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Validation and Topic-driven Ranking for Biomedical Hypothesis Generation Systems
[article]
2018
bioRxiv
pre-print
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Using an in-progress system, MOLIERE, as a case-study, we show the utility of our validation and ranking methods. ...
To expedite their searches, some scientists leverage hypothesis generation (HG) systems, which can automatically inspect published papers to uncover novel implicit connections. ...
Another extremely important use case of ranking is related to massive query runs in hypothesis generation systems. ...
doi:10.1101/263897
fatcat:rd3exyewxzd5fnepjjrctzuaxy
AGATHA: Automatic Graph-mining And Transformer based Hypothesis generation Approach
[article]
2020
arXiv
pre-print
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We present AGATHA, a deep-learning hypothesis generation system that can introduce data-driven insights earlier in the discovery process. ...
Hypothesis generation systems address this challenge by mining the wealth of publicly available scientific information to predict plausible research directions. ...
Moliere, our prior hypothesis generation system [39] , produces data for scientific interpretation in the form of LDA topic models [7] . ...
arXiv:2002.05635v1
fatcat:t6jbr53fqrhytm2avreoufvs4y
Large-Scale Validation of Hypothesis Generation Systems via Candidate Ranking
[article]
2018
arXiv
pre-print
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Finally, we demonstrate that our proposed validation method aligns with real-world research goals by deploying our method within Moliere, our recent topic-driven HG system, in order to automatically generate ...
The first step of many research projects is to define and rank a short list of candidates for study. ...
Our contribution: In this paper we propose novel hypothesis ranking methods and a method to validate HG systems that does not require expert input and allows for large validation sets. ...
arXiv:1802.03793v4
fatcat:27scdbhytvbc7k232wtmcblpiq
Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
2006
Biomedical Digital Libraries
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Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. ...
Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians ...
This is a major problem for developers of hypothesis generating systems. However, a variant of this approach is possible. ...
doi:10.1186/1742-5581-3-2
pmid:16584552
pmcid:PMC1459187
fatcat:43hj56ap6zd4jbr53vf5mwq7ra
Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems
2016
Journal of Proteome Research
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Much of biomedical research concerns interrogating disease signature proteins and defining their roles in disease mechanisms. ...
The general approach and protein lists presented here may be used to guide rational experimental design in optimizing MRM transitions for any given topic for which there have been literature publications ...
Their effective dissemination for clinical and hypothesis-testing applications is becoming a pressing objective that promises a transformative impact on biomedical research, both within individual laboratories ...
doi:10.1021/acs.jproteome.6b00095
pmid:27356587
pmcid:PMC5120959
fatcat:xelitadkkfevjhes74xyyvdp6i
Combining literature text mining with microarray data: advances for system biology modeling
2011
Briefings in Bioinformatics
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genes with elements for biological understanding and for generating and validating new biological hypothesis. ...
Under this scenario, this article reviews the knowledge discovery systems that fuse information from the literature, gathered by text mining, with microarray data for enriching the lists of down and upregulated ...
Usually, this is performed either with the goal of enriching the lists of down and up-regulated genes with elements for biological understanding or for generating and validating new biological hypothesis ...
doi:10.1093/bib/bbr018
pmid:21677032
fatcat:lvtg7ea74ngb5h6i2ywss6cjru
Knowledge-based biomedical Data Science
2017
Data Science
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Knowledge-based biomedical Data Science involves the design and implementation of computer systems that act as if they knew about biomedicine. ...
There are many ways in which a computational approach might act as if it knew something: for example, it might be able to answer a natural language question about a biomedical topic, or pass an exam; it ...
[40] and those aimed at hypothesis generation or refinement from data [11, 38] , as well as mixed initiative human-computer hypothesis generation [29] . ...
doi:10.3233/ds-170001
pmid:30294517
pmcid:PMC6171523
fatcat:d5kjfs24nvdsne4mmzrdfb5wsq
Predicting MeSH Beyond MEDLINE
2017
Proceedings of the 1st Workshop on Scholarly Web Mining - SWM '17
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Medical subject headings (MeSH) are a flexible and useful tool for describing biomedical concepts. ...
Here, we present MeSHier, a tool for assigning MeSH terms to biomedical documents based on abstract similarity and references to MEDLINE records. ...
The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. ...
doi:10.1145/3057148.3057155
pmid:30417176
pmcid:PMC6221467
dblp:conf/wsdm/KehoeTRS17
fatcat:z5xh3j2mfbaifpbtm3hsztw4da
Quantifying hyperoxia-mediated damage to mammalian respiratory cilia-driven fluid flow using particle tracking velocimetry optical coherence tomography
2015
Journal of Biomedical Optics
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The ability of PTV-OCT to detect biomedically relevant flow perturbations in the sub-100 μm∕s regime was validated by quantifying temperature-and drug-mediated modulation of flow performance in ex vivo ...
