相关论文: Discriminatory proofreading regimes in non-equilib…

We propose a novel framework for structured prediction via adversarial learning. Existing adversarial learning methods involve two separate networks, i.e., the structured prediction models and the discriminative models, in the training. The…

Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…

Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…

A hallmark of living systems is the ability to employ a common set of versatile building blocks that can self-organize into a multitude of different structures, in a way that can be controlled with minimal cost. This capability can only be…

Many complex systems share two characteristics: 1) they are stochastic in nature, and 2) they are characterized by a large number of factors. At the same time, various natural complex systems appear to have two types of intertwined…

Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task, examples include ecosystems, financial markets, complex diseases, etc. In this paper, we…

Many natural systems undergo critical transitions, i.e. sudden shifts from one dynamical regime to another. In the climate system, the atmospheric boundary layer can experience sudden transitions between fully turbulent states and…

The equilibrium behavior of binary mixtures can be understood through the competition of energy scales, which classifies their corresponding phase diagrams into distinct topological regimes (Types I-IV). However, in many soft-matter…

Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and…

We introduce and solve a general model of dynamic response under external perturbations. This model captures a wide range of systems out of equilibrium including Ising models of physical systems, social opinions, and population genetics.…

Non-equilibrium states of quantum systems in contact with thermal baths help telling environments with different temperatures or different statistics apart. We extend these studies to a more generic problem that consists in discriminating…

Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…

The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…

In the task of discriminating between nonorthogonal quantum states from multiple copies, the key parameters are the error probability and the resources (number of copies) used. Previous studies have considered the task of minimizing the…

First order phase transitions proceed via nucleation. The rate of nucleation varies exponentially with the free-energy barrier to nucleation, and so is highly sensitive to variations in this barrier. In practice, very few systems are…

Networked systems that occur in various domains, such as the power grid, the brain, and opinion networks, are known to obey conservation laws. For instance, electric networks obey Kirchoff's laws, and social networks display opinion…

Complex systems can convert energy imparted by nonequilibrium forces to regulate how quickly they transition between long lived states. While such behavior is ubiquitous in natural and synthetic systems, currently there is no general…

External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical…

Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems,…

The persistence of biodiversity of species is a challenging proposition in ecological communities in the face of Darwinian selection. The present article investigates beyond the pairwise competitive interactions and provides a novel…