Udesh Habaraduwa

Udesh Habaraduwa, Andrei Lixandru

The advancement of human healthspan and bioengineering relies heavily on predicting the behavior of complex biological systems. While high-throughput multiomics data is becoming increasingly abundant, converting this data into actionable predictive models remains a bottleneck. High-capacity, datadriven simulation systems are critical in this landscape; unlike classical mechanistic models restricted by prior knowledge, these architectures can infer latent interactions directly from observational data, allowing for the simulation of temporal trajectories and the anticipation of downstream intervention effects in personalized medicine and synthetic biology. To address this challenge, we introduce Neural Ordinary Differential Equations (NODEs) as a dynamic framework for learning the complex interplay between the proteome and metabolome. We applied this framework to time-series data derived from engineered Escherichia coli strains, modeling the continuous dynamics of metabolic pathways. The proposed NODE architecture demonstrates superior performance in capturing system dynamics compared to traditional machine learning pipelines. Our results show a greater than 90% improvement in root mean squared error over baselines across both Limonene (up to 94.38% improvement) and Isopentenol (up to 97.65% improvement) pathway datasets. Furthermore, the NODE models demonstrated a 1000x acceleration in inference time, establishing them as a scalable, high-fidelity tool for the next generation of metabolic engineering and biological discovery.

Udesh Habaraduwa

This paper discusses the limitations of machine learning (ML), particularly deep artificial neural networks (ANNs), which are effective at approximating complex functions but often lack transparency and explanatory power. It highlights the `problem of induction' : the philosophical issue that past observations may not necessarily predict future events, a challenge that ML models face when encountering new, unseen data. The paper argues for the importance of not just making predictions but also providing good explanations, a feature that current models often fail to deliver. It suggests that for AI to progress, we must seek models that offer insights and explanations, not just predictions.