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PubMed2001

Information theory in ecology.

The application of information theory (IT) to ecology has occurred along two separate lines: (1) it has been used to quantify the distribution of stocks and numbers of organisms; and (2) it has been employed to quantify the pattern of interactions of trophic processes. By and large, the first endeavor has resulted in relatively few insights into ecosystem dynamics and has generated much ambiguity and disappointment, so that most ecologists remain highly skeptical about the advisability of applying IT to ecology. By contrast, the second, and less well-known application has shed light on the possibility that ecosystem behavior is the most palpable example of a purely natural 'infodynamics' that transcends classical dynamics, but remains well within the realm of quantitative description.

Ecology↗
PubMed1996

Emergent information. Towards a unified information theory.

This paper proposes the restoration of information theory by means of a philosophy of evolutionary systems. What this philosophy implies for the conception of information may be called a multi-stage model, comprising both the history and the ordering of information processing by real-world systems. Such a unifying information concept may assist suitable research in the coming field of information science.

Biological Evolution↗
PubMed1990

Quantitative densitometry from the point of view of information theory.

The process of quantitative densitometry is analyzed with methods developed in information theory. It is shown that the steps involved in densitometry, e.g. gel staining, mechanical, optical and electronic processing, as well as all the steps of data processing, can be viewed as communication channels. The factors affecting both the relevant and irrelevant part of the total information passed through these channels are discussed in the consistent frame provided by information theory. This view leads to a unifying context for analyzing the performance of quantitative densitometers.

Densitometry↗
PubMed2001

Prediction of protein surface accessibility with information theory.

A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in various states defined by their different thresholds. Prediction is achieved by the application of information obtained from a single amino acid position or pair-information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than results from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60 %, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case.

Algorithms↗
PubMed2006

Bayesian and information theory analysis of MAS sideband patterns in spin 1/2 systems.

Bayesian statistics and information theory are used to analyze the reliability of extracting chemical shift parameters from spinning sideband patterns of spin 1/2 systems. Efficient code has been written to calculate the two-dimensional posterior probability as a function of the chemical shift anisotropy, delta, and the asymmetry parameter, eta, given the sideband intensities and the signal-to-noise ratio. This method has the advantage of assuming only that the noise in the sideband intensities is distributed as a Gaussian. It assumes nothing about the distribution of the values of parameters delta and eta, which are shown in some cases to be highly non-Gaussian. The utility of Bayesian analysis is demonstrated on 1D slow-spinning MAS spectra and on sideband patterns extracted from 2D PASS spectra. Previous investigations have shown that there is an optimal range of spinning frequencies for determining delta. In this study, information theory is used to determine the signal-to-noise ratio dependence of the entropy in delta, eta, and total entropy in spinning sideband spectra. The entropy is a measure of the information content of a probability distribution. When the entropy is zero, there is perfect information on a system, while if it is infinite, there is no information on the system. It is found that for all values of eta and for signal-to-noise ratios in the range 50-1000, an entropy minimum in nudelta/nur occurs for values 1.5<or=nudelta/nur<or=3. In the same range of signal-to-noise ratios, the entropy in eta is a monotonically decreasing function of nudelta/nur. The global information content of a spinning sideband pattern (i.e., the total entropy) is dependent on the signal-to-noise ratio and has an optimal value at nudelta/nur approximately 2 at a signal-to-noise ratio of 50 and increasing to approximately 2.5 for signal-to-noise ratios of 1000. Finally, the increase of information in a sideband pattern as a function of the number of sidebands used in the analysis is examined. Most of the information about delta and eta is contained in the five central sidebands; i.e., sidebands -2 to 2.

Algorithms↗
PubMed1994

[Reflexions on the usage of information theory in biology].

For living beings, information is as fundamental as matter or energy. In this paper we show: a) inadequacies of quantitative theories of information, b) how a qualitative analysis leads to a classification of information systems and to a modelling of intercellular communication. From a quantitative point of view, the application in biology of information theories borrowed from communication techniques proved to be disappointing. These theories ignore deliberately the significance of messages, and do not give any definition of information. They refer to quantities, based upon arbitrarily defined probabilistic events. Probability is subjective. The receiver of the message needs to have 'meta-knowledge' of the events. The quantity of information depends on language, coding, and arbitrary definition of disorder. The suggested objectivity is fallacious. In common language, the word 'information' is synonymous with knowledge of order. Following common sense a message (letters, coded signals, etc.) is information just in case it is interpretable, i.e. if it fits to a previously acquired meaning (the words of an available language, etc.). The consequence is that calculation of quantities in the sense of Shannon can be used for transmissions, but it is itself meaningless (has no significance). In linguistics and semantics, information is composed of a 'signifier', a physical medium (letters, coded signals, etc.), and a 'signified' or significance. The nature of information is complex. The laws of linguistics and semantics are valid not only at the human, organismic level, but also at the cellular and molecular level. The physiology of sensations gives us many examples for application of a concept of information An electromagnetic wave of 0.7% give us the sensation of a red colour. Sensations have no physical reality. They are purely subjective. At the cellular level communication operates by means of chemical messengers (first messengers), which generally do not penetrate the plasmic membrane. Specific captors operate as transductors: external factors are converted into secondary messengers (cyclic AMP, Ca ion, etc.). Sometimes, electric signals (like depolarization waves) may also play a part in the intercellular communication. Such processes are characterized by changes in a sequence of different molecules carried by a physical signal. What is transmitted is the meaning of the message (significance) which can be memorized by the cell, providing a possible following use. At the molecular level one can find also the processes of linguistic nature. We know that the significance of a word is changed with changing the order of letters (ADD-->DAD, etc.).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1989

Effects of information conflict and complexity in visual figures on voluntary visual exploration, using structural information theory.