Overall, PTV-OCT imaging of cilia-driven fluid flow in ex vivo mouse trachea is a powerful and straightforward approach for studying factors that modulate and damage mammalian respiratory ciliary physiology ...
[8] [9] [10] [11] To date, the optimum dosage of oxygen for both adults 12, 13 and neonates 14 remains a topic of debate. ...
doi:10.1117/1.jbo.20.8.080505
pmid:26308164
pmcid:PMC4874052
fatcat:hmj5ke344jbyhib23wjadauq54
Formalising Hypothesis Virtues in Knowledge Graphs: A General Theoretical Framework and its Validation in Literature-Based Discovery Experiments
[article]
2015
arXiv
pre-print
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We present a framework for formalising so called hypothesis virtues within knowledge graphs. ...
We validate the proposed framework by experiments in literature-based discovery. The experiments have demonstrated the utility of our work and its superiority w.r.t. related approaches. ...
The terms in the topic refer to features of a biomedically relevant relationship that can be traced in literature. 2. ...
arXiv:1503.09137v2
fatcat:cefrm37m25aevcrq537umybevq
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP)
[article]
2021
arXiv
pre-print
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2020 pre-print arXiv:2010.16413v1 fatcat:ybe3qgvvtjey5jjrw24vyqn7ieOther Versions
This review surveys approximately 150 NLP studies and more than 50 systems and datasets addressing the COVID-19 pandemic. ...
We also describe work that directly addresses aspects of the pandemic through four additional tasks: topic modeling, sentiment and emotion analysis, caseload forecasting, and misinformation detection. ...
Second, model-driven processing methods are also used where a question needs to be processed into a compatible format for the later ranking models. ...
arXiv:2010.16413v2
fatcat:cxzxmnnbfrednpto4zkpnemltm
BEERE: a web server for biomedical entity expansion, ranking and explorations
2019
Nucleic Acids Research
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The output from BEERE includes: a list of the original entities matched with known relationships in databases; any expanded entities that may be generated from the analysis; the ranks and ranking scores ...
BEERE (Biomedical Entity Expansion, Ranking and Explorations) is a new web-based data analysis tool to help biomedical researchers characterize any input list of genes/proteins, biomedical terms or their ...
Meanwhile, conventional hypothesis-driven researchers, after performing literature studies of a biological research topic, may also find it challenging to follow through a comprehensive list of candidate ...
doi:10.1093/nar/gkz428
pmid:31114876
pmcid:PMC6602520
fatcat:vws52uajyreefdr53tos2beuo4
Mining On Alzheimer's Diseases Related Knowledge Graph to Identity Potential AD-related Semantic Triples for Drug Repurposing
[article]
2022
arXiv
pre-print
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The knowledge graph constructed can facilitate data-driven knowledge discoveries and the generation of novel hypotheses. ...
Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. ...
The knowledge graph we constructed can facilitate data-driven knowledge discovery and new hypothesis generation. A breadth of possibilities exists to further improve this framework. ...
arXiv:2202.08712v3
fatcat:do3sgo7b2rebhfaadd2k2mm57e
Biomedical text mining and its applications in cancer research
2013
Journal of Biomedical Informatics
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This integrated but unstructured biomedical text is of great value for cancer diagnostics, treatment, and prevention. ...
To address this issue, we describe the general workflow of text mining in cancer systems biology and each phase of the workflow. ...
BioText-Quest [73] is a biomedical text mining system for concept discovery that provides services such as biomedical named entity recognition, concept association, and hypothesis generation. ...
doi:10.1016/j.jbi.2012.10.007
pmid:23159498
fatcat:xd7j77sbwfhklkat6tael64lbq
Automatically extracting information needs from complex clinical questions
2010
Journal of Biomedical Informatics
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We achieved an F1 score of 76.0% for the task of general topic classification and 58.0% for keyword extraction. Our systems have been implemented into the larger question answering system AskHERMES. ...
We speculate that the performance of general topic classification and keyword extraction can be further improved if consistently annotated data are made available. ...
Any opinions, findings, or recommendations are those of the authors and do not necessarily reflect the views of the NIH and UWM. ...
doi:10.1016/j.jbi.2010.07.007
pmid:20670693
pmcid:PMC2991382
fatcat:rm3hug5kkzfkhf3t55ssgtf6tq
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