Bayesian Inference

With the publication of Wilfred Bion’s text 'Learning from Experience', psychoanalysis was afforded a new schema for understanding the processes and implications involved in an infant’s contact with their caregivers. As a result, our conception of some of the most fundamental phenomena of psychic life was significantly enriched. By proposing his theory of alpha-functioning, Bion mapped out how meaningful connections to the internal and external worlds become established in the mind. In contrast, and through working clinically with psychotic patients, Bion revealed how these ties can catastrophically come undone. It is with these ideas, as well as their links to a corresponding set of neuroscientific constructs relating to the Markov blanket and principally developed by Karl Friston, that this paper is concerned. Through an investigation of the psychic functioning originally dubbed ‘dream-work-alpha’, the paper’s first section focuses on how Bion conceived of the creation of a ‘contact-barrier’ that allows for the differentiation of consciousness from an unconscious mind. Casting the ramifications of this organisation in sharp relief, the psychotic disorganisation of the contact-barrier is then explored. The discussion subsequently broadens to incorporate contemporary theories from free energy neuroscience that bear significant and illuminating relations to the psychoanalytic ideas espoused by Bion over half a century ago. Finally, through posing a series of three questions with accompanying discussions, a superimposition of these theoretical schemas is attempted. These suggestions directly address 1. whether there is an intimate connection between the interoceptive contact-barrier and the exteroceptive Markov blanket, 2. whether a disobjectalising of the contact-barrier may be reflected as a tear in the functional fabric of the Markov blanket, and 3. what the clinical implications are of working at the level of the projected surface. Ultimately, the aim of the paper is to expose relevant points of contact within and between the varying conceptual frameworks; frameworks that ultimately derive from disciplines that are both concerned with examining the underlying mechanisms of the mind-brain.

Intelligent design theorist William Dembski hasproposed an``explanatory filter''fordistinguishing between events due to chance, lawful regularity or design. We show that ifDembski's filter were adopted as a scientificheuristic, some classical developments inscience would not be rational, and thatDembski's assertion that the filter reliablyidentifies rarefied design requires ignoringthe state of background knowledge. Ifbackground information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to ...

Recent developments in ecological statistics have reached behavioral ecology, and an increasing number of studies now apply analytical tools that incorporate alternatives to the conventional null hypothesis testing based on significance levels. However, these approaches continue to receive mixed support in our field. Because our statistical choices can influence research design and the interpretation of data, there is a compelling

Iverson, Lee, and Wagenmakers (2009) claimed that Killeen's statistic prep overestimated the “true probability of replication.”  We show that Iverson et al. confused the probability of replication of an observed direction of effect with a probability of coincidence—the probability that two future experiments will return the same sign. We emphasize throughout that prep is intended to evaluate the probability of a replication outcome after observations, not to estimate a parameter. Hence, the usual conventional criteria (unbiasedness, minimum variance estimator) for judging estimators are not appropriate for probabilities such as p and prep.