This study was designed to examine the effects of information conflict and complexity on voluntary visual exploration quantitatively. 31 adults viewed each of 16 slides of geometrical figures and places for as long as they wished. The stimuli had two values of information conflict and complexity which had been calculated by means of structural information theory. Free looking times indicated that only when information conflict was low, voluntary visual exploration was positively correlated with complexity. Furthermore, voluntary visual exploration correlated positively with information conflict when complexity was low.

Adult↗
PubMed1979

An analysis of case mix complexity using information theory and diagnostic related grouping.

Case mix complexity measurements are essential to determine health care efficiency and effectiveness. Measures of patient care processes and outcomes must be adjusted for case mix before valid comparisons can be made. Hospital reimbursement, particularly prospective reimbursement, must take into account differences in case mix. In addition, a key variable for hospital classification is case mix. There are, however, no widely accepted easily computed case mix measures. Information theory measures of case mix have been developed but their acceptance has been limited by a lack of verification of their basic assumption that concentration of disease is related to clinical complexity. We discuss the rationale underlying the mathematical computaton of information theory measures and demonstrate a statistically significant relationship between clinical measures of case mix complexity and information theory measures of case mix complexity.

Costs and Cost Analysis↗
PubMed2005

Information theory in prediction of cleavage sites of signal peptides.

Information theory is used to analyze the character of signal peptide quantitatively, especially residents. On the basis of the above analysis, a method named simplified information-matrix has been developed to predict the cleavage sites of signal peptides. A comparison between the results of weight-matrix and simplified information-matrix is presented.

Computational Biology↗
PubMed1981

Application of information theory to clinical diagnostic testing. The electrocardiographic stress test.

The inherent imperfection of clinical diagnostic tests introduces uncertainty into their interpretation. The magnitude of diagnostic uncertainty after any test may be quantified by information theory. THe information content of the electrocardiographic ST-segment response to exercise, relative to the diagnosis of angiographic coronary artery disease, was determined using literature-based pooled estimates of the true- and false-positive rates for various magnitudes of ST depression from less than 0.5 mm to greater than or equal to 2.5 mm. This analysis allows three conclusions of clinical relevance. First, the diagnostic information content of exercise-induced ST-segment depression, interpreted by the standard 1.0-mm criterion, averages only 15% of that of coronary angiography. Second, there is a 41% increase in information content when the specific magnitude of ST-segment depression is analyzed, as opposed to the single, categorical 1-mm criterion. Third, the information obtained from ECG stress testing is markedly influenced by the prevalence of disease in the population tested, being low in the asymptomatic and typical angina groups and substantially greater in groups with nonanginal chest pain and atypical angina. The quantitation of information has broad relevance to selection and use of diagnostic tests, because one can analyze objectively the value of different interpretation criteria, compare one test with another and evaluate the cost-effectiveness of both a single test and potential testing combination.

Electrocardiography↗
PubMed2004

Information theory for evaluating environmental classification systems.

Environmental pollution data are often ranked in rule-based classification systems. These environmental data are separated in predetermined classes of a classification system for a better and smarter characterization of the state of pollution. Often the measured values are transformed, e.g. in pseudocolor maps, and can then be presented in maps. For some environmental compartments different classification systems for evaluating environmental loadings are used. Because of the dissimilarity of the various classification systems direct visual comparison is difficult. However, by means of information theory an objective comparison of these various classification systems based on their information content enables a decision to be made about which system is the most informative for objective assessment of the state of pollution. By means of the new measure "multiple medium information content" (multiple entropy) objective and simultaneous comparison of all channels (in an environmental classification system: pollutants) of each classification system is now possible. Furthermore the development of the state of pollution over the whole investigation period can be detected by means of information theory. On the basis of the conditions of the established rule-based systems the use of information theory enables definition of new ranges of classes in order to reach the optimum of information during conversion into the environmental classification system.

Journal Article↗
PubMed1991

Comparison of the predictive abilities of different methods based on information theory: searching for receptor-binding sites.

A comparison of a new method of searching for functionally important sites in proteins and peptide hormones with a previously published method is presented. All methods are based on information theory that holds that rare oligomers contain much information and, thus, are likely to be important for specific functional activity. Twenty-five proteins and peptide hormones with known receptor-binding sites were studied; the new method showed good predictive ability. However, taking into account short-range sequential preferences in protein structures, the predictive ability of methods based on information theory, at least for the receptor-binding site predictions, was not greatly improved.

