6,820 research outputs found
Entropy and Graph Based Modelling of Document Coherence using Discourse Entities: An Application
We present two novel models of document coherence and their application to
information retrieval (IR). Both models approximate document coherence using
discourse entities, e.g. the subject or object of a sentence. Our first model
views text as a Markov process generating sequences of discourse entities
(entity n-grams); we use the entropy of these entity n-grams to approximate the
rate at which new information appears in text, reasoning that as more new words
appear, the topic increasingly drifts and text coherence decreases. Our second
model extends the work of Guinaudeau & Strube [28] that represents text as a
graph of discourse entities, linked by different relations, such as their
distance or adjacency in text. We use several graph topology metrics to
approximate different aspects of the discourse flow that can indicate
coherence, such as the average clustering or betweenness of discourse entities
in text. Experiments with several instantiations of these models show that: (i)
our models perform on a par with two other well-known models of text coherence
even without any parameter tuning, and (ii) reranking retrieval results
according to their coherence scores gives notable performance gains, confirming
a relation between document coherence and relevance. This work contributes two
novel models of document coherence, the application of which to IR complements
recent work in the integration of document cohesiveness or comprehensibility to
ranking [5, 56]
The lifecycle of provenance metadata and its associated challenges and opportunities
This chapter outlines some of the challenges and opportunities associated
with adopting provenance principles and standards in a variety of disciplines,
including data publication and reuse, and information sciences
The Phyre2 web portal for protein modeling, prediction and analysis
Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission
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