A comprehensive analysis of early dinosaur relationships raised the possibility that the group may have originated in Laurasia (Northern Hemisphere), rather than Gondwana (Southern Hemisphere) as often thought. However, that study focused solely on morphology and phylogenetic relationships and did not quantitatively evaluate this issue. Here, we investigate dinosaur origins using a novel Bayesian framework uniting tip-dated phylogenetics with dynamic, time-sliced biogeographic methods, which explicitly account for the age and locality of fossils and the changing interconnections of areas through time due to tectonic and eustatic change. Our analysis finds strong support for a Gondwanan origin of Dinosauria, with 99 % probability for South America (83 % for southern South America). Parsimony analysis gives concordant results. Inclusion of time-sliced biogeographic information affects ancestral state reconstructions (e.g., high connectivity between two regions increases uncertainty over which is the ancestral area) and influences tree topology (disfavouring uniting fossil taxa from localities that were widely separated during the relevant time slice). Our approach directly integrates plate tectonics with phylogenetics and divergence dating, and in doing so reaffirms southern South America as the most likely area for the geographic origin of Dinosauria. Dinosaurs are one of the most charismatic and heavily studied groups of vertebrates (e.g., Sereno 1999), but despite ongoing work and many recent discoveries, certain aspects of early dinosaurian evolution remain unclear. A recent study of early dinosaur relationships presented a new phylogeny that departs radically from existing models, but forms a broader framework for inferring dinosaur evolutionary history than those that were previously available (Baron et al. 2017a). While that study was focused primarily on early dinosaurian anatomy and relationships, a general observation was made: based upon the geographic locations of key taxa in their phylogeny, a Laurasian setting for dinosaur origin may have been plausible. This proposal ran contrary to an established consensus based on earlier phylogenies that favoured a Gondwanan and, more specifically, South American setting for this event (Nesbitt et al. 2009; Brusatte et al. 2010; Langer et al. 2010; Sues et al. 2011; Boyd 2015). In particular, the European presence of silesaurids, a close outgroup to dinosaurs, and some early dinosaur taxa (e.g., Saltopus) hinted that northern Pangaea may have played an important role in the earliest stages of dinosaur diversification. However, given the space limitations associated with the original article, no quantitative analyses were carried out to evaluate this alternative hypothesis rigorously. Here, we test the alternative hypothesis implicit in Baron et al. (2017a) by analysing their early dinosaur dataset using a novel integration of time-sliced Bayesian biogeographic models (Landis 2016) and tip-dated Bayesian phylogenetics (Drummond et al. 2012; Bielejec et al. 2014; Gavryushkina et al. 2017). The current method simultaneously estimates phylogenetic relationships, divergence dates, evolutionary rates and biogeographic patterns. Biogeographical changes are inferred using models that account for the changing relationships of continents (and thus dispersal abilities) over time-a 'chronobiogeographical' paradigm (Hunn & Upchurch 2001)-and this information provides potentially critical information for improving estimates of tree topology and divergence dates. For comparison, we also perform analogous analyses using traditional biogeographic parsimony-based methods. Previous studies have advocated a similar approach to integrating phylogeny, stratigraphy, morphology and bio-geography in a parsimony framework (reviewed in Rossie & Seiffert 2006). However, that implementation was problematic: as parsimony trees lack an explicit time element, only very simple time-sliced biogeographic models were possible (e.g., three areas and three time slices) and tree topology and divergence dates had to be assessed manually. The analyses attempted here tackle this complex multidimensional problem more efficiently , using explicit Bayesian computational approaches.

We perceive the shapes and material properties of objects quickly and reliably despite the complexity and objective ambiguities of natural images. Typical images are highly complex because they consist of many objects embedded in background clutter. Moreover, the image features of ...

In classical econometric binary regression models, the logistic regression model has been used associated to the logit symmetric link. The purpose of this paper is to present binary regression models with rather asymmetric links —not yet available as commercial software—, when this asymmetry is more appropriate to the researcher. In addition, a utility program called BAYES-PUCP is implemented. BAYES-PUCP uses a bayesian approach with the program WinBUGS and will facilitate the writing of the syntax for the models reviewed. It also generates both the syntax and the structure of the data. The method is illustrated for a sample of farmers who consider the decision to eradicate illegal crops of coca leaf. Factors associated with this decision are also explored.

The core of D. Lewis' many con tribution to philosophy, including his work in philosophical ontolo gy, intensional logic and semantics, probability and decision theory, and topics within philosophy of science as well as a distinguished philosophy of mind, dan ve understood as the development of a philosophical postion that is centered around his conception of Humean supervenience. If we accept the thesis that i t is physical science and not philosophical reasoning that will eventually arrive at the basic constituents of all matter pertaining in our world will supervene on the class of physical truht in the following sense: there are no truth in any compartment of our world that cannot be accounted for in terms of differences and similarities among those properties and external space-time relationsthat are fundamental to our world accordint to physical science.
Together the published essays challenge  aspects of Lewis' philosophy, posing new questions  and opening up new points of view in one of contemporary philosophy's most  ingenious and independent authors.

