Human Minds

Articl

RankPL: A Qualitative Probabilistic Programming Language

In this paper we introduce RankPL, a modeling language that can be thought of as a qualitative variant of a probabilistic programming language with a semantics based on Spohn's ranking theory. Broadly speaking, RankPL can be used to represent and reason about processes that exhibit uncertainty expressible by distinguishing "normal" from" surprising" events. RankPL allows (iterated) revision of rankings over alternative program states and supports various types of reasoning, including abduction and causal inference. We present the language, its denotational semantics, and a number of practical examples. We also discuss an implementation of RankPL that is available for download

Are Reasons Causally Relevant for Action? Dharmakīrti and the Embodied Cognition Paradigm

How do mental states come to be about something other than their own operations, and thus to serve as ground for effective action? This papers argues that causation in the mental domain should be understood to function on principles of intelligibility (that is, on principles which make it perfectly intelligible for intentions to have a causal role in initiating behavior) rather than on principles of mechanism (that is, on principles which explain how causation works in the physical domain). The paper considers Dharmakīrti’s kāryānumāna argument (that is, the argument that an inference is sound only when one infers from the effect to the cause and not vice versa), and proposes a naturalized account of reasons. On this account, careful scrutiny of the effect can provide a basis for ascertaining the unique causal totality that is its source, but only for reasoning that is context‐specific

Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes

Causal inference approaches in systems genetics exploit quantitative trait loci (QTL) genotypes to infer causal relationships among phenotypes. The genetic architecture of each phenotype may be complex, and poorly estimated genetic architectures may compromise the inference of causal relationships among phenotypes. Existing methods assume QTLs are known or inferred without regard to the phenotype network structure. In this paper we develop a QTL-driven phenotype network method (QTLnet) to jointly infer a causal phenotype network and associated genetic architecture for sets of correlated phenotypes. Randomization of alleles during meiosis and the unidirectional influence of genotype on phenotype allow the inference of QTLs causal to phenotypes. Causal relationships among phenotypes can be inferred using these QTL nodes, enabling us to distinguish among phenotype networks that would otherwise be distribution equivalent. We jointly model phenotypes and QTLs using homogeneous conditional Gaussian regression models, and we derive a graphical criterion for distribution equivalence. We validate the QTLnet approach in a simulation study. Finally, we illustrate with simulated data and a real example how QTLnet can be used to infer both direct and indirect effects of QTLs and phenotypes that co-map to a genomic region.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS288 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Learning Bayesian Networks with the bnlearn R Package

bnlearn is an R package which includes several algorithms for learning the structure of Bayesian networks with either discrete or continuous variables. Both constraint-based and score-based algorithms are implemented, and can use the functionality provided by the snow package to improve their performance via parallel computing. Several network scores and conditional independence algorithms are available for both the learning algorithms and independent use. Advanced plotting options are provided by the Rgraphviz package.Comment: 22 pages, 4 picture