scholarly journals On the Need for Mechanistic Models in Computational Genomics and Metagenomics

2013 ◽  
Vol 5 (10) ◽  
pp. 2008-2018 ◽  
Author(s):  
David A. Liberles ◽  
Ashley I. Teufel ◽  
Liang Liu ◽  
Tanja Stadler
2021 ◽  
Vol 35 (8) ◽  
pp. 6765-6775
Author(s):  
Rebecca E. Harmon ◽  
Gorugantu SriBala ◽  
Linda J. Broadbelt ◽  
Alan K. Burnham

2021 ◽  
Vol 69 (3) ◽  
Author(s):  
Michael Vigdorowitsch ◽  
Valery V. Ostrikov ◽  
Sergey N. Sazonov ◽  
Valentin V. Safonov ◽  
Vladimir I. Orobinsky

2021 ◽  
Vol 134 ◽  
pp. 171-180
Author(s):  
Nariman Shahhosseini ◽  
Christina Frederick ◽  
Marie-Pierre Letourneau-Montminy ◽  
Benoit-Biancamano Marie-Odile ◽  
Gary P. Kobinger ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jared L. Callaham ◽  
James V. Koch ◽  
Bingni W. Brunton ◽  
J. Nathan Kutz ◽  
Steven L. Brunton

AbstractThroughout the history of science, physics-based modeling has relied on judiciously approximating observed dynamics as a balance between a few dominant processes. However, this traditional approach is mathematically cumbersome and only applies in asymptotic regimes where there is a strict separation of scales in the physics. Here, we automate and generalize this approach to non-asymptotic regimes by introducing the idea of an equation space, in which different local balances appear as distinct subspace clusters. Unsupervised learning can then automatically identify regions where groups of terms may be neglected. We show that our data-driven balance models successfully delineate dominant balance physics in a much richer class of systems. In particular, this approach uncovers key mechanistic models in turbulence, combustion, nonlinear optics, geophysical fluids, and neuroscience.


Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 755
Author(s):  
Eric B. Searle ◽  
F. Wayne Bell ◽  
Guy R. Larocque ◽  
Mathieu Fortin ◽  
Jennifer Dacosta ◽  
...  

In the past two decades, forest management has undergone major paradigm shifts that are challenging the current forest modelling architecture. New silvicultural systems, guidelines for natural disturbance emulation, a desire to enhance structural complexity, major advances in successional theory, and climate change have all highlighted the limitations of current empirical models in covering this range of conditions. Mechanistic models, which focus on modelling underlying ecological processes rather than specific forest conditions, have the potential to meet these new paradigm shifts in a consistent framework, thereby streamlining the planning process. Here we use the NEBIE (a silvicultural intervention scale that classifies management intensities as natural, extensive, basic, intensive, and elite) plot network, from across Ontario, Canada, to examine the applicability of a mechanistic model, ZELIG-CFS (a version of the ZELIG tree growth model developed by the Canadian Forest Service), to simulate yields and species compositions. As silvicultural intensity increased, overall yield generally increased. Species compositions met the desired outcomes when specific silvicultural treatments were implemented and otherwise generally moved from more shade-intolerant to more shade-tolerant species through time. Our results indicated that a mechanistic model can simulate complex stands across a range of forest types and silvicultural systems while accounting for climate change. Finally, we highlight the need to improve the modelling of regeneration processes in ZELIG-CFS to better represent regeneration dynamics in plantations. While fine-tuning is needed, mechanistic models present an option to incorporate adaptive complexity into modelling forest management outcomes.


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