Cancers are complex dynamical systems. They remain the leading cause of disease-related pediatric mortality in North America. To overcome this burden, we must decipher the state-space attractor dynamics of gene expression patterns and protein oscillations orchestrated by cancer stemness networks. The review provides an overview of dynamical systems theory to steer cancer research in pattern science. While most of our current tools in network medicine rely on statistical correlation methods, causality inference remains primitively developed. As such, a survey of attractor reconstruction methods and machine algorithms for the detection of causal structures applicable in experimentally derived time series cancer datasets is presented. A toolbox of complex systems approaches are discussed for reconstructing the signaling state space of cancer networks, interpreting causal relationships in their time series gene expression patterns, and assisting clinical decision making in computational oncology. As a proof of concept, the applicability of some algorithms are demonstrated on pediatric brain cancer datasets and the requirement of their time series analysis is highlighted. ll

No abstract

Cancers remain the leading cause of disease-related pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system. Herein, a tumor and its heterogeneous phenotypes are discussed as dynamical systems having multiple strange attractors. Machine learning, network science and algorithmic information dynamics are discussed as current tools for cancer network reconstruction. Deep learning architectures and computational fluid models are proposed for better forecasting gene expression patterns in cancer ecosystems. Cancer cell decision-making is investigated within the framework of complex systems and complexity theory.

Cancers are complex, adaptive ecosystems. It remains the lead cause of disease-related, pediatric death in North America. The emerging field of complexity science has redefined cancer as a computational system with intractable, algorithmic complexity. Herein, a tumor and its heterogeneous phenotypes are discussed as dynamical systems having multiple, chaotic attractors. Machine learning, Network science and information theory are discussed as current tools for cancer network reconstruction. The fluid dynamics of cancer-cell fate transitions and chemical pattern formation are briefly reviewed. Deep Learning architectures, delay-embedding algorithms and computational fluid models are proposed for better forecasting gene expression patterns in cancer ecosystems. Cancer cell decision-making is investigated within the framework of complexity theory.

Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires the integration of information dynamics across multidimensional spatiotemporal scales, including genetic, transcriptional, metabolic, proteomic, epigenetic, and multi-cellular networks. However, the time-series analysis of these complex networks remains vastly absent in cancer research. With longitudinal screening and time-series analysis of cellular dynamics, universally observed causal patterns pertaining to dynamical systems, may self-organize in the signaling or gene expression state-space of cancer triggering processes. A class of these patterns, strange attractors, may be mathematical biomarkers of cancer progression. The emergence of intracellular chaos and chaotic cell population dynamics remains a new paradigm in systems medicine. As such, chaotic and complex dynamics are discussed as mathematical hallmarks of cancer cell fate dynamics herein. Given the assumption that time-resolved single-cell datasets are made available, a survey of interdisciplinary tools and algorithms from complexity theory, are hereby reviewed to investigate critical phenomena and chaotic dynamics in cancer ecosystems. To conclude, the perspective cultivates an intuition for computational systems oncology in terms of nonlinear dynamics, information theory, inverse problems, and complexity. We highlight the limitations we see in the area of statistical machine learning but the opportunity at combining it with the symbolic computational power offered by the mathematical tools explored.

No abstract

No abstract

No abstract