Control of stochastic and induced switching in biophysical networks

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 to induce a desired cell state. Here we present a scalable, quantitative method based on the Freidlin-Wentzell action to predict and control noise-induced switching between different states in genetic networks that, conveniently, can also control transitions between stable states in the absence of noise. We apply this methodology to models of cell differentiation and show how predicted manipulations of tunable factors can induce lineage changes, and further utilize it to identify new candidate strategies for cancer therapy in a cell death pathway model. This framework offers a systems approach to identifying the key factors for rationally manipulating biophysical dynamics, and should also find use in controlling other classes of noisy complex networks.Comment: A ready-to-use code package implementing the method described here is available from the authors upon reques

Imitative Follower Deception in Stackelberg Games

Information uncertainty is one of the major challenges facing applications of game theory. In the context of Stackelberg games, various approaches have been proposed to deal with the leader's incomplete knowledge about the follower's payoffs, typically by gathering information from the leader's interaction with the follower. Unfortunately, these approaches rely crucially on the assumption that the follower will not strategically exploit this information asymmetry, i.e., the follower behaves truthfully during the interaction according to their actual payoffs. As we show in this paper, the follower may have strong incentives to deceitfully imitate the behavior of a different follower type and, in doing this, benefit significantly from inducing the leader into choosing a highly suboptimal strategy. This raises a fundamental question: how to design a leader strategy in the presence of a deceitful follower? To answer this question, we put forward a basic model of Stackelberg games with (imitative) follower deception and show that the leader is indeed able to reduce the loss due to follower deception with carefully designed policies. We then provide a systematic study of the problem of computing the optimal leader policy and draw a relatively complete picture of the complexity landscape; essentially matching positive and negative complexity results are provided for natural variants of the model. Our intractability results are in sharp contrast to the situation with no deception, where the leader's optimal strategy can be computed in polynomial time, and thus illustrate the intrinsic difficulty of handling follower deception. Through simulations we also examine the benefit of considering follower deception in randomly generated games

Roadmap on semiconductor-cell biointerfaces.

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world

Action and behavior: a free-energy formulation

We have previously tried to explain perceptual inference and learning under a free-energy principle that pursues Helmholtz’s agenda to understand the brain in terms of energy minimization. It is fairly easy to show that making inferences about the causes of sensory data can be cast as the minimization of a free-energy bound on the likelihood of sensory inputs, given an internal model of how they were caused. In this article, we consider what would happen if the data themselves were sampled to minimize this bound. It transpires that the ensuing active sampling or inference is mandated by ergodic arguments based on the very existence of adaptive agents. Furthermore, it accounts for many aspects of motor behavior; from retinal stabilization to goal-seeking. In particular, it suggests that motor control can be understood as fulfilling prior expectations about proprioceptive sensations. This formulation can explain why adaptive behavior emerges in biological agents and suggests a simple alternative to optimal control theory. We illustrate these points using simulations of oculomotor control and then apply to same principles to cued and goal-directed movements. In short, the free-energy formulation may provide an alternative perspective on the motor control that places it in an intimate relationship with perception

Near-Optimal Deviation-Proof Medium Access Control Designs in Wireless Networks

Distributed medium access control (MAC) protocols are essential for the proliferation of low cost, decentralized wireless local area networks (WLANs). Most MAC protocols are designed with the presumption that nodes comply with prescribed rules. However, selfish nodes have natural motives to manipulate protocols in order to improve their own performance. This often degrades the performance of other nodes as well as that of the overall system. In this work, we propose a class of protocols that limit the performance gain which nodes can obtain through selfish manipulation while incurring only a small efficiency loss. The proposed protocols are based on the idea of a review strategy, with which nodes collect signals about the actions of other nodes over a period of time, use a statistical test to infer whether or not other nodes are following the prescribed protocol, and trigger a punishment if a departure from the protocol is perceived. We consider the cases of private and public signals and provide analytical and numerical results to demonstrate the properties of the proposed protocols.Comment: 14 double-column pages, submitted to ACM/IEEE Trans Networkin