Calculation Of Information Content Research Articles

Bias-free estimation of information content in temporally sparse neuronal activity.

Applying information theoretic measures to neuronal activity data enables the quantification of neuronal encoding quality. However, when the sample size is limited, a naïve estimation of the information content typically contains a systematic overestimation (upward bias), which may lead to misinterpretation of coding characteristics. This bias is exacerbated in Ca2+ imaging because of the temporal sparsity of elevated Ca2+ signals. Here, we introduce methods to correct for the bias in the naïve estimation of information content from limited sample sizes and temporally sparse neuronal activity. We demonstrate the higher accuracy of our methods over previous ones, when applied to Ca2+ imaging data recorded from the mouse hippocampus and primary visual cortex, as well as to simulated data with matching tuning properties and firing statistics. Our bias-correction methods allowed an accurate estimation of the information place cells carry about the animal’s position (spatial information) and uncovered the spatial resolution of hippocampal coding. Furthermore, using our methods, we found that cells with higher peak firing rates carry higher spatial information per spike and exposed differences between distinct hippocampal subfields in the long-term evolution of the spatial code. These results could be masked by the bias when applying the commonly used naïve calculation of information content. Thus, a bias-free estimation of information content can uncover otherwise overlooked properties of the neural code.

Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a.

Data pathologies caused by effects such as diffraction anisotropy and translational noncrystallographic symmetry (tNCS) can dramatically complicate the solution of the crystal structures of macromolecules. Such problems were encountered in determining the structure of a mutant form of Rab27a, a member of the Rab GTPases. Mutant Rab27a constructs that crystallize in the free form were designed for use in the discovery of drugs to reduce primary tumour invasiveness and metastasis. One construct, hRab27aMut, crystallized within 24 h and diffracted to 2.82 Å resolution, with a unit cell possessing room for a large number of protein copies. Initial efforts to solve the structure using molecular replacement by Phaser were not successful. Analysis of the data set revealed that the crystals suffered from both extreme anisotropy and strong tNCS. As a result, large numbers of reflections had estimated standard deviations that were much larger than their measured intensities and their expected intensities, revealing problems with the use of such data at the time in Phaser. By eliminating extremely weak reflections with the largest combined effects of anisotropy and tNCS, these problems could be avoided, allowing a molecular-replacement solution to be found. The lessons that were learned in solving this structure have guided improvements in the numerical analysis used in Phaser, particularly in identifying diffraction measurements that convey very little information content. The calculation of information content could also be applied as an alternative to ellipsoidal truncation. The post-mortem analysis also revealed an oversight in accounting for measurement errors in the fast rotation function. While the crystal of mutant Rab27a is not amenable to drug screening, the structure can guide new modifications to obtain more suitable crystal forms.

Bayesian-based information extraction and aggregation approach for multilevel systems with multi-source data

The ever-increasing complexity of industry facilities has made the reliability analysis and assessment an imperative yet tough work. Motivated by practical engineering requirement, this paper develops a Bayesian-based information extraction and aggregation (BIEA) approach for system level reliability estimation of a complex system. It takes both subjective judgments and objective field outputs into consideration. Novel features of this approach is a unique information content based aggregation process, which allows a flexible application of this framework in separated modules on account for purpose. The coherency of which is guaranteed by the objective information content calculation. This work goes beyond the alternatives that deal with solely attributed data under ideal information circumstance, and investigates a more generic tool for real engineering application. Limitations embedded in traditional statistical modeling methods have been eliminated in a nature manner by information transition and integration. In addition, a double axis driving mechanism (DADM) for erecting the antenna of a satellite is demonstrated as case study for benefit illustration and effectiveness verification.

Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics

The evaluation of the Fisher information matrix for the probability density of trajectories generated by the over-damped Langevin dynamics at equilibrium is presented. The framework we developed is general and applicable to any arbitrary potential of mean force where the parameter set is now the full space dependent function. Leveraging an innovative Hermitian form of the corresponding Fokker-Planck equation allows for an eigenbasis decomposition of the time propagation probability density. This formulation motivates the use of the square root of the equilibrium probability density as the basis for evaluating the Fisher information of trajectories with the essential advantage that the Fisher information matrix in the specified parameter space is constant. This outcome greatly eases the calculation of information content in the parameter space via a line integral. In the continuum limit, a simple analytical form can be derived to explicitly reveal the physical origin of the information content in equilibrium trajectories. This methodology also allows deduction of least informative dynamics models from known or available observables that are either dynamical or static in nature. The minimum information optimization of dynamics is performed for a set of different constraints to illustrate the generality of the proposed methodology.

