16,502 research outputs found
Data-driven discovery of coordinates and governing equations
The discovery of governing equations from scientific data has the potential
to transform data-rich fields that lack well-characterized quantitative
descriptions. Advances in sparse regression are currently enabling the
tractable identification of both the structure and parameters of a nonlinear
dynamical system from data. The resulting models have the fewest terms
necessary to describe the dynamics, balancing model complexity with descriptive
ability, and thus promoting interpretability and generalizability. This
provides an algorithmic approach to Occam's razor for model discovery. However,
this approach fundamentally relies on an effective coordinate system in which
the dynamics have a simple representation. In this work, we design a custom
autoencoder to discover a coordinate transformation into a reduced space where
the dynamics may be sparsely represented. Thus, we simultaneously learn the
governing equations and the associated coordinate system. We demonstrate this
approach on several example high-dimensional dynamical systems with
low-dimensional behavior. The resulting modeling framework combines the
strengths of deep neural networks for flexible representation and sparse
identification of nonlinear dynamics (SINDy) for parsimonious models. It is the
first method of its kind to place the discovery of coordinates and models on an
equal footing.Comment: 25 pages, 6 figures; added acknowledgment
Mechanism Deduction from Noisy Chemical Reaction Networks
We introduce KiNetX, a fully automated meta-algorithm for the kinetic
analysis of complex chemical reaction networks derived from semi-accurate but
efficient electronic structure calculations. It is designed to (i) accelerate
the automated exploration of such networks, and (ii) cope with model-inherent
errors in electronic structure calculations on elementary reaction steps. We
developed and implemented KiNetX to possess three features. First, KiNetX
evaluates the kinetic relevance of every species in a (yet incomplete) reaction
network to confine the search for new elementary reaction steps only to those
species that are considered possibly relevant. Second, KiNetX identifies and
eliminates all kinetically irrelevant species and elementary reactions to
reduce a complex network graph to a comprehensible mechanism. Third, KiNetX
estimates the sensitivity of species concentrations toward changes in
individual rate constants (derived from relative free energies), which allows
us to systematically select the most efficient electronic structure model for
each elementary reaction given a predefined accuracy. The novelty of KiNetX
consists in the rigorous propagation of correlated free-energy uncertainty
through all steps of our kinetic analyis. To examine the performance of KiNetX,
we developed AutoNetGen. It semirandomly generates chemistry-mimicking reaction
networks by encoding chemical logic into their underlying graph structure.
AutoNetGen allows us to consider a vast number of distinct chemistry-like
scenarios and, hence, to discuss assess the importance of rigorous uncertainty
propagation in a statistical context. Our results reveal that KiNetX reliably
supports the deduction of product ratios, dominant reaction pathways, and
possibly other network properties from semi-accurate electronic structure data.Comment: 36 pages, 4 figures, 2 table
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