17 papers · ranked by Valyu relevance
Bryan C. Daniels, Ilya Nemenman
Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the…
Usha Kadiyala, David Sprinzak, Nicholas A. M. Monk, Shannon E. Taylor + 6 more
'Shannon E. Taylor' 'Berta Verd' 'Katharina F. Sonnen' 'Lauren Moon' 'Adrienne H. K. Roeder' 'Ruben Perez-Carrasco' 'Pau Formosa-Jordan'] Title: ABSTRACT Developmental biology seeks to unravel the intricate regulatory mechanisms orchestrating the transformation of a single cell into a complex, multicellular organism.…
Bryan C. Daniels, Ilya Nemenman, Magnus Rattray
The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the S-system formalism, which is a sensible representation of nonlinear mass-action…
Lois A. Gelfand, Sally Engelhart
Dynamical Systems Theory (DST) has generated interest and excitement in psychological research, as demonstrated by the recent statement, “…the dynamical perspective has emerged as a primary paradigm for the investigation of psychological processes at different levels of personal and social reality” (Vallacher et al.…
Gemma Massonis, Alejandro F. Villaverde, Julio R. Banga, Marc R Birtwistle
'Marc R Birtwistle'] Mechanistic dynamical models allow us to study the behavior of complex biological systems. They can provide an objective and quantitative understanding that would be difficult to achieve through other means. However, the systematic development of these models is a non-trivial exercise and an open…
Xiaojun Wu, MeiLu McDermott, Adam L MacLean, Mark Alber
Biological systems exhibit complex dynamics that differential equations can often adeptly represent. Ordinary differential equation models are widespread; until recently their construction has required extensive prior knowledge of the system. Machine learning methods offer alternative means of model construction…
Mengman Wei, Qian Peng
Human behavioral and mental health outcomes arise from interactions among genetic, environmental, and neurobiological systems. Existing frameworks often model these components jointly, but many treat variables independently or use static representations. This limits their ability to capture system-level dynamics and…
William Sulis
The full range of biopsychosocial complexity is mind-boggling, spanning a vast range of spatiotemporal scales with complicated vertical, horizontal, and diagonal feedback interactions between contributing systems. It is unlikely that such complexity can be dealt with by a single model. One approach is to focus on a…
Nestor V. Torres, Guido Santos
In this communication, we introduce a general framework and discussion on the role of models and the modeling process in the field of biosciences. The objective is to sum up the common procedures during the formalization and analysis of a biological problem from the perspective of Systems Biology, which approaches the…
Daniel V. Holt, Magda Osman
Much of human decision making occurs in dynamic situations where decision makers have to control a number of interrelated elements (dynamic systems control). Although in recent years progress has been made toward assessing individual differences in control performance, the cognitive processes underlying exploration and…
Tatiana Baumuratova, Simona Dobre, Thierry Bastogne, Thomas Sauter + 1 more
'Gennady Cymbalyuk'] Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several…
Ezio Bartocci, Pietro Lió, Marta Zofia Kwiatkowska
As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable…
Benjamin Engelhardt, Holger Frőhlich, Maik Kschischo
Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open.…
Maximilien Cosme, Colin Thomas, Cédric Gaucherel, Tomas Veloz
Ecosystem modeling is a complex and multidisciplinary modeling problem which emerged in the 1950s. It takes advantage of the computational turn in sciences to better understand anthropogenic impacts and improve ecosystem management. For that purpose, ecosystem simulation models based on difference or differential…
Malgorzata Kardynska, Daria Kogut, Marcin Pacholczyk, Jaroslaw Smieja
'Jaroslaw Smieja'] Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract…
R. Bardini, G. Politano, A. Benso, S. Di Carlo
During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an…
Rachel A. Hillmer, Heather L. True-Krob
A mathematical model is a set of relationships, usually written as equations, that describe how the parts of the system respond to system inputs, regulate each other, and control system output. Why do we need math to do this? Math is just formalized logic, so in theory we could just use descriptive sentences. But for…