Dataset Information

Assessing semantic coherence in conditional probability estimates.

ABSTRACT: Semantic coherence is a higher-order coherence benchmark that assesses whether a constellation of estimates--P(A), P(B), P(B | A), and P(A | B)--maps onto the relationship between sets implied by the description of a given problem. We present an automated method for evaluating semantic coherence in conditional probability estimates that efficiently reduces a large problem space into five meaningful patterns: identical sets, subsets, mutually exclusive sets, overlapping sets, and independent sets. It also identifies three theoretically interesting nonfallacious errors. We discuss unique issues in evaluating semantic coherence in conditional probabilities that are not present in joint probability judgments, such as errors resulting from dividing by zero and the use of a tolerance parameter to manage rounding errors. A spreadsheet implementing the methods described above can be downloaded as a supplement from www.springerlink.com .

SUBMITTER: Fisher CR

PROVIDER: S-EPMC3746019 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Assessing semantic coherence in conditional probability estimates.

Fisher Christopher R CR Wolfe Christopher R CR

Behavior research methods 20111201 4

Semantic coherence is a higher-order coherence benchmark that assesses whether a constellation of estimates--P(A), P(B), P(B | A), and P(A | B)--maps onto the relationship between sets implied by the description of a given problem. We present an automated method for evaluating semantic coherence in conditional probability estimates that efficiently reduces a large problem space into five meaningful patterns: identical sets, subsets, mutually exclusive sets, overlapping sets, and independent sets ...[more]

PMID: 21512870

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Project description:BackgroundThe increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Named entity recognition of well-defined objects, such as genes or proteins, has achieved a sufficient level of maturity such that it can form the basis for the next step: the extraction of relations that exist between the recognized entities. Whereas most early work focused on the mere detection of relations, the classification of the type of relation is also of great importance and this is the focus of this work. In this paper we describe an approach that extracts both the existence of a relation and its type. Our work is based on Conditional Random Fields, which have been applied with much success to the task of named entity recognition.ResultsWe benchmark our approach on two different tasks. The first task is the identification of semantic relations between diseases and treatments. The available data set consists of manually annotated PubMed abstracts. The second task is the identification of relations between genes and diseases from a set of concise phrases, so-called GeneRIF (Gene Reference Into Function) phrases. In our experimental setting, we do not assume that the entities are given, as is often the case in previous relation extraction work. Rather the extraction of the entities is solved as a subproblem. Compared with other state-of-the-art approaches, we achieve very competitive results on both data sets. To demonstrate the scalability of our solution, we apply our approach to the complete human GeneRIF database. The resulting gene-disease network contains 34758 semantic associations between 4939 genes and 1745 diseases. The gene-disease network is publicly available as a machine-readable RDF graph.ConclusionWe extend the framework of Conditional Random Fields towards the annotation of semantic relations from text and apply it to the biomedical domain. Our approach is based on a rich set of textual features and achieves a performance that is competitive to leading approaches. The model is quite general and can be extended to handle arbitrary biological entities and relation types. The resulting gene-disease network shows that the GeneRIF database provides a rich knowledge source for text mining. Current work is focused on improving the accuracy of detection of entities as well as entity boundaries, which will also greatly improve the relation extraction performance.

Project description:Functional connectivity concerns the correlated activity between neuronal populations in spatially segregated regions of the brain, which may be studied using functional magnetic resonance imaging (fMRI). This coupled activity is conveniently expressed using covariance, but this measure fails to distinguish between direct and indirect effects. A popular alternative that addresses this issue is partial correlation, which regresses out the signal of potentially confounding variables, resulting in a measure that reveals only direct connections. Importantly, provided the data are normally distributed, if two variables are conditionally independent given all other variables, their respective partial correlation is zero. In this paper, we propose a probabilistic generative model that allows us to estimate functional connectivity in terms of both partial correlations and a graph representing conditional independencies. Simulation results show that this methodology is able to outperform the graphical LASSO, which is the de facto standard for estimating partial correlations. Furthermore, we apply the model to estimate functional connectivity for twenty subjects using resting-state fMRI data. Results show that our model provides a richer representation of functional connectivity as compared to considering partial correlations alone. Finally, we demonstrate how our approach can be extended in several ways, for instance to achieve data fusion by informing the conditional independence graph with data from probabilistic tractography. As our Bayesian formulation of functional connectivity provides access to the posterior distribution instead of only to point estimates, we are able to quantify the uncertainty associated with our results. This reveals that while we are able to infer a clear backbone of connectivity in our empirical results, the data are not accurately described by simply looking at the mode of the distribution over connectivity. The implication of this is that deterministic alternatives may misjudge connectivity results by drawing conclusions from noisy and limited data.

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Assessing semantic coherence in conditional probability estimates.

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Assessing semantic coherence in conditional probability estimates.

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