Rowman & Littlefield, Lanham, Maryland.

https://rowman.com/ISBN/9780742512009/Reality-and-Humean-Supervenience-Essays-on-the-Philosophy-of-David-Lewis

The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai’i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographical distributions of their closest living relatives. We sequenced two chloroplast DNA fragments, rbcL and the trnL-F intergenic spacer (IGS), for 18 Hawaiian taxa, 45 non-Hawaiian taxa, and two outgroup species. For individual fragments, we estimated phylogenetic relationships using Bayesian inference and maximum parsimony. We performed a combined analysis of both cpDNA fragments employing Bayesian inference, maximum parsimony, and maximum likelihood. These analyses indicate that Hawaiian Dryopteris is not monophyletic, and that there were at least five separate colonizations of the Hawaiian Islands by different species of dryopteroid ferns, with most of the five groups having closest relatives in SE Asia. The results suggest that one colonizing ancestor, perhaps from SE Asia, gave rise to eight endemic taxa (the glabra group). Another colonizing ancestor, also possibly from SE Asia, gave rise to a group of five endemic taxa (the exindusiate group). Dryopteris fusco-atra and its two varieties, which are endemic to Hawai’i, most likely diversified from a SE Asian ancestor. The Hawaiian endemic Nothoperanema rubiginosum has its closest relatives in SE Asia, and while the remaining two species, D. wallichiana and D. subbipinnata, are sister species, their biogeographical origins could not be determined from these analyses due to the widespread distributions of D. wallichiana and its closest non-Hawaiian relative.

In this paper concerned with the study of queueing model for teletraffic. In teletraffic data are related to internet and other complex
telecommunications systems. They include packet sizes, inter-arrival times, download times and transmission times, among others. Such
times are follows to Gumbel distribution. The limiting distribution, expected waiting time and expected busy period time are derived by
using embedded Markov chain technique. Finally the computational performances are carried out for this model.

Keywords: M/G/1 queue, Gumbel distribution, embedded Markov chain, teletraffic data.

Multi-sensor networks can alleviate the need for high-cost, high-accuracy, single-sensor tracking in favor of an abundance of lower-cost and lower-accuracy sensors to perform multi-sensor tracking. The use of a multi-sensor network gives rise to the need for a fusion step that combines the outputs of all sensor nodes into a single probabilistic state description. When considering Gaussian uncertainties, the well-known covariance intersection technique may be used. In the more general, non-Gaussian case, covariance intersection is not sufficient. This paper examines a fusion method based on logarithmic opinion pools and develops algorithms for multi-sensor data fusion as well as investigates weight selection schemes for the opinion pool. The proposed fusion rules are applied to the tracking of a space object using multiple ground-based optical sensors. Non-Gaussian orbit determination methods are applied to each sensor individually, and the fusion rule is applied to the combined outputs of each sensor node. It is shown that the multi-sensor fusion rule leads to an increase of nearly two orders of magnitude in the position tracking accuracy as compared to the traditional single-sensor tracking method.

We propose Bayesian inference in hazard regression models where the baseline hazard is unknown, covariate effects are possibly agevarying (non-proportional), and there is multiplicative frailty with arbitrary distribution. Our framework incorporates a wide variety of order restrictions on covariate dependence and duration dependence (ageing). We propose estimation and evaluation of age-varying covariate e¤ects when covariate dependence is monotone rather than proportional. In particular, we consider situations where the lifetime conditional on a higher value of the covariate ages faster or slower than that conditional on a lower value; this kind of situation is common in applications. In addition, there may be restrictions on the nature of ageing. For example, relevant theory may suggest that the baseline hazard function decreases with age. The proposed framework enables evaluation of order restrictions in the nature of both covariate and duration dependence as well as estimation of...

Given the reproducibility crisis (or replication crisis), more psychologists and social-cultural scientists are getting involved with Bayesian inference. Therefore, the current article provides a brief overview of programs (or software) and steps to conduct Bayesian data analysis in social sciences.

