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Lexical patterns, features and knowledge resources for coreference resolution in clinical notes
Generation of entity coreference chains provides a means to extract linked narrative events from clinical notes, but despite being a well-researched topic in natural language processing, general- purpose coreference tools perform poorly on clinical texts. This paper presents a knowledge-centric and pattern-based approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA). In addition, a method for generating coreference chains using progressively pruned linked lists is demonstrated that reduces the search space and facilitates evaluation by a number of metrics. Independent evaluation results show an F-measure for each corpus of 79.2% and 87.5%, respectively, which offers performance at least as good as human annotators, greatly increased performance over general- purpose tools, and improvement on previously reported clinical coreference systems. The system uses a number of open-source components that are available to download
A Relation Extraction Approach for Clinical Decision Support
In this paper, we investigate how semantic relations between concepts
extracted from medical documents can be employed to improve the retrieval of
medical literature. Semantic relations explicitly represent relatedness between
concepts and carry high informative power that can be leveraged to improve the
effectiveness of retrieval functionalities of clinical decision support
systems. We present preliminary results and show how relations are able to
provide a sizable increase of the precision for several topics, albeit having
no impact on others. We then discuss some future directions to minimize the
impact of negative results while maximizing the impact of good results.Comment: 4 pages, 1 figure, DTMBio-KMH 2018, in conjunction with ACM 27th
Conference on Information and Knowledge Management (CIKM), October 22-26
2018, Lingotto, Turin, Ital
On the Effect of Semantically Enriched Context Models on Software Modularization
Many of the existing approaches for program comprehension rely on the
linguistic information found in source code, such as identifier names and
comments. Semantic clustering is one such technique for modularization of the
system that relies on the informal semantics of the program, encoded in the
vocabulary used in the source code. Treating the source code as a collection of
tokens loses the semantic information embedded within the identifiers. We try
to overcome this problem by introducing context models for source code
identifiers to obtain a semantic kernel, which can be used for both deriving
the topics that run through the system as well as their clustering. In the
first model, we abstract an identifier to its type representation and build on
this notion of context to construct contextual vector representation of the
source code. The second notion of context is defined based on the flow of data
between identifiers to represent a module as a dependency graph where the nodes
correspond to identifiers and the edges represent the data dependencies between
pairs of identifiers. We have applied our approach to 10 medium-sized open
source Java projects, and show that by introducing contexts for identifiers,
the quality of the modularization of the software systems is improved. Both of
the context models give results that are superior to the plain vector
representation of documents. In some cases, the authoritativeness of
decompositions is improved by 67%. Furthermore, a more detailed evaluation of
our approach on JEdit, an open source editor, demonstrates that inferred topics
through performing topic analysis on the contextual representations are more
meaningful compared to the plain representation of the documents. The proposed
approach in introducing a context model for source code identifiers paves the
way for building tools that support developers in program comprehension tasks
such as application and domain concept location, software modularization and
topic analysis
Mining Domain-Specific Thesauri from Wikipedia: A case study
Domain-specific thesauri are high-cost, high-maintenance, high-value knowledge structures. We show how the classic thesaurus structure of terms and links can be mined automatically from Wikipedia. In a comparison with a professional thesaurus for agriculture we find that Wikipedia contains a substantial proportion of its concepts and semantic relations; furthermore it has impressive coverage of contemporary documents in the domain. Thesauri derived using our techniques capitalize on existing public efforts and tend to reflect contemporary language usage better than their costly, painstakingly-constructed manual counterparts
Effect of heuristics on serendipity in path-based storytelling with linked data
Path-based storytelling with Linked Data on the Web provides users the ability to discover concepts in an entertaining and educational way. Given a query context, many state-of-the-art pathfinding approaches aim at telling a story that coincides with the user's expectations by investigating paths over Linked Data on the Web. By taking into account serendipity in storytelling, we aim at improving and tailoring existing approaches towards better fitting user expectations so that users are able to discover interesting knowledge without feeling unsure or even lost in the story facts. To this end, we propose to optimize the link estimation between - and the selection of facts in a story by increasing the consistency and relevancy of links between facts through additional domain delineation and refinement steps. In order to address multiple aspects of serendipity, we propose and investigate combinations of weights and heuristics in paths forming the essential building blocks for each story. Our experimental findings with stories based on DBpedia indicate the improvements when applying the optimized algorithm
Designing Semantic Kernels as Implicit Superconcept Expansions
Recently, there has been an increased interest in the exploitation of background knowledge in the context of text mining tasks, especially text classification. At the same time, kernel-based learning algorithms like Support Vector Machines have become a dominant paradigm in the text mining community. Amongst other reasons, this is also due to their capability to achieve more accurate learning results by replacing standard linear kernel (bag-of-words) with customized kernel functions which incorporate additional apriori knowledge. In this paper we propose a new approach to the design of âsemantic smoothing kernelsâ by means of an implicit superconcept expansion using well-known measures of term similarity. The experimental evaluation on two different datasets indicates that our approach consistently improves performance in situations where (i) training data is scarce or (ii) the bag-ofwords representation is too sparse to build stable models when using the linear kernel
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