scholarly journals Identification of Novel Plant Peroxisomal Targeting Signals by a Combination of Machine Learning Methods and in Vivo Subcellular Targeting Analyses

2011 ◽  
Vol 23 (4) ◽  
pp. 1556-1572 ◽  
Author(s):  
Thomas Lingner ◽  
Amr R. Kataya ◽  
Gerardo E. Antonicelli ◽  
Aline Benichou ◽  
Kjersti Nilssen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Subcellular Targeting ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Peroxisomal Targeting ◽  
Targeting Signals

scholarly journals Electrical impedance characterization of in vivo porcine tissue using machine learning

2021 ◽  
Vol 12 (1) ◽  
pp. 26-33
Author(s):  
Stephen Chiang ◽  
Matthew Eschbach ◽  
Robert Knapp ◽  
Brian Holden ◽  
Andrew Miesse ◽  
...  
Keyword(s):  
Machine Learning ◽  
Small Bowel ◽  
Electrical Impedance ◽  
Tissue Type ◽  
Support Vector ◽  
Learning Methods ◽  
K Nearest Neighbors ◽  
Porcine Tissue ◽  
Machine Learning Methods

Abstract The incorporation of sensors onto the stapling platform has been investigated to overcome the disconnect in our understanding of tissue handling by surgical staplers. The goal of this study was to explore the feasibility of in vivo porcine tissue differentiation using bioimpedance data and machine learning methods. In vivo electrical impedance measurements were obtained in 7 young domestic pigs, using a logarithmic sweep of 50 points over a frequency range of 100 Hz to 1 MHz. Tissues studied included lung, liver, small bowel, colon, and stomach, which was further segmented into fundus, body, and antrum. The data was then parsed through MATLAB's classification learner to identify the best algorithm for tissue type differentiation. The most effective classification scheme was found to be cubic support vector machines with 86.96% accuracy. When fundus, body and antrum were aggregated together as stomach, the accuracy improved to 88.03%. The combination of stomach, small bowel, and colon together as GI tract improved accuracy to 99.79% using fine k nearest neighbors. The results suggest that bioimpedance data can be effectively used to differentiate tissue types in vivo. This study is one of the first that combines in vivo bioimpedance tissue data across multiple tissue types with machine learning methods.

scholarly journals An Open Drug Discovery Competition: Experimental Validation of Predictive Models in a Series of Novel Antimalarials

2020 ◽  
Author(s):  
Edwin Tse ◽  
Laksh Aithani ◽  
Mark Anderson ◽  
Jonathan Cardoso-Silva ◽  
Giovanni Cincilla ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Predictive Models ◽  
Structural Information ◽  
Open Data ◽  
Ion Pump ◽  
Learning Methods ◽  
Machine Learning Methods

<p>The discovery of new antimalarial medicines with novel mechanisms of action is key to combating the problem of increasing resistance to our frontline treatments. The Open Source Malaria (OSM) consortium has been developing compounds ("Series 4") that have potent activity against <i>Plasmodium falciparum</i> <i>in vitro</i> and <i>in vivo</i> and that have been suggested to act through the inhibition of <i>Pf</i>ATP4, an essential membrane ion pump that regulates the parasite’s intracellular Na<sup>+</sup> concentration. The structure of <i>Pf</i>ATP4 is yet to be determined. In the absence of structural information about this target, a public competition was created to develop a model that would allow the prediction of anti-<i>Pf</i>ATP4 activity among Series 4 compounds, thereby reducing project costs associated with the unnecessary synthesis of inactive compounds.</p>In the first round, in 2016, six participants used the open data collated by OSM to develop moderately predictive models using diverse methods. Notably, all submitted models were available to all other participants in real time. Since then further bioactivity data have been acquired and machine learning methods have rapidly developed, so a second round of the competition was undertaken, in 2019, again with freely-donated models that other participants could see. The best-performing models from this second round were used to predict novel inhibitory molecules, of which several were synthesised and evaluated against the parasite. One such compound, containing a motif that the human chemists familiar with this series would have dismissed as ill-advised, was active. The project demonstrated the abilities of new machine learning methods in the prediction of active compounds where there is no biological target structure, frequently the central problem in phenotypic drug discovery. Since all data and participant interactions remain in the public domain, this research project “lives” and may be improved by others.

scholarly journals An Open Drug Discovery Competition: Experimental Validation of Predictive Models in a Series of Novel Antimalarials

2020 ◽  
Author(s):  
Edwin Tse ◽  
Laksh Aithani ◽  
Mark Anderson ◽  
Jonathan Cardoso-Silva ◽  
Giovanni Cincilla ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Predictive Models ◽  
Structural Information ◽  
Open Data ◽  
Ion Pump ◽  
Learning Methods ◽  
Machine Learning Methods

<p>The discovery of new antimalarial medicines with novel mechanisms of action is key to combating the problem of increasing resistance to our frontline treatments. The Open Source Malaria (OSM) consortium has been developing compounds ("Series 4") that have potent activity against <i>Plasmodium falciparum</i> <i>in vitro</i> and <i>in vivo</i> and that have been suggested to act through the inhibition of <i>Pf</i>ATP4, an essential membrane ion pump that regulates the parasite’s intracellular Na<sup>+</sup> concentration. The structure of <i>Pf</i>ATP4 is yet to be determined. In the absence of structural information about this target, a public competition was created to develop a model that would allow the prediction of anti-<i>Pf</i>ATP4 activity among Series 4 compounds, thereby reducing project costs associated with the unnecessary synthesis of inactive compounds.</p>In the first round, in 2016, six participants used the open data collated by OSM to develop moderately predictive models using diverse methods. Notably, all submitted models were available to all other participants in real time. Since then further bioactivity data have been acquired and machine learning methods have rapidly developed, so a second round of the competition was undertaken, in 2019, again with freely-donated models that other participants could see. The best-performing models from this second round were used to predict novel inhibitory molecules, of which several were synthesised and evaluated against the parasite. One such compound, containing a motif that the human chemists familiar with this series would have dismissed as ill-advised, was active. The project demonstrated the abilities of new machine learning methods in the prediction of active compounds where there is no biological target structure, frequently the central problem in phenotypic drug discovery. Since all data and participant interactions remain in the public domain, this research project “lives” and may be improved by others.

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