Bayesian Inference in Processing Experimental Data: Principles and Basic Applications

This report introduces general ideas and some basic methods of the Bayesian probability theory applied to physics measurements. Our aim is to make the reader familiar, through examples rather than rigorous formalism, with concepts such as: model comparison (including the automatic Ockham's Razor filter provided by the Bayesian approach); parametric inference; quantification of the uncertainty about the value of physical quantities, also taking into account systematic effects; role of marginalization; posterior characterization; predictive distributions; hierarchical modelling and hyperparameters; Gaussian approximation of the posterior and recovery of conventional methods, especially maximum likelihood and chi-square fits under well defined conditions; conjugate priors, transformation invariance and maximum entropy motivated priors; Monte Carlo estimates of expectation, including a short introduction to Markov Chain Monte Carlo methods.Comment: 40 pages, 2 figures, invited paper for Reports on Progress in Physic

The BLue Amazon Brain (BLAB): A Modular Architecture of Services about the Brazilian Maritime Territory

We describe the first steps in the development of an artificial agent focused on the Brazilian maritime territory, a large region within the South Atlantic also known as the Blue Amazon. The "BLue Amazon Brain" (BLAB) integrates a number of services aimed at disseminating information about this region and its importance, functioning as a tool for environmental awareness. The main service provided by BLAB is a conversational facility that deals with complex questions about the Blue Amazon, called BLAB-Chat; its central component is a controller that manages several task-oriented natural language processing modules (e.g., question answering and summarizer systems). These modules have access to an internal data lake as well as to third-party databases. A news reporter (BLAB-Reporter) and a purposely-developed wiki (BLAB-Wiki) are also part of the BLAB service architecture. In this paper, we describe our current version of BLAB's architecture (interface, backend, web services, NLP modules, and resources) and comment on the challenges we have faced so far, such as the lack of training data and the scattered state of domain information. Solving these issues presents a considerable challenge in the development of artificial intelligence for technical domains

Compulsory admissions of patients with mental disorders : State of the art on ethical and legislative aspects in 40 European countries

Copyright: This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of MedicineBACKGROUND.: Compulsory admission procedures of patients with mental disorders vary between countries in Europe. The Ethics Committee of the European Psychiatric Association (EPA) launched a survey on involuntary admission procedures of patients with mental disorders in 40 countries to gather information from all National Psychiatric Associations that are members of the EPA to develop recommendations for improving involuntary admission processes and promote voluntary care. METHODS.: The survey focused on legislation of involuntary admissions and key actors involved in the admission procedure as well as most common reasons for involuntary admissions. RESULTS.: We analyzed the survey categorical data in themes, which highlight that both medical and legal actors are involved in involuntary admission procedures. CONCLUSIONS.: We conclude that legal reasons for compulsory admission should be reworded in order to remove stigmatization of the patient, that raising awareness about involuntary admission procedures and patient rights with both patients and family advocacy groups is paramount, that communication about procedures should be widely available in lay-language for the general population, and that training sessions and guidance should be available for legal and medical practitioners. Finally, people working in the field need to be constantly aware about the ethical challenges surrounding compulsory admissions.Peer reviewe

Compulsory admissions of patients with mental disorders : State of the art on ethical and legislative aspects in 40 European countries

Background. Compulsory admission procedures of patients with mental disorders vary between countries in Europe. The Ethics Committee of the European Psychiatric Association (EPA) launched a survey on involuntary admission procedures of patients with mental disorders in 40 countries to gather information from all National Psychiatric Associations that are members of the EPA to develop recommendations for improving involuntary admission processes and promote voluntary care. Methods. The survey focused on legislation of involuntary admissions and key actors involved in the admission procedure as well as most common reasons for involuntary admissions. Results. We analyzed the survey categorical data in themes, which highlight that both medical and legal actors are involved in involuntary admission procedures. Conclusions. We conclude that legal reasons for compulsory admission should be reworded in order to remove stigmatization of the patient, that raising awareness about involuntary admission procedures and patient rights with both patients and family advocacy groups is paramount, that communication about procedures should be widely available in lay-language for the general population, and that training sessions and guidance should be available for legal and medical practitioners. Finally, people working in the field need to be constantly aware about the ethical challenges surrounding compulsory admissions.Peer reviewe

Biomedical Discovery Acceleration, with Applications to Craniofacial Development

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work

Uncertainty, learning, and the “Problem” of dilation

Imprecise probabilism—which holds that rational belief/credence is permissibly represented by a set of probability functions—apparently suffers from a problem known as dilation. We explore whether this problem can be avoided or mitigated by one of the following strategies: (a) modifying the rule by which the credal state is updated, (b) restricting the domain of reasonable credal states to those that preclude dilation