Related papers: Reconstructing an epigenetic landscape using a gen…
We propose a new procedure to monitor and forecast the onset of transitions in high dimensional complex systems. We describe our procedure by an application to the Tangled Nature model of evolutionary ecology. The quasi-stable…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
The quasipotential is a natural generalization of the concept of energy functions to non-equilibrium systems. In the analysis of rare events in stochastic dynamics, it plays a central role in characterizing the statistics of transition…
Networks (graphs) in psychology are often restricted to settings without interventions. Here we consider a framework borrowed from biology that involves multiple interventions from different contexts (observations and experiments) in a…
Modern methods for sampling rugged landscapes in state space mainly rely on knowledge of the relative probabilities of microstates, which is given by the Boltzmann factor for equilibrium systems. In principle, trajectory reweighting…
In this paper we study how to shape temporal pulses to switch a bistable system between its stable steady states. Our motivation for pulse-based control comes from applications in synthetic biology, where it is generally difficult to…
We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early-stage drug discovery, where such responses can offer insights into gene function and inform…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…
Darwinian evolution can be illustrated as an uphill walk in a landscape, where the surface consists of genotypes, the height coordinates represent fitness, and each step corresponds to a point mutation. Epistasis, roughly defined as the…
To provide a phenomenological theory for the various interesting transitions in restructuring networks we employ a statistical mechanical approach with detailed balance satisfied for the transitions between topological states. This enables…
Random Boolean networks have been used widely to explore aspects of gene regulatory networks. A modified form of the model through which to systematically explore the effects of increasing the number of gene states has previously been…
In this paper, we consider the problem of optimal exogenous control of gene regulatory networks. Our approach consists in adapting an established reinforcement learning algorithm called the fitted Q iteration. This algorithm infers the…
Nonequilibrium statistical mechanics exhibit a variety of complex phenomena far from equilibrium. It inherits challenges of equilibrium, including accurately describing the joint distribution of a large number of configurations, and also…
Noise caused by fluctuations at the molecular level is a fundamental part of intracellular processes. While the response of biological systems to noise has been studied extensively, there has been limited understanding of how to exploit it…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…
Quantifying the adaptive landscape in a given dynamical processes has been one of most important goals in theoretical biology. It can have immediate implications for many dynamical properties, such as robustness and plasticity. Based on…
We consider regression in which one predicts a response $Y$ with a set of predictors $X$ across different experiments or environments. This is a common setup in many data-driven scientific fields and we argue that statistical inference can…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical…