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Interpretable Drug Target Prediction Using Deep Neural Representation

Kyle Yingkai Gao, Achille Fokoue, Heng Luo, Arun Iyengar, Sanjoy Dey, Ping Zhang
2018 Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence  
The identification of drug-target interactions (DTIs) is a key task in drug discovery, where drugs are chemical compounds and targets are proteins.  ...  Overall, the results show that our model outperforms other approaches without requiring domain knowledge and feature engineering.  ...  Meanwhile, machine learning approaches are very promising as they enable large scale testing of candidates in a relatively short time.  ... 
doi:10.24963/ijcai.2018/468 dblp:conf/ijcai/GaoFLIDZ18 fatcat:gtgxi2cfdzd45jjbnorpndonxe

Predicting Rich Drug-Drug Interactions via Biomedical Knowledge Graphs and Text Jointly Embedding [article]

Meng Wang
2018 arXiv   pre-print
First, a large-scale drug knowledge graph is generated from different sources. Then, the knowledge graph is embedded with comprehensive biomedical text into a common low dimensional space.  ...  Most existing studies focus on predicting binary drug-drug interactions between drug pairs but ignore other interactions.  ...  Independent similarity scores for a candidate pair of drugs are computed and used as the input for a machine learning classifier (e.g., a logistic regression model), which outputs a binary prediction.  ... 
arXiv:1712.08875v4 fatcat:byh5k47nb5axhgfyn3vgnqawqu

An effective algorithm for hyperparameter optimization of neural networks [article]

Gonzalo Diaz, Achille Fokoue, Giacomo Nannicini, Horst Samulowitz
2017 arXiv   pre-print
The performance of the proposed methodology is assessed on benchmark sets and in the context of predicting drug-drug interactions, showing promising results.  ...  A major challenge in designing neural network (NN) systems is to determine the best structure and parameters for the network given the data for the machine learning problem at hand.  ...  22] that was built to receive various sources of drug-related data and knowledge as inputs, and provide drug-drug interaction (DDI) predictions as outputs.  ... 
arXiv:1705.08520v1 fatcat:zmmfiiicozau5h2ocbgxqbn27u

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings

Remzi Celebi, Huseyin Uyar, Erkan Yasar, Ozgur Gumus, Oguz Dikenelli, Michel Dumontier
2019 BMC Bioinformatics  
We also tested RDF2Vec on various drug knowledge graphs such as DrugBank, PharmGKB and KEGG to predict unknown drug-drug interactions.  ...  Predicting potential drug-drug interaction helps reduce unanticipated drug interactions and drug development costs and optimizes the drug design process.  ...  Emre Guney for providing his feedback on proposed cross-validation method.  ... 
doi:10.1186/s12859-019-3284-5 pmid:31852427 pmcid:PMC6921491 fatcat:qd7ugkxhpzhszmk6dtv6dt63qm

Simultaneous learning of individual microRNA-gene interactions and regulatory comodules

Michael Roth, Pranjal Jain, Jinkyu Koo, Somali Chaterji
2021 BMC Bioinformatics  
We developed Theia, an effective method for simultaneously predicting miRNA-gene interactions and regulatory comodules, which group functionally related miRNAs and genes via non-negative matrix factorization  ...  Although it is known that miRNAs act combinatorially to regulate genes, precise identification of miRNA-gene interactions and their specific functional roles in regulatory comodules remains a challenge  ...  The ARI for Tiresias cannot be calculated because Tiresias only predicts miRNA-gene interactions; thus, we plot the F 1 score a second time (bottom left) with a different axis to show Tiresias reaching  ... 
doi:10.1186/s12859-021-04151-2 pmid:33971820 fatcat:kg6a4pmfgreu7mbymut3geqfei

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches

Pantelis Natsiavas, Andigoni Malousi, Cédric Bousquet, Marie-Christine Jaulent, Vassilis Koutkias
2019 Frontiers in Pharmacology  
Knowledge Engineering (KE) is the Computer Science discipline elaborating on methods and tools for developing "knowledge-intensive" systems, depending on a conceptual "knowledge" schema and some kind of  ...  Various exemplar applications were identified with promising results, e.g., improvement in Adverse Drug Reaction (ADR) prediction, detection of drug interactions, and novel ADE profiles related with specific  ...  Finally, Tiresias, a DDI prediction system relying on a large integrated RDF knowledge base, was successfully used to predict DDIs, identifying 68% of all DDIs found after 2011, using only information  ... 
doi:10.3389/fphar.2019.00415 pmid:31156424 pmcid:PMC6533857 fatcat:pljcyqcp6red7pdwa5burxgbx4

THE UNIVERSITY OF NEW SOUTH WALES

1961 Medical Journal of Australia  
At LOBE I learned the skills necessary for the production of large scale, large format images from Dr Nicole Aebischer.  ...  The concrete holographic image which is of a sufficiently large format and scale has qualities which are perceptually interpreted as 'presence'.  ...  Rather the image simulates the environment/habitat as accompaniment. 384 "Let the word 'melody' as I have discussed it from Proust therefore serve as a name both for an actual melody and for any other  ... 
doi:10.5694/j.1326-5377.1961.tb69461.x fatcat:xjlce5jn25edzoiqwwijlhsojy

