The architecture of information processing in biological systems

Biological systems process information at different scales and adapt to their changing environment. Informed both by experimental observations and theoretical constraints, we propose a chemical model for sensing that incorporates energy consumption, information storage, and negative feedback. We show that a biochemical architecture enclosing these minimal mechanisms leads to the emergence of dynamical memory and adaptation. Crucially, adaptation is associated with both an increase in the mutual information between external and internal variables and a reduction of dissipation of the internal chemical processes. By simultaneously minimizing energy consumption and maximizing information, we find that far-from-equilibrium sensing dominates in the low-noise regime. Our results, in principle, can be declined at different biological scales. We employ our model to shed light on large-scale neural adaptation in zebrafish larvae under repeated visual stimulation. We find striking similarities between predicted and observed behaviors, capturing the emergent adaptation of neural response. Our framework draws a path toward the unraveling of the essential ingredients that connect information processing, adaptation, and memory in biological systems

Multi-hop Diffusion LMS for Energy-constrained Distributed Estimation

We propose a multi-hop diffusion strategy for a sensor network to perform distributed least mean-squares (LMS) estimation under local and network-wide energy constraints. At each iteration of the strategy, each node can combine intermediate parameter estimates from nodes other than its physical neighbors via a multi-hop relay path. We propose a rule to select combination weights for the multi-hop neighbors, which can balance between the transient and the steady-state network mean-square deviations (MSDs). We study two classes of networks: simple networks with a unique transmission path from one node to another, and arbitrary networks utilizing diffusion consultations over at most two hops. We propose a method to optimize each node's information neighborhood subject to local energy budgets and a network-wide energy budget for each diffusion iteration. This optimization requires the network topology, and the noise and data variance profiles of each node, and is performed offline before the diffusion process. In addition, we develop a fully distributed and adaptive algorithm that approximately optimizes the information neighborhood of each node with only local energy budget constraints in the case where diffusion consultations are performed over at most a predefined number of hops. Numerical results suggest that our proposed multi-hop diffusion strategy achieves the same steady-state MSD as the existing one-hop adapt-then-combine diffusion algorithm but with a lower energy budget.Comment: 14 pages, 12 figures. Submitted for publicatio

Joint Energy Efficient and QoS-aware Path Allocation and VNF Placement for Service Function Chaining

Service Function Chaining (SFC) allows the forwarding of a traffic flow along a chain of Virtual Network Functions (VNFs, e.g., IDS, firewall, and NAT). Software Defined Networking (SDN) solutions can be used to support SFC reducing the management complexity and the operational costs. One of the most critical issues for the service and network providers is the reduction of energy consumption, which should be achieved without impact to the quality of services. In this paper, we propose a novel resource (re)allocation architecture which enables energy-aware SFC for SDN-based networks. To this end, we model the problems of VNF placement, allocation of VNFs to flows, and flow routing as optimization problems. Thereafter, heuristic algorithms are proposed for the different optimization problems, in order find near-optimal solutions in acceptable times. The performance of the proposed algorithms are numerically evaluated over a real-world topology and various network traffic patterns. The results confirm that the proposed heuristic algorithms provide near optimal solutions while their execution time is applicable for real-life networks.Comment: Extended version of submitted paper - v7 - July 201

Bounded Rational Decision-Making in Changing Environments

A perfectly rational decision-maker chooses the best action with the highest utility gain from a set of possible actions. The optimality principles that describe such decision processes do not take into account the computational costs of finding the optimal action. Bounded rational decision-making addresses this problem by specifically trading off information-processing costs and expected utility. Interestingly, a similar trade-off between energy and entropy arises when describing changes in thermodynamic systems. This similarity has been recently used to describe bounded rational agents. Crucially, this framework assumes that the environment does not change while the decision-maker is computing the optimal policy. When this requirement is not fulfilled, the decision-maker will suffer inefficiencies in utility, that arise because the current policy is optimal for an environment in the past. Here we borrow concepts from non-equilibrium thermodynamics to quantify these inefficiencies and illustrate with simulations its relationship with computational resources.Comment: 9 pages, 2 figures, NIPS 2013 Workshop on Planning with Information Constraint