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"Inferencing is defined as 'the act of deriving logical conclusions from premises known or assumed to be true', and it is one of the most important processes necessary for successful comprehension during reading. This volume features contributions by distinguished researchers in cognitive psychology, educational psychology, and neuroscience on topics central to our understanding of the inferential process during reading. The chapters cover aspects of inferencing that range from the fundamental bottom up processes that form the basis for an inference to occur, to the more strategic processes that transpire when a reader is engaged in literary understanding of a text. Basic activation mechanisms, word-level inferencing, methodological considerations, inference validation, causal inferencing, emotion, development of inferences processes as a skill, embodiment, contributions from neuroscience, and applications to naturalistic text are all covered as well as expository text and online learning materials, and literary immersion"--

Cognitive psychology --- Inference

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This paper summarizes recent advances in causal inference and underscores the paradigmatic shifts that must be undertaken in moving from traditional statistical analysis to causal analysis of multivariate data. Special emphasis is placed on the assumptions that underlie all causal inferences, the languages used in formulating those assumptions, the conditional nature of all causal and counterfactual claims, and the methods that have been developed for the assessment of such claims. These advances are illustrated using a general theory of causation based on the Structural Causal Model (SCM) described in Pearl (2000a), which subsumes and unifies other approaches to causation, and provides a coherent mathematical foundation for the analysis of causes and counterfactuals. In particular, the paper surveys the development of mathematical tools for inferring (from a combination of data and assumptions) answers to three types of causal queries: those about (1) the effects of potential interventions, (2) probabilities of counterfactuals, and (3) direct and indirect effects (also known as "mediation"). Finally, the paper defines the formal and conceptual relationships between the structural and potential-outcome frameworks and presents tools for a symbiotic analysis that uses the strong features of both. The tools are demonstrated in the analyses of mediation, causes of effects, and probabilities of causation.

Mathematical statistics --- Multivariate analysis --- Probabilities --- Causation --- Inference

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Scientists today have access to an unprecedented arsenal of high-tech tools that can be used to thoroughly characterize biological systems of interest. High-throughput “omics” technologies enable to generate enormous quantities of data at the DNA, RNA, epigenetic and proteomic levels. One of the major challenges of the post-genomic era is to extract functional information by integrating such heterogeneous high-throughput genomic data. This is not a trivial task as we are increasingly coming to understand that it is not individual genes, but rather biological pathways and networks that drive an organism’s response to environmental factors and the development of its particular phenotype. In order to fully understand the way in which these networks interact (or fail to do so) in specific states (disease for instance), we must learn both, the structure of the underlying networks and the rules that govern their behavior. In recent years there has been an increasing interest in methods that aim to infer biological networks. These methods enable the opportunity for better understanding the interactions between genomic features and the overall structure and behavior of the underlying networks. So far, such network models have been mainly used to identify and validate new interactions between genes of interest. But ultimately, one could use these networks to predict large-scale effects of perturbations, such as treatment by multiple targeted drugs. However, currently, we are still at an early stage of comprehending methods and approaches providing a robust statistical framework to quantitatively assess the quality of network inference and its predictive potential. The scope of this Research Topic in Bioinformatics and Computational Biology aims at addressing these issues by investigating the various, complementary approaches to quantify the quality of network models. These “validation” techniques could focus on assessing quality of specific interactions, global and local structures, and predictive ability of network models. These methods could rely exclusively on in silico evaluation procedures or they could be coupled with novel experimental designs to generate the biological data necessary to properly validate inferred networks.

Validation --- Gene Expression --- Network Inference --- bioinformatics

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Inferencing is defined as 'the act of deriving logical conclusions from premises known or assumed to be true', and it is one of the most important processes necessary for successful comprehension during reading. This volume features contributions by distinguished researchers in cognitive psychology, educational psychology, and neuroscience on topics central to our understanding of the inferential process during reading. The chapters cover aspects of inferencing that range from the fundamental bottom up processes that form the basis for an inference to occur, to the more strategic processes that transpire when a reader is engaged in literary understanding of a text. Basic activation mechanisms, word-level inferencing, methodological considerations, inference validation, causal inferencing, emotion, development of inferences processes as a skill, embodiment, contributions from neuroscience, and applications to naturalistic text are all covered as well as expository text, online learning materials, and literary immersion.

Cognitive psychology. --- Inference. --- Knowledge, Theory of. --- Inference --- Cognitive psychology --- Social Sciences --- Psychology --- Psychology, Cognitive --- Cognitive science --- Ampliative induction --- Induction, Ampliative --- Inference (Logic) --- Reasoning

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Philosophy --- Knowledge, Theory of. --- Inference. --- Thought and thinking.