2,202 research outputs found
Disambiguation of biomedical text using diverse sources of information
Background: Like text in other domains, biomedical documents contain a range of terms with more than one possible meaning. These ambiguities form a significant obstacle to the automatic processing of biomedical texts. Previous approaches to resolving this problem have made use of various sources of information including linguistic features of the context in which the ambiguous term is used and domain-specific resources, such as UMLS.
Materials and methods: We compare various sources of information including ones which have been previously used and a novel one: MeSH terms. Evaluation is carried out using a standard test set (the NLM-WSD corpus).
Results: The best performance is obtained using a combination of linguistic features and MeSH terms. Performance of our system exceeds previously published results for systems evaluated using the same data set.
Conclusion: Disambiguation of biomedical terms benefits from the use of information from a variety of sources. In particular, MeSH terms have proved to be useful and should be used if available
Knowledge will Propel Machine Understanding of Content: Extrapolating from Current Examples
Machine Learning has been a big success story during the AI resurgence. One
particular stand out success relates to learning from a massive amount of data.
In spite of early assertions of the unreasonable effectiveness of data, there
is increasing recognition for utilizing knowledge whenever it is available or
can be created purposefully. In this paper, we discuss the indispensable role
of knowledge for deeper understanding of content where (i) large amounts of
training data are unavailable, (ii) the objects to be recognized are complex,
(e.g., implicit entities and highly subjective content), and (iii) applications
need to use complementary or related data in multiple modalities/media. What
brings us to the cusp of rapid progress is our ability to (a) create relevant
and reliable knowledge and (b) carefully exploit knowledge to enhance ML/NLP
techniques. Using diverse examples, we seek to foretell unprecedented progress
in our ability for deeper understanding and exploitation of multimodal data and
continued incorporation of knowledge in learning techniques.Comment: Pre-print of the paper accepted at 2017 IEEE/WIC/ACM International
Conference on Web Intelligence (WI). arXiv admin note: substantial text
overlap with arXiv:1610.0770
Medical WordNet: A new methodology for the construction and validation of information resources for consumer health
A consumer health information system must be able to comprehend both expert and non-expert medical vocabulary and to map between the two. We describe an ongoing
project to create a new lexical database called Medical WordNet (MWN), consisting of
medically relevant terms used by and intelligible to non-expert subjects and supplemented by a corpus of natural-language sentences that is designed to provide
medically validated contexts for MWN terms. The corpus derives primarily from online health information sources targeted to consumers, and involves two sub-corpora, called Medical FactNet (MFN) and Medical BeliefNet (MBN), respectively. The former consists of statements accredited as true on the basis of a rigorous process of validation, the latter of statements which non-experts believe to be true. We summarize the MWN / MFN / MBN project, and describe some of its applications
Hi, how can I help you?: Automating enterprise IT support help desks
Question answering is one of the primary challenges of natural language
understanding. In realizing such a system, providing complex long answers to
questions is a challenging task as opposed to factoid answering as the former
needs context disambiguation. The different methods explored in the literature
can be broadly classified into three categories namely: 1) classification
based, 2) knowledge graph based and 3) retrieval based. Individually, none of
them address the need of an enterprise wide assistance system for an IT support
and maintenance domain. In this domain the variance of answers is large ranging
from factoid to structured operating procedures; the knowledge is present
across heterogeneous data sources like application specific documentation,
ticket management systems and any single technique for a general purpose
assistance is unable to scale for such a landscape. To address this, we have
built a cognitive platform with capabilities adopted for this domain. Further,
we have built a general purpose question answering system leveraging the
platform that can be instantiated for multiple products, technologies in the
support domain. The system uses a novel hybrid answering model that
orchestrates across a deep learning classifier, a knowledge graph based context
disambiguation module and a sophisticated bag-of-words search system. This
orchestration performs context switching for a provided question and also does
a smooth hand-off of the question to a human expert if none of the automated
techniques can provide a confident answer. This system has been deployed across
675 internal enterprise IT support and maintenance projects.Comment: To appear in IAAI 201
Improving Broad-Coverage Medical Entity Linking with Semantic Type Prediction and Large-Scale Datasets
Medical entity linking is the task of identifying and standardizing medical
concepts referred to in an unstructured text. Most of the existing methods
adopt a three-step approach of (1) detecting mentions, (2) generating a list of
candidate concepts, and finally (3) picking the best concept among them. In
this paper, we probe into alleviating the problem of overgeneration of
candidate concepts in the candidate generation module, the most under-studied
component of medical entity linking. For this, we present MedType, a fully
modular system that prunes out irrelevant candidate concepts based on the
predicted semantic type of an entity mention. We incorporate MedType into five
off-the-shelf toolkits for medical entity linking and demonstrate that it
consistently improves entity linking performance across several benchmark
datasets. To address the dearth of annotated training data for medical entity
linking, we present WikiMed and PubMedDS, two large-scale medical entity
linking datasets, and demonstrate that pre-training MedType on these datasets
further improves entity linking performance. We make our source code and
datasets publicly available for medical entity linking research.Comment: 35 page
Knowledge-Driven Methods for Geographic Information Extraction in the Biomedical Domain
abstract: Accounting for over a third of all emerging and re-emerging infections, viruses represent a major public health threat, which researchers and epidemiologists across the world have been attempting to contain for decades. Recently, genomics-based surveillance of viruses through methods such as virus phylogeography has grown into a popular tool for infectious disease monitoring. When conducting such surveillance studies, researchers need to manually retrieve geographic metadata denoting the location of infected host (LOIH) of viruses from public sequence databases such as GenBank and any publication related to their study. The large volume of semi-structured and unstructured information that must be reviewed for this task, along with the ambiguity of geographic locations, make it especially challenging. Prior work has demonstrated that the majority of GenBank records lack sufficient geographic granularity concerning the LOIH of viruses. As a result, reviewing full-text publications is often necessary for conducting in-depth analysis of virus migration, which can be a very time-consuming process. Moreover, integrating geographic metadata pertaining to the LOIH of viruses from different sources, including different fields in GenBank records as well as full-text publications, and normalizing the integrated metadata to unique identifiers for subsequent analysis, are also challenging tasks, often requiring expert domain knowledge. Therefore, automated information extraction (IE) methods could help significantly accelerate this process, positively impacting public health research. However, very few research studies have attempted the use of IE methods in this domain.
This work explores the use of novel knowledge-driven geographic IE heuristics for extracting, integrating, and normalizing the LOIH of viruses based on information available in GenBank and related publications; when evaluated on manually annotated test sets, the methods were found to have a high accuracy and shown to be adequate for addressing this challenging problem. It also presents GeoBoost, a pioneering software system for georeferencing GenBank records, as well as a large-scale database containing over two million virus GenBank records georeferenced using the algorithms introduced here. The methods, database and software developed here could help support diverse public health domains focusing on sequence-informed virus surveillance, thereby enhancing existing platforms for controlling and containing disease outbreaks.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201
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