Algorithms↗
PubMed2005

Information theory, novelty and hippocampal responses: unpredicted or unpredictable?

Shannon's information theory provides a principled framework for the quantitative analysis of brain responses during the encoding and representation of event streams. In particular, entropy measures the expected uncertainty of events in a given context. This contextual uncertainty or unpredictability may, itself, be important for balancing [bottom-up] sensory information and [top-down] prior expectations during perceptual synthesis. Using event-related functional magnetic resonance imaging (fMRI), we found that the anterior hippocampus is sensitive to the entropy of a visual stimulus stream. In contrast, activity in an extensive bilateral cortico-thalamic network was dictated by the surprise or information associated with each particular stimulus. In short, we show that the probabilistic structure or context in which events occur is an important predictor of hippocampal activity.

Adult↗
PubMed1984

The need-informational theory of emotions.

As an evolvement of Pavlov ideas on higher nervous (psychic) activity 'the need-informational theory of emotions' was suggested by the author in 1964. According to it an emotion is a function of two major factors: (1) power and quality of actual need (or drive, or motivation) and (2) estimation of probability (possibility) of need satisfaction on the basis of phylo- and ontogenetic experience. In the process of experimental testing of 'the need-informational theory of emotions' the role of different cerebral structures (frontal neocortex, hippocampus, amygdala, hypothalamus) in the genesis of emotional states and in the organization of goal-directed behavior was elucidated. The experimental data showed that these 4 brain structures play the major role in estimation of signals coming from environment and in the choice of subject's reactions. The individual characteristics of the interaction between the 4 brain structures must be taken into consideration in discussing neurophysiological backgrounds of different types of the higher nervous activity (temperaments), parameters of extra-introversion and neurotism (emotionality), the formation of main types of neurosis.

Amygdala↗
PubMed1986

Application of information theory to decision analysis in potentially prostaglandin-responsive neonates.

To define settings in which use of prostaglandin E1 before transfer from a community hospital to a tertiary care center benefits neonates with possible heart disease, information theory was used to predict the probability of a favorable response to prostaglandin therapy from the limited information of clinical variables. Records of 250 patients, newborn to 7 days old, with suspected heart disease were reviewed to assess six clinical variables (cyanosis, respiratory distress, heart murmur, pulse contour, hepatomegaly and prematurity). According to the anatomic and hemodynamic cardiovascular condition, each case was categorized as to whether a favorable response to prostaglandin E1 could be anticipated. Information content of each clinical variable with respect to prostaglandin responsiveness was determined, and patients were classified according to the most informative clinical variable. Stepwise extraction of information proceeded until remaining clinical variables added no significant information. Bayes' rule gave estimates of probability of prostaglandin-responsive defect in final subgroups for use in decision analysis. Cyanosis, murmur, small volume pulses and prematurity gave information about prostaglandin-responsive defects. Decision analysis indicated that frequency of poor outcome is minimized by early prostaglandin treatment of cyanotic term infants with a murmur or poor pulses, regardless of how ill they appear, and by treating any critically ill term newborn who has either cyanosis or poor pulses. Acyanotic patients with normal pulses are best untreated with prostaglandin until after definitive diagnosis is made. Advantage to either course was not seen in some small subgroups. Information theory with decision analysis is a rigorous approach to identify relevant clinical variables and define their roles in critical decisions in pediatric cardiology.

Algorithms↗
PubMed2003

Regime changes in ecological systems: an information theory approach.

We present our efforts at developing an ecological system index using information theory. Specifically, we derive an expression for Fisher Information based on sampling of the system trajectory as it evolves in the space defined by the state variables of the system, i.e. its state space. The Fisher Information index, as we have derived it, is a measure of system order, and captures the characteristic variation in speed and acceleration along the system's periodic steady-state trajectories. When calculated repeatedly over the system period, this index tracks steady states and transient behavior. We believe that such an index could be useful in detecting system 'flips' associated with a regime change, i.e. determining when systems are in a transient between one steady state and another. We illustrate the concepts using model ecosystems.

Animals↗
PubMed2003

Information theory applied to chromatographic fingerprint of herbal medicine for quality control.

At present, the construction of chromatographic fingerprints plays an important role in the quality control of complex herbal medicines. In this work, information theory was applied to obtain chromatographic fingerprints with good performance. Moreover, according to the characteristics of the chromatographic fingerprints obtained, some modifications of the calculation of the information content were conducted. In comparison with the information content from several chromatographic fingerprints obtained, reliable chromatographic fingerprints with a high separation degree and uniform concentration distribution of chemical components could be determined. The successful application of information theory with modification to simulated chromatographic fingerprints together with real herbal medicines such as Rhizoma chuanxiong and Ginkgo biloba from different sources demonstrated clearly that the proposed method to determine chromatographic fingerprints was reasonable and reliable and it was user-friendly. Chromatographic fingerprints determined with high separation degrees and uniform concentration distribution of chemical ingredients might also chemically represent characteristic components of herbal medicines for quality control.

Chromatography↗