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Validation and Topic-driven Ranking for Biomedical Hypothesis Generation Systems [article]

Justin Sybrandt, Ilya Safro
2018 bioRxiv   pre-print
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]

Justin Sybrandt, Ilya Tyagin, Michael Shtutman, Ilya Safro
2020 arXiv   pre-print
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]

Justin Sybrandt, Michael Shtutman, Ilya Safro
2018 arXiv   pre-print
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

Tanja Bekhuis
2006 Biomedical Digital Libraries  
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

Maggie P. Y. Lam, Vidya Venkatraman, Yi Xing, Edward Lau, Quan Cao, Dominic C. M. Ng, Andrew I. Su, Junbo Ge, Jennifer E. Van Eyk, Peipei Ping
2016 Journal of Proteome Research  
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

A. Faro, D. Giordano, C. Spampinato
2011 Briefings in Bioinformatics  
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

Lawrence E. Hunter, Tobias Kuhn
2017 Data Science  
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

Adam K. Kehoe, Vetle I. Torvik, Matthew B. Ross, Neil R. Smalheiser
2017 Proceedings of the 1st Workshop on Scholarly Web Mining - SWM '17  
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

Ute A. Gamm, Brendan K. Huang, Mansoor Syed, Xuchen Zhang, Vineet Bhandari, Michael A. Choma
2015 Journal of Biomedical Optics  
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]

Vit Novacek
2015 arXiv   pre-print
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]

Qingyu Chen, Robert Leaman, Alexis Allot, Ling Luo, Chih-Hsuan Wei, Shankai Yan, Zhiyong Lu
2021 arXiv   pre-print
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  
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]

Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Yong Chen, Cui Tao
2022 arXiv   pre-print
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

Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
2013 Journal of Biomedical Informatics  
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

Yong-gang Cao, James J. Cimino, John Ely, Hong Yu
2010 Journal of Biomedical Informatics  
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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