The cocktail party problem is a multi-faceted challenge which encompasses various aspects of auditory perception. Its processes underlie the brain's ability to detect, identify and classify sound objects; to robustly represent and maintain speech intelligibility amidst severe distortions; and to guide actions and behaviors in line with complex goals and shifting acoustic soundscapes. Here, we present a perspective that considers the powerful Bayesian inference as a unifying framework to integrate the role of sensory cues as well as stimulus-driven priors and top-down schemas including attention.

The purpose of this study is to compare the maximum likelihood (ML) and Bayesian estimation methods for polychoric correlation (PCC) under diverse conditions using a Monte Carlo simulation. Two new Bayesian estimates, maximum a posteriori (MAP) and expected a posteriori (EAP), are compared to ML, the classic solution, to estimate PCC. Different types of prior distributions are used to investigate the sensitivity of a prior distribution onto the Bayesian PCC estimation. In this simulation study, it appears that the MAP would be the estimator of choice for the PCC. The performance of the MAP is not only better than the ML but also appears to overcome the limitations of the EAP (i.e., the shrinkage effect).

MrBayes is a program for the Bayesian inference of phylogeny. This manual explains Bayesian inference of phylogeny and how to use the program. The program has a command-line interface and should run on a variety of computer platforms. Note that the computer should have a ...

We formulate the inverse problem of solving Fredholm integral equa- tions of the first kind as a nonparametric Bayesian inference problem, using Levy random fields (and their mixtures) as prior distributions. Posterior distributions for all featues of interest are computed using novel Markov chain Monte Carlo numerical methods in infinite-dimensional spaces, based on generalizations and extensions of the authors' Inverse

The theory of dual numerical means of random and experienced variables is briefly described in the framework of the new theory of experience and the chance that arises as an axiomatic synthesis of two dual theories — the Kolmogorov theory of probability and the theory of believability. A new term is introduced for the numerical mean of the experienced variable — mathematical reflection, which is dual to the mathematical expectation of a random variable within the framework of the new theory. The basic properties and examples of dual numerical means are considered.

La progressiva affermazione della prova scientifica nel processo penale come nuova regina probationum ha innescato una lenta, ma inesorabile sollecitazione delle logiche qualitative del ragionamento probabilistico, così come descritte dalla sentenza Franzese. Gli argomenti allora utilizzati per confutare gli sterili e opposti approcci quantitativi all’accertamento del nesso causale si scontrano con i recenti tentativi di applicare la matematica alla valutazione e combinazione delle prove. Dagli Stati Uniti d’America e dalla Scandinavia è giunta l’eco travolgente di raffinate teorie per l’algoritmizzazione del giudizio attraverso la quantificazione della credenza soggettiva in un’ipotesi alla luce delle risultanze istruttorie. Compito del giurista e del legislatore è analizzare tali approcci comprendendone il funzionamento, approntando i necessari strumenti per resistere al rischio di degenerazioni meccanicistiche del ricorso ai big data, senza rinunciare agli indubbi vantaggi che i mathematical tools offrono al processo. Invero, l’attuale diffusione anche su scala europea di applicazioni sperimentali del teorema di Bayes e dell’E.V.M. sta cambiando silenziosamente il ragionamento probatorio, proponendo sfide inimmaginabili fino al decennio scorso.
http://www.questionegiustizia.it/rivista/pdf/QG_2018-4_16.pdf

We discuss epistemological and methodological aspects of the Bayesian approach in astrophysics and cosmology. The introduction to the Bayesian framework is given for a further discussion concerning the Bayesian inference in physics. The interplay between the modern cosmology, Bayesian statistics, and philosophy of science is presented. We consider paradoxes of confirmation, like Goodman's paradox, appearing in the Bayesian theory of confirmation. As in Goodman's paradox the Bayesian inference is susceptible to some epistemic limitations in the logic of induction. However Goodman's paradox applied to cosmological hypotheses seems to be resolved due to the evolutionary character of cosmology and accumulation new empirical evidences. We argue that the Bayesian framework is useful in the context of falsificability of quantum cosmological models, as well as contemporary dark energy and dark matter problem.