It is increasingly common for experiments in biology and medicine to involve large numbers of hypothesis tests. A natural graphical method for visualizing these tests is to construct a histogram from the p-values of these tests. In this article, we examine the shapes, both normal and abnormal, that these histograms can take on, as well as present simple inferential procedures that help to interpret the shapes in terms of diagnosing potential problems with the experiment. We examine potential causes of these problems in detail, and discuss potential remedies. Throughout, examples of abnormal-looking p-value histograms are provided and based on case studies involving real biological experiments.

The mutual information between the state of a neural network and the state of the external world represents the amount of information stored in the neural network that is associated with the external world. In contrast, the surprise of the sensory input indicates the unpredictability of the current input. In other words, this is a measure of inference ability, and an upper bound of the surprise is known as the variational free energy. According to the free-energy principle (FEP), a neural network continuously minimizes the free energy to perceive the external world. For the survival of animals, inference ability is considered to be more important than simply memorized information. In this study, the free energy is shown to represent the gap between the amount of information stored in the neural network and that available for inference. This concept involves both the FEP and the infomax principle, and will be a useful measure for quantifying the amount of information available for inference.

A general framework for inference in dynamical systems is described, based on the language of Bayesian probability theory and making use of the maximum entropy principle. Taking as fundamental the concept of a path, the continuity equation and Cauchy's equation for fluid dynamics arise naturally, while the specific information about the system can be included using the Maximum Caliber (or maximum path entropy) principle.

Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data.These data have different types (discrete,real,string etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data(copy number variation, single nucleotide polymorphisms), GO annotations, protein-protein interaction and disease-gene association data are some of the commonly used genomic datasets to study biological processes. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about their regulatory mechanisms. In order to understand the functions of genes, proteins and analyze mechanisms arising out of their interactions, information provided by each of these datasets individually may not be sufficient. Therefore integrating these multi-omic data and inferring regulatory interactions from the integrated dataset provides a system level biological insights in predicting gene functions and their phenotypic outcomes. To study genome functionality through interaction networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here data integration approaches using state-of-the-art techniques such as network integration, Bayesian networks, regularized regression (LASSO) and multiple kernel learning methods.

Education outside the classroom (EOtC) can be beneficial for students. The relationship between biological stress markers and sedentary behavior (SB) plus physical activity (PA) is insufficiently evaluated in school settings. This exploratory study aims to evaluate the association between students’ cortisol, plus circulating cell-free deoxyribonucleic acid (cfDNA) levels, and their SB, light PA (LPA) and moderate-to-vigorous PA (MVPA) during outdoor and indoor classes in different seasons. We assessed data from an education outside the classroom (EOtC) program (n = 48; intervention group [IG], n = 37; control group [CG], n = 11). We sampled data on 3 school-days in three seasons (fall, spring, and summer) in normal teaching indoors (CG) and outdoor lessons (IG) in the forest. SB and PA were evaluated by accelerometry, and cortisol and cfDNA levels by saliva samples. The compositional data analysis approach analyzed SB and PA. Fitted Bayesian hierarchical linear models evaluated the association between cortisol and cfDNA, and SB/LPA/MVPA. A steady decline of cortisol in the outdoor setting is associated with relatively high levels of LPA. SB and MVPA tended to exhibit a similar effect in the indoor setting. CfDNA is positively associated with a relatively high amount of SB in the IG, the same association is likely for LPA and MVPA in both groups. LPA seems to support a healthy cortisol decrease in children during outdoor lessons. The relevance of SB/PA as a composition in relation to students stress response in school should be emphasized. This study facilitates the formulation of straightforward and directed hypotheses for further research.

Grading of rice grains has gain attentions due its requirement of quality assessment during import or export. Rice grain quality depends on milling operation, where rice hull is removed with a huller system followed by whitening operation. In such process, adjustment of rollers, control, and operation is important in terms of quality of milled rice. Especially, the basmati rice needed more quality assurance as it is not parboiled rice and exported globally with a high product value. In this present work, the basic problem of quality assessment in rice industry is addressed with digital image processing based technique. Machine vision and digital image processing provide an alternative with the automated, nondestructive, cost-effective, and fast approach as compared with traditional method which is done manually by human inspectors. A model of quality grade testing and identification is built based on morphological features using digital image processing and knowledge based adaptive neuro-fuzzy inference system (ANFIS). The qualities of rice kernels are determined with the help of shape descriptors and geometric features using the sample images of milled rice. The adopted technique has been tested on a sufficient number of training images of basmati rice grain. The proposed method gives a promising result in an evaluation of rice quality with 100% classification accuracy for broken and whole grain. The milling efficiency is also assessed using the ratio between head rice and broken rice percentage and it is 77.27% for the test sample. The overall results of the adopted methodology are promising in terms of classification accuracy and efficiency.

Geometric Akaike Information Criteria (G-AICs) for generalized noise-level dependent crystallographic symmetry classifications of two-dimensional (2D) images that are more or less periodic in either two or one dimensions as well as Akaike weights for multi-model inferences and predictions are reviewed. Such novel classifications do not refer to a single crystallographic symmetry class exclusively in a qualitative and definitive way. Instead, they are quantitative, spread over a range of crystallographic symmetry classes, and provide opportunities for inferences from all classes (within the range) simultaneously. The novel classifications are based on information theory and depend only on information that has been extracted from the images themselves by means of maximal likelihood approaches so that these classifications are objective. This is in stark contrast to the common practice whereby arbitrarily set thresholds or null hypothesis tests are employed to force crystallographic symmetry classifications into apparently definitive/exclusive states, while the geometric feature extraction results on which they depend are never definitive in the presence of generalized noise, i.e. in all real world applications. Thus, there is unnecessary subjectivity in the currently practiced ways of making crystallographic symmetry classifications, which can be overcome by the approach outlined in this review.

