arXiv subjects

Alexander S. Moffett

Publications and source records attributed to Alexander S. Moffett.

5 recordsLinked to original sources

arXiv2025

Kelly Bets and Single-Letter Codes: Optimal Information Processing in Natural Systems

In an information-processing investment game, such as the growth of a population of organisms in a changing environment, Kelly betting maximizes the expected log rate of growth. In this paper, we show that Kelly bets are closely related to optimal single-letter codes (i.e., they can achieve the rate-distortion bound with equality). Thus, natural information processing systems with limited computational resources can achieve information-theoretically optimal performance. We show that the rate-distortion tradeoff for an investment game has a simple linear bound, and that the bound is achievable at the point where the corresponding single-letter code is optimal. This interpretation has two interesting consequences. First, we show that increasing the organism's portfolio of potential strategies can lead to optimal performance over a continuous range of channels, even if the strategy portfolio is fixed. Second, we show that increasing an organism's number of phenotypes (i.e., its number of possible behaviours in response to the environment) can lead to higher growth rate, and we give conditions under which this occurs. Examples illustrating the results in simplified biological scenarios are presented.

cs.IT↗

arXiv2021

Minimal informational requirements for fitness

The existing concept of the "fitness value of information" provides a theoretical upper bound on the fitness advantage of using information concerning a fluctuating environment. Using concepts from rate-distortion theory, we develop a theoretical framework to answer a different pair of questions: What is the minimal amount of information needed for a population to achieve a certain growth rate? What is the minimal amount of information gain needed for one sub-population to achieve a certain average selection coefficient over another? We introduce a correspondence between fitness and distortion and solve for the rate-distortion functions of several systems using analytical and numerical methods. Because accurate information processing is energetically costly, our approach provides a theoretical basis for understanding evolutionary "design principles" underlying information-cost trade-offs.

q-bio.PE↗

arXiv2021

A factor graph EM algorithm for inference of kinetic microstates from patch clamp measurements

We derive a factor graph EM (FGEM) algorithm, a technique that permits combined parameter estimation and statistical inference, to determine hidden kinetic microstates from patch clamp measurements. Using the cystic fibrosis transmembrane conductance regulator (CFTR) and nicotinic acetylcholine receptor (nAChR) as examples, we perform {\em Monte Carlo} simulations to demonstrate the performance of the algorithm. We show that the performance, measured in terms of the probability of estimation error, approaches the theoretical performance limit of maximum {\em a posteriori} estimation. Moreover, the algorithm provides a reliability score for its estimates, and we demonstrate that the score can be used to further improve the performance of estimation. We use the algorithm to estimate hidden kinetic states in lab-obtained CFTR single channel patch clamp traces.

q-bio.QM↗

arXiv2020

The Fitness Value of Information with Delayed Phenotype Switching: Optimal Performance with Imperfect Sensing

The ability of organisms to accurately sense their environment and respond accordingly is critical for evolutionary success. However, exactly how the sensory ability influences fitness is a topic of active research, while the necessity of a time delay between when unreliable environmental cues are sensed and when organisms can mount a response has yet to be explored at any length. Accounting for this delay in phenotype response in models of population growth, we find that a critical error probability can exist under certain environmental conditions: an organism with a sensory system with any error probability less than the critical value can achieve the same long-term growth rate as an organism with a perfect sensing system. We also observe a trade off between the evolutionary value of sensory information and robustness to error, mediated by the rate at which the phenotype distribution relaxes to steady-state. The existence of the critical error probability could have several important evolutionary consequences, primarily that sensory systems operating at the non-zero critical error probability may be evolutionarily optimal.

q-bio.PE↗

arXiv2017

On the transferability of time-lagged independent components between similar molecular dynamics systems

Dimensionality reduction techniques have found great success in a wide range of fields requiring analysis of high-dimensional datasets. Time-lagged independent components analysis (TICA), which finds independent components (TICs) with maximal autocorrelation, is often applied to atomistic biomolecular simulations, where the full molecular configuration can be projected onto only a few TICs describing the slowest modes of motion. Recently, Sultan and Pande have proposed the use of TICs as collective variables for enhanced sampling. However, it is unclear what the best strategy for estimating the TICs of a system is a priori. In order to evaluate the utility of TICs calculated on one system to describe the slow dynamics of similar systems, we develop a methodology for measuring the transferability of TICs and apply it to a wide range of systems. We find that transferred TICs can approximate the slowest dynamics of some systems surprisingly well, while failing to transfer between other sets of systems, highlighting the inherent difficulties of predicting TIC transferability. Additionally, we use two dimensional Brownian dynamics simulations on similar potential surfaces to gain insight into the relationship between TIC transferability and potential surface changes.

q-bio.BM↗