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The concept of nestedness, in particular for ecological and economical networks, has been introduced as a structural characteristic of real interacting systems. We suggest that the nestedness is in fact another way to express a mesoscale…
Many researchers have voiced their support towards Pearl's counterfactual theory of causation as a stepping stone for AI/ML research's ultimate goal of intelligent systems. As in any other growing subfield, patience seems to be a virtue…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
Graph-based signal processing techniques have become essential for handling data in non-Euclidean spaces. However, there is a growing awareness that these graph models might need to be expanded into `higher-order' domains to effectively…
The claim that life is an emergent phenomenon exhibiting novel properties and principles is often criticized for being in conflict with causal closure at the microscopic level. I argue that advances in cosmological theory suggesting an…
Cell complexes (CCs) are a higher-order network model deeply rooted in algebraic topology that has gained interest in signal processing and network science recently. However, while the processing of signals supported on CCs can be described…
The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…
Engineering methods are centered around traditional notions of decomposition and recomposition that rely on partitioning the inputs and outputs of components to allow for component-level properties to hold after their composition. In…
A major challenge of interdisciplinary description of complex system behaviour is whether real systems of higher complexity levels can be understood with at least the same degree of objective, "scientific" rigour and universality as…
The origin of cellular life can be described in terms of the transition from inorganic matter: solids, liquids and gases, to the emergence of cooperative assemblies of organic matter, DNA and proteins,capable of replication and metabolism.…
A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and…
Emergence and causality are two fundamental concepts for understanding complex systems. They are interconnected. On one hand, emergence refers to the phenomenon where macroscopic properties cannot be solely attributed to the cause of…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
If a concept is not well defined, there are grounds for its abuse. This is particularly true of complexity, an inherently interdisciplinary concept that has penetrated very different fields of intellectual activity from physics to…
The advent of molecular biology has led to the identification of definitive causative factors for a number of diseases, most of which are monogenic. Causes for most common diseases across the population, however, seem elusive and cannot be…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors.…
Lateral organization in the plane of the plasma membrane is an important driver of biological processes. The past dozen years have seen increasing experimental support for the notion that lipid organization plays an important role in…