How Sustainable Enterprises Can Drive The Sustainable Development

Patrizia Gazzola, Eka Sepashvili, Roberta Pezzetti
2018 European Scientific Journal  
Acknowledgement We wish to acknowledge Román Salgado Maximiliano, Ramirez Miranda María Alejandra, Jaimes Pérez Josué Iván, Martínez Carrillo Eligio, and González Torres Arturo for their advice, guidance  ...  , and direction in the course of this study.  ...  For this purpose, the patient accepts techniques and methods to facilitate behavioral control and coping with the need for psychoactive drugs.  ... 
doi:10.19044/esj.2018.c3p3 fatcat:bfdk5wm6wvbg5ann2tzuymivdq

William Faulkner: From Jefferson to the World

William Van O'Connor, Hyatt H. Waggoner
1962 American Literature  
drug store fiction.  ...  The interaction of these perspectives has prepared us to accept the interpretation implicit in the impersonal reporting of the last section.  ... 
doi:10.2307/2923753 fatcat:3brgtx7jojcy7k2tbwhteyf7ri

K–O [chapter]

2021 Dictionary of World Biography  
A guerilla and bandit for 30 years, his forces overthrew *Mobutu in July 1997 and he became President of the Democratic Republic of the Congo (formerly Zaire).  ...  In 2018, a corrupt and violent election was won by an opposition candidate Félix Tshisekedi; a bizarre result that appeared to be a democratic transition but was engineered to guarantee Kabila's continuing  ...  drugs.  ... 
doi:10.22459/dwb.2021.06 fatcat:vmshfpjaxzgldcqatjrznpujay

LANGUAGE IN INDIA Strength for Today and Bright Hope for Tomorrow

J Sundarsingh, M Thirumalai, B Mallikarjun, Sam, B A Sharada, A R Fatihi, Lakhan, K Karunakaran, Marie Jennifer, Bayer, J Sundarsingh
unpublished
This is based on the Greek mythology, in which, Tiresias was a blind prophet of Thebes, known for being transformed into a woman for seven years (http://en.wikipedia.org/wiki/Tiresias).  ...  for evaluation are the features of the laboratory that makes teaching learning more individualized, interactive, innovative and interesting.  ...  The challenge for teachers is to make judicious use of the machine. The machine is always under the control of the teacher.  ... 
fatcat:7sefwvrs5nahln4io7k5onqzk4

Freud, Fiction, and the Articulation of Truth in Modern Psychological Science Perspectives in Medical Humanities General Editor Recent Titles

-Joseph Martin, Anne Lefler, Dean Emeritus, Brian Dolan, Henry Bourne
unpublished
The book is a treasure with deep significance for everyone. A fresh, lucid, and imaginative look at Freud's influence on how we read ourselves and the work-art and love-we undertake.  ...  Our series invites scholars from the humanities and health care professions to share narratives and analysis on health, healing, and the contexts of our beliefs and practices that impact biomedical inquiry  ...  Cardozo in Boston and Patricia van der Leun in New York for their encouragement in this project, and, for my education at every turn, to those persons to whom the book is dedicated.  ... 
fatcat:opc2dqnkjrfbxl2x5vdzjpujsq

ISBN 9780983463962 Author Publication Date Freud, Fiction, and the Articulation of Truth in Modern Psychological Science Perspectives in Medical Humanities General Editor Recent Titles

Miyawaki, -Joseph Martin, Anne Lefler, Dean Emeritus, Brian Dolan, Henry Bourne
2012 unpublished
The book is a treasure with deep significance for everyone. A fresh, lucid, and imaginative look at Freud's influence on how we read ourselves and the work-art and love-we undertake.  ...  Our series invites scholars from the humanities and health care professions to share narratives and analysis on health, healing, and the contexts of our beliefs and practices that impact biomedical inquiry  ...  Cardozo in Boston and Patricia van der Leun in New York for their encouragement in this project, and, for my education at every turn, to those persons to whom the book is dedicated.  ... 
fatcat:unjuk6rlizcrdondhdrsv54flu

Whole Issue

Diana Villanueva-Romero
2018 Ecozon@  
This interpretation of myth is particularly compelling for those narratives that indeed portray the origins of human society in their foundational interactions with nonhuman nature.  ...  Mortimer has applied her impressive book learning to her new career, gleaning valuable knowledge from "agricultural reports and farm publications" (279).  ...  There is not merely one way for humans to interact with or experience ecologies and environments, and the more often we are reminded of this, the better.  ... 
doi:10.37536/ecozona.2018.9.2.2807 fatcat:ck6thqvfqjgqve5ug22j7yz6fy

Possible knowledge: forms of literary and scientific thought in early modern England

Debapriya Sarkar
2014
Possible knowledge emerges from elements crucial to our understanding of the literary, including mimesis, utopian discourse, and dramatic enactment, and it crosses generic boundaries.  ...  I engage with the history and philosophy of science to show how the techniques of writing associated with possible knowledge are visible across modern disciplinary divides: the error and the endlessness  ...  This analogical reasoning relies largely on the regularity of surroundings and on the predictability of the past.  ... 
doi:10.7282/t3s75dpg fatcat:x2zgimvhareczesm4flerzj3k4
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