A Novel Approach for Product Design Scheme Evaluation with Non-Functional Attributes

Axiomatic design theory is a popular methodology for product design scheme evaluation in recent years. However, as information axiom has some limitation for information content of non-functional attributes, the application of axiomatic design theory is bound. Therefore, a new method is proposed for product design scheme evaluation in this paper, which is the generalized information content calculation, and the proposed method avoids the shortcoming of traditional information content calculations. Finally, the proposed method is applied in a case study, and experimental result shows the feasibility of the proposed method.

Estimation of Word Net-Based Lexical Semantic Similarity Measure for Telugu Documents

The estimation of lexical semantic relatedness has numerous applications in NLP. Several measures are available for the evaluation of lexical semantic relatedness. This paper presents two approaches for measuring semantic similarity/distance between words and concepts with the help of WordNet-Telugu. The edge-based approach of the edge counting scheme and the node-based approach of the information content calculation have been explored. In the field of concepts, the measure of Wu and Palmer has the advantage of being simple to implement and have good performances compared to the other similarity measures. The obtained results show that the Wu and Palmer approach presents a better performance in terms of relevance.

SEWAL: an open-source platform for next-generation sequence analysis and visualization

Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (∼108 sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (∼107 sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith’s adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets. Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal.

Chromatographic fingerprinting and related chemometric techniques for quality control of traditional Chinese medicines

Development of chromatographic fingerprint (CF) and related chemometric methods and their applications to quality control of traditional Chinese medicines (TCMs) were discussed. CF is essentially a kind of quality control method for TCMs (or Chinese herbal medicines). Also, it is a quality-relevant-data high-throughput and integral tool to explore chemically the complexity of TCMs. With the help of chemometrics, some difficulties in evaluation and analysis of CFs, such as calculation of information content, peak alignment, pattern analysis, deconvolution of overlapping peaks, etc. could be well solved. To further explore TCMs synergic quality, intensive study of CF coupled with chemometrics will create the possibility to achieve the aim to reveal the working mechanisms of TCMs and to further control and strengthen TCMs' intrinsic quality in a comprehensive manner.

A More Complex Isoleucine Aptamer with a Cognate Triplet

The simplest RNA that can meet a column affinity selection for isoleucine was previously defined using selection amplification with decreasing numbers of randomized nucleotides. This simplest UAUU motif was a small asymmetric internal loop. Conserved positions of the loop include isoleucine codon and anticodon triplets (Lozupone C., Changayil, S., Majerfeld, I., and Yarus, M. (2003) RNA (N. Y.) 9, 1315-1322). Using new primer sequences, we now select a somewhat more complex isoleucine binding RNA, requiring 4.7 more bits of information to describe. The newly selected structure is a terminal or hairpin loop of 20 nucleotides, 15 being invariant. An information profile shows that the new binding site contains five short functional loop regions joined by less significant single nucleotide positions. Among the important nucleotides is a conserved isoleucine anticodon, supporting the escaped triplet theory, which posits a stereochemical genetic code originating in RNA amino acid binding sites.

Axiomatc design in ergonomics and an extension of the information axiom

Axiomatic design as a design principle has been used increasingly in product and system development. This paper introduces axiomatic design as a foundation to ergonomic design. Three examples demonstrate how axiomatic design can be used for biomechanics design of hand tools and for anthropometric design of workplaces. The independence axiom was used to demonstrate how design activity can be structured to avoid time-consuming iterative improvements of design solutions: a decoupled design can indicate the ideal design sequence. For one case study it was demonstrated that the number of design iterations would be reduced if the Environment or Machine would first be designed followed by the Operator's workstation and the task. The information axiom was used for anthropometric design of a work place. Direct application of the information axiom is not appropriate for ergonomic design. A new way of calculating the information contents in anthropometric design is suggested. This involves a re-definition of the concepts of system range and design range, and results in a new formulation for calculation of information content. Through these design examples the application of axiomatic design in ergonomics seems promising.