Information theoretic approach to interactive learning

The principles of statistical mechanics and information theory play an important role in learning and have inspired both theory and the design of numerous machine learning algorithms. The new aspect in this paper is a focus on integrating feedback from the learner. A quantitative approach to interactive learning and adaptive behavior is proposed, integrating model- and decision-making into one theoretical framework. This paper follows simple principles by requiring that the observer's world model and action policy should result in maximal predictive power at minimal complexity. Classes of optimal action policies and of optimal models are derived from an objective function that reflects this trade-off between prediction and complexity. The resulting optimal models then summarize, at different levels of abstraction, the process's causal organization in the presence of the learner's actions. A fundamental consequence of the proposed principle is that the learner's optimal action policies balance exploration and control as an emerging property. Interestingly, the explorative component is present in the absence of policy randomness, i.e. in the optimal deterministic behavior. This is a direct result of requiring maximal predictive power in the presence of feedback.Comment: 6 page

The thermodynamics of prediction

A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations, and a fraction of this information is predictive of future ones. The remaining nonpredictive information reflects model complexity that does not improve predictive power, and thus represents the ineffectiveness of the model. We expose the fundamental equivalence between this model inefficiency and thermodynamic inefficiency, measured by dissipation. Our results hold arbitrarily far from thermodynamic equilibrium and are applicable to a wide range of systems, including biomolecular machines. They highlight a profound connection between the effective use of information and efficient thermodynamic operation: any system constructed to keep memory about its environment and to operate with maximal energetic efficiency has to be predictive.Comment: 5 pages, 1 figur

Network information and connected correlations

Entropy and information provide natural measures of correlation among elements in a network. We construct here the information theoretic analog of connected correlation functions: irreducible $N$--point correlation is measured by a decrease in entropy for the joint distribution of $N$ variables relative to the maximum entropy allowed by all the observed $N-1$ variable distributions. We calculate the ``connected information'' terms for several examples, and show that it also enables the decomposition of the information that is carried by a population of elements about an outside source.Comment: 4 pages, 3 figure

Second law, entropy production, and reversibility in thermodynamics of information

We present a pedagogical review of the fundamental concepts in thermodynamics of information, by focusing on the second law of thermodynamics and the entropy production. Especially, we discuss the relationship among thermodynamic reversibility, logical reversibility, and heat emission in the context of the Landauer principle and clarify that these three concepts are fundamentally distinct to each other. We also discuss thermodynamics of measurement and feedback control by Maxwell's demon. We clarify that the demon and the second law are indeed consistent in the measurement and the feedback processes individually, by including the mutual information to the entropy production.Comment: 43 pages, 10 figures. As a chapter of: G. Snider et al. (eds.), "Energy Limits in Computation: A Review of Landauer's Principle, Theory and Experiments

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Quantifying Endangerment Value: a Promising Tool to Support Curation Decisions

Botanic garden collections are increasingly seeking to quantify and improve the value of their collections for science, horticulture, conservation and other uses. Quantifying the value of a collection depends on the mission of the institution. Many botanic gardens are prioritising the conservation of rare and threatened species towards preventing plant extinctions. In doing so, botanic gardens must make decisions about which plants should remain, be replaced or be added to their collections, and how to allocate staff and resources to care for individual plants, while considering funding and space limits. So, how can curators make the biggest impact towards conserving plant species? We present a promising method to quantitatively assess which plant species might be higher or lower conservation priority to an ex situ collection, using what we term ‘endangerment value’ – the value of collections for preventing plant extinction. We apply this method to four genera of high importance at The Morton Arboretum and showcase advantages of this approach as well as pitfalls. We found this method useful for priority setting, but note that the inclusion and exclusion of different data and how they are weighted impacts the ranking of priority species – an important lesson for any prioritisation method. We hope this method will inspire and help other botanic gardens to evaluate their current and future endangerment value and set priorities for maintaining and growing ex situ collections globally

Experimental and Theoretical Study of the Kinetics and Mechanism of the Reaction of OH Radicals with Dimethyl Ether

The reaction of OH with dimethyl ether (CH₃OCH₃) has been studied from 195 to 850 K using laser flash photolysis coupled to laser induced fluorescence detection of OH radicals. The rate coefficient from this work can be parametrized by the modified Arrhenius expression <i>k</i> = (1.23 ± 0.46) × 10^–12 (<i>T</i>/298)^2.05±0.23 exp((257 ± 107)/<i>T</i>) cm³ molecule^–1 s^–1. Including other recent literature data (923–1423 K) gives a modified Arrhenius expression of <i>k</i>₁ = (1.54 ± 0.48) × 10^–12 (<i>T</i>/298 K)^1.89±0.16 exp((184 ± 112)/<i>T</i>) cm³ molecule^–1 s^–1 over the range 195–1423 K. Various isotopomeric combinations of the reaction have also been investigated with deuteration of dimethyl ether leading to a normal isotope effect. Deuteration of the hydroxyl group leads to a small inverse isotope effect. To gain insight into the reaction mechanisms and to support the experimental work, theoretical studies have also been undertaken calculating the energies and structures of the transition states and complexes using high level ab initio methods. The calculations also identify pre- and post-reaction complexes. The calculations show that the pre-reaction complex has a binding energy of ∼22 kJ mol^–1. Stabilization into the complex could influence the kinetics of the reaction, especially at low temperatures (<300 K), but there is no direct evidence of this occurring under the experimental conditions of this study. The experimental data have been modeled using the recently developed MESMER (master equation solver for multi energy well reactions) code; the calculated rate coefficients lie within 16% of the experimental values over the temperature range 200–1400 K with a model based on a single transition state. This model also qualitatively reproduces the observed isotope effects, agreeing closely above ∼600 K but overestimating them at low temperatures. The low temperature differences may derive from an inadequate treatment of tunnelling and/or from an enhanced role of an outer transition state leading to the pre-reaction complex