1,114 research outputs found
Advancing Biomedicine with Graph Representation Learning: Recent Progress, Challenges, and Future Directions
Graph representation learning (GRL) has emerged as a pivotal field that has
contributed significantly to breakthroughs in various fields, including
biomedicine. The objective of this survey is to review the latest advancements
in GRL methods and their applications in the biomedical field. We also
highlight key challenges currently faced by GRL and outline potential
directions for future research.Comment: Accepted by 2023 IMIA Yearbook of Medical Informatic
DHLP 1&2: Giraph based distributed label propagation algorithms on heterogeneous drug-related networks
Background and Objective: Heterogeneous complex networks are large graphs
consisting of different types of nodes and edges. The knowledge extraction from
these networks is complicated. Moreover, the scale of these networks is
steadily increasing. Thus, scalable methods are required. Methods: In this
paper, two distributed label propagation algorithms for heterogeneous networks,
namely DHLP-1 and DHLP-2 have been introduced. Biological networks are one type
of the heterogeneous complex networks. As a case study, we have measured the
efficiency of our proposed DHLP-1 and DHLP-2 algorithms on a biological network
consisting of drugs, diseases, and targets. The subject we have studied in this
network is drug repositioning but our algorithms can be used as general methods
for heterogeneous networks other than the biological network. Results: We
compared the proposed algorithms with similar non-distributed versions of them
namely MINProp and Heter-LP. The experiments revealed the good performance of
the algorithms in terms of running time and accuracy.Comment: Source code available for Apache Giraph on Hadoo
Knowledge graphs for covid-19: An exploratory review of the current landscape
Background: Searching through the COVID-19 research literature to gain actionable clinical insight is a formidable task, even for experts. The usefulness of this corpus in terms of improving patient care is tied to the ability to see the big picture that emerges when the studies are seen in conjunction rather than in isolation. When the answer to a search query requires linking together multiple pieces of information across documents, simple keyword searches are insufficient. To answer such complex information needs, an innovative artificial intelligence (AI) technology named a knowledge graph (KG) could prove to be effective. Methods: We conducted an exploratory literature review of KG applications in the context of COVID-19. The search term used was "covid-19 knowledge graph". In addition to PubMed, the first five pages of search results for Google Scholar and Google were considered for inclusion. Google Scholar was used to include non-peer-reviewed or non-indexed articles such as pre-prints and conference proceedings. Google was used to identify companies or consortiums active in this domain that have not published any literature, peer-reviewed or otherwise. Results: Our search yielded 34 results on PubMed and 50 results each on Google and Google Scholar. We found KGs being used for facilitating literature search, drug repurposing, clinical trial mapping, and risk factor analysis. Conclusions: Our synopses of these works make a compelling case for the utility of this nascent field of research
Knowledge-based Biomedical Data Science 2019
Knowledge-based biomedical data science (KBDS) involves the design and
implementation of computer systems that act as if they knew about biomedicine.
Such systems depend on formally represented knowledge in computer systems,
often in the form of knowledge graphs. Here we survey the progress in the last
year in systems that use formally represented knowledge to address data science
problems in both clinical and biological domains, as well as on approaches for
creating knowledge graphs. Major themes include the relationships between
knowledge graphs and machine learning, the use of natural language processing,
and the expansion of knowledge-based approaches to novel domains, such as
Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages
with 3 table
Natural Language Processing for Drug Discovery Knowledge Graphs: promises and pitfalls
Building and analysing knowledge graphs (KGs) to aid drug discovery is a
topical area of research. A salient feature of KGs is their ability to combine
many heterogeneous data sources in a format that facilitates discovering
connections. The utility of KGs has been exemplified in areas such as drug
repurposing, with insights made through manual exploration and modelling of the
data. In this article, we discuss promises and pitfalls of using natural
language processing (NLP) to mine unstructured text typically from scientific
literature as a data source for KGs. This draws on our experience of initially
parsing structured data sources such as ChEMBL as the basis for data within a
KG, and then enriching or expanding upon them using NLP. The fundamental
promise of NLP for KGs is the automated extraction of data from millions of
documents a task practically impossible to do via human curation alone.
However, there are many potential pitfalls in NLP-KG pipelines such as
incorrect named entity recognition and ontology linking all of which could
ultimately lead to erroneous inferences and conclusions.Comment: 17 pages, 7 figure
Exposing Provenance Metadata Using Different RDF Models
A standard model for exposing structured provenance metadata of scientific
assertions on the Semantic Web would increase interoperability,
discoverability, reliability, as well as reproducibility for scientific
discourse and evidence-based knowledge discovery. Several Resource Description
Framework (RDF) models have been proposed to track provenance. However,
provenance metadata may not only be verbose, but also significantly redundant.
Therefore, an appropriate RDF provenance model should be efficient for
publishing, querying, and reasoning over Linked Data. In the present work, we
have collected millions of pairwise relations between chemicals, genes, and
diseases from multiple data sources, and demonstrated the extent of redundancy
of provenance information in the life science domain. We also evaluated the
suitability of several RDF provenance models for this crowdsourced data set,
including the N-ary model, the Singleton Property model, and the
Nanopublication model. We examined query performance against three commonly
used large RDF stores, including Virtuoso, Stardog, and Blazegraph. Our
experiments demonstrate that query performance depends on both RDF store as
well as the RDF provenance model
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