). In the presence of disparate timescales, the linear noise approximation admits a quasi-steady-state reduction referred to as the \textit{slow scale} linear noise approximation (ssLNA). Curiously, the ssLNAs reported in the literature are slightly different. The differences in the reported ssLNAs lie at the mathematical heart of the derivation. In this work, we derive the ssLNA directly from geometric singular perturbation theory and explain the origin of the different ssLNAs in the literature. Moreover, we discuss the loss of normal hyperbolicity and we extend the ssLNA derived from geometric singular perturbation theory to a non-classical singularly perturbed problem. In so doing, we disprove a commonly-accepted qualifier for the validity of stochastic quasi-steady-state approximation of the Michaelis--Menten reaction mechanism.

physics.chem-ph↗