3,261 research outputs found
Evaluating Pre-trained Word Embeddings in domain specific Ontology Matching
Tese de mestrado, Ciência de Dados, Universidade de Lisboa, Faculdade de Ciências, 2022The ontology matching process focuses on discovering mappings between two concepts from distinct
ontologies, a source and a target. It is a fundamental step when trying to integrate heterogeneous data
sources that are described in ontologies. This data represents an even more challenging problem since
we are working with complex data as biomedical data. Thus, derived from the necessity of keeping on
improving ontology matching techniques, this dissertation focused on implementing a new approach to
the AML pipeline to calculate similarities between entities from two distinct ontologies.
For the implementation of this dissertation, we used some of the OAEI tracks, such as Anatomy
and LargeBio, to apply a new algorithm and evaluate if it improves AML’s results against a refer ence alignment. This new approach consisted of using pre-trained word embeddings of five different
types, BioWordVec Extrinsic, BioWordVec Intrinsic, PubMed+PC, PubMed+PC+Wikipedia and English
Wikipedia. These pre-trained word embeddings use a machine learning technique, Word2Vec, and were
used in this work since it allows to carry the semantic meaning inherent to the words represented with
the corresponding vector. Word embeddings allowed that each concept of each ontology was represented
with a corresponding vector to see if, with that information, it was possible to improve how relations
between concepts were determined in the AML system. The similarity between concepts was calculated
through the cosine distance and the evaluation of the new alignment used the metrics precision recall
and F-measure. Although we could not prove that word embeddings improve AML current results, this
implementation could be refined, and the technique can be still an option to consider in future work if
applied in some other way
Biomedical ontology alignment: An approach based on representation learning
While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results
Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules
Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed method is adequate in practice and can be integrated within the workflow of systems unable to cope with very large ontologies
Cross-lingual Entity Alignment via Joint Attribute-Preserving Embedding
Entity alignment is the task of finding entities in two knowledge bases (KBs)
that represent the same real-world object. When facing KBs in different natural
languages, conventional cross-lingual entity alignment methods rely on machine
translation to eliminate the language barriers. These approaches often suffer
from the uneven quality of translations between languages. While recent
embedding-based techniques encode entities and relationships in KBs and do not
need machine translation for cross-lingual entity alignment, a significant
number of attributes remain largely unexplored. In this paper, we propose a
joint attribute-preserving embedding model for cross-lingual entity alignment.
It jointly embeds the structures of two KBs into a unified vector space and
further refines it by leveraging attribute correlations in the KBs. Our
experimental results on real-world datasets show that this approach
significantly outperforms the state-of-the-art embedding approaches for
cross-lingual entity alignment and could be complemented with methods based on
machine translation
Ranking Significant Discrepancies in Clinical Reports
Medical errors are a major public health concern and a leading cause of death
worldwide. Many healthcare centers and hospitals use reporting systems where
medical practitioners write a preliminary medical report and the report is
later reviewed, revised, and finalized by a more experienced physician. The
revisions range from stylistic to corrections of critical errors or
misinterpretations of the case. Due to the large quantity of reports written
daily, it is often difficult to manually and thoroughly review all the
finalized reports to find such errors and learn from them. To address this
challenge, we propose a novel ranking approach, consisting of textual and
ontological overlaps between the preliminary and final versions of reports. The
approach learns to rank the reports based on the degree of discrepancy between
the versions. This allows medical practitioners to easily identify and learn
from the reports in which their interpretation most substantially differed from
that of the attending physician (who finalized the report). This is a crucial
step towards uncovering potential errors and helping medical practitioners to
learn from such errors, thus improving patient-care in the long run. We
evaluate our model on a dataset of radiology reports and show that our approach
outperforms both previously-proposed approaches and more recent language models
by 4.5% to 15.4%.Comment: ECIR 2020 (short
NLSC: Unrestricted Natural Language-based Service Composition through Sentence Embeddings
Current approaches for service composition (assemblies of atomic services)
require developers to use: (a) domain-specific semantics to formalize services
that restrict the vocabulary for their descriptions, and (b) translation
mechanisms for service retrieval to convert unstructured user requests to
strongly-typed semantic representations. In our work, we argue that effort to
developing service descriptions, request translations, and matching mechanisms
could be reduced using unrestricted natural language; allowing both: (1)
end-users to intuitively express their needs using natural language, and (2)
service developers to develop services without relying on syntactic/semantic
description languages. Although there are some natural language-based service
composition approaches, they restrict service retrieval to syntactic/semantic
matching. With recent developments in Machine learning and Natural Language
Processing, we motivate the use of Sentence Embeddings by leveraging richer
semantic representations of sentences for service description, matching and
retrieval. Experimental results show that service composition development
effort may be reduced by more than 44\% while keeping a high precision/recall
when matching high-level user requests with low-level service method
invocations.Comment: This paper will appear on SCC'19 (IEEE International Conference on
Services Computing) on July 1
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