The relationship of the animal with its environment has been of longstanding interest in philosophy and science. Here I provide a brief introduction to concepts that place an emphasis on mutualism as the basis of organism - environment interaction, in contrast to the long standing view that the environment exerts an instrumental role in shaping the organism. Two influential theories have been von Uexküll’s theory of umwelt and Gibson’s theory of affordances. The former envisioned the animal as immersed in its surroundings (umwelt) to form a functional unit. In a similar manner, the latter theory describes a unity between 1) environmental information that provides the animal with opportunities for action (affordances) and 2) the ability of the animal to perceive and engage with those affordances. These views have influenced more recent ecological models of the organism as the functional unit of biology and have also influenced models of immune function. In ecological models, agency is seen as the ability of the organism to predict and control its engagement with the environment in order to maintain its integrity. The predominant contemporary model of neural function in which perception and action are understood to operate through Bayes-like active inference complements the concept of agency as proposed by the mutualism models. However, it is suggested that rather than a constant mutualism, encounters between organism and environment range over a dynamic spectrum from dualism to mutualism. It is also suggested that along this spectrum, agency emerges when the balance of instrumentality shifts from the environment to the organism, and that the balance of this relationship can further progress towards a felicitous mutualism. Meaning emerges between environmental information and an agent as opportunity for action. Implications for opportunities to foster agency in animals within our care is noted.

We find that the standard relative entropy and the Umegaki entropy are designed for the purpose of inferentially updating probability and density matrices respectively. From the same set of inferentially guided design criteria, both of the previously stated entropies are derived in parallel. This formulates a quantum maximum entropy method for the purpose of inferring density matrices in the absence of complete information.

This paper attempts at applying adaptive network-based fuzzy inference system (ANFIS) for analysis of the resonant frequency of a microstrip rectangular patch antenna with two equal size slots which are placed on the patch vertically. The resonant frequency is calculated as the position of slots is shifted to the right and left sides on the patch. As a result , the antenna resonates at more than one frequency . Commonly, machine algorithms based on artificial neural networks are employed to recognize the whole resonant frequencies. However ,they fail to estimate the resonant frequencies correctly as in some cases variations are not very sensible and the resonant frequencies overlap each other . It can be concluded that artificial neural networks could be replaced in such designs by the adaptive network-based fuzzy Inference system due to its high approximation capability and much faster convergence rate.

An approach to the assessment of probabilistic inference is described which quantifies the performance on the probability scale. From both information and Bayesian theory, the central tendency of an inference is proven to be the geometric mean of the probabilities reported for the actual outcome and is referred to as the “Accuracy.” Upper and lower error bars on the accuracy are provided by the arithmetic mean and the -2/3 mean. The arithmetic is called the “Decisiveness” due to its similarity with the cost of a decision and the -2/3 mean is called the “Robustness”, due to its sensitivity to outlier errors. Visualization of inference performance is facilitated by plotting the reported model probabilities versus the histogram calculated source probabilities. The visualization of the calibration between model and source is summarized on both axes by the arithmetic, geometric, and -2/3 means. From information theory, the performance of the inference is related to the cross-entropy between the model and source distribution. Just as cross-entropy is the sum of the entropy and the divergence; the accuracy of a model can be decomposed into a component due to the source uncertainty and the divergence between the source and model. Translated to the probability domain these quantities are plotted as the average model probability versus the average source probability. The divergence probability is the average model probability divided by the average source probability. When an inference is over/under-confident, the arithmetic mean of the model increases/decreases, while the -2/3 mean decreases/increases, respectively.

Historic expeditions are events that are flavored by exploratory, scientific, military or geographic characteristics. Such events are often documented in literature, journey notes or personal diaries. A typical historic expedition involves multiple site visits and their descriptions contain spatiotemporal and attributive contexts. Expeditions involve movements in space that can be represented by triplet features (location, time and description). However, such features are implicit and innate parts of textual documents. Extracting the geospatial information from these documents requires understanding the contextualized entities in the text. To this end, we developed a semi-automated framework that has multiple Information Retrieval and Natural Language Processing components to extract the spatiotemporal information from a two-volumes historic expedition gazetteer. Our framework has three basic components, namely, the Text Preprocessor, the Gazetteer Processing Machine and the JAPE (Java Annotation Pattern Engine) Transducer. We used the Brazilian Ornithological Gazetteer as an experimental dataset and extracted the spatial and temporal entities from entries that refer to three expeditioners’ site visits and mapped the trajectory of each expedition using the extracted information. Finally, one of the mapped trajectories was manually compared with a historical reference map of that expedition to assess the reliability of our framework. The reference map was manually prepared in previous research work by others.

Predicting electricity prices is a very important issue in modern society, because the associated decision process under uncertainty requires accurate forecasts for the economic agents involved. In this paper, we apply the decision tree extension of Random Forests to the prediction of electricity prices in Spain, but with the novelty of modeling prices jointly with demand, with the purpose of achieving greater accuracy than with univariate response Random Forests, particularly in price prediction, as well as understanding the effect of the input variables (lagged values of price and demand, current production levels of available energy sources) on the joint of the two outputs. The results are very encouraging, providing significant increase in price prediction accuracy. Also, interesting methodological challenges appear as far as the appropriate choice of the relative weights of price and demand in the joint modeling is concerned and a new procedure to provide the importance variable ranking is proposed. The partykit (package of R software) library allowing for multivariate Random Forests has been used.