2014
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Are Bigger Data Sets Better for Machine Learning? Fusing Single-Point and Dual-Event Dose Response Data for Mycobacterium tuberculosis
Abstract: Tuberculosis is a major neglected disease for which the quest to find new treatments continues. There is an abundance of data from large phenotypic screens in the public domain against Mycobacterium tuberculosis (Mtb). Since machine learning methods can learn from past data, we were interested in addressing whether more data builds better models. We now describe using Bayesian machine learning to assess whether we can improve our models by combining the large quantities of single-point data with the much small… Show more
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“…The high-throughput docking/Bayesian workflow was, thus, able to find a small molecule (JSF-2164) with promising InhA inhibition, whole-cell activity, and modest SI versus Vero cells for a virtual screening hit. The hit rate of 2/19 (10.5%) compounds with acceptable antitubercular efficacy is similar to hit rates we have witnessed when implementing Bayesian models in previous ligand-based screens, which are more cost- and time-efficient than experimental HTS against M. tuberculosis (hit rates <1%). Additionally, the Bayesian approach removed from consideration whole-cell inactive compounds, as the TAACF-CB2 model’s lowest scoring five candidates all exhibited MIC values between 125 and 250 μM.…”
Section: Discussionsupporting
confidence: 71%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD).
Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD.
The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC).
Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
“…The high-throughput docking/Bayesian workflow was, thus, able to find a small molecule (JSF-2164) with promising InhA inhibition, whole-cell activity, and modest SI versus Vero cells for a virtual screening hit. The hit rate of 2/19 (10.5%) compounds with acceptable antitubercular efficacy is similar to hit rates we have witnessed when implementing Bayesian models in previous ligand-based screens, which are more cost- and time-efficient than experimental HTS against M. tuberculosis (hit rates <1%). Additionally, the Bayesian approach removed from consideration whole-cell inactive compounds, as the TAACF-CB2 model’s lowest scoring five candidates all exhibited MIC values between 125 and 250 μM.…”
Section: Discussionsupporting
confidence: 71%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD).
Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD.
The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC).
Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
“…We found that the larger Mtb model slightly edged out the smaller ChEMBL data set, but the statistics were nearly identical. In a previous study we saw a similar plateauing of model ROC when assessing different dataset sizes 18 .…”
Section: Discussionsupporting
confidence: 67%
“…In a previous study, we saw a similar plateauing of model ROC when assessing different data set sizes. 18 One method to expand the usefulness of these larger models using Bayesian models would be to utilize a nearest neighbors approach. If a model weighted the final prediction score based on both the Bayesian score and the kNN score (weighted by the model size), this may yield more accurate predictions.…”
Section: Molecular Pharmaceuticssupporting
confidence: 76%
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD).
Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD.
The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC).
Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
“…The ROC values for the M. tuberculosis models are comparable to those published recently using a commercial tool. For example, in this study MLSMR single-point model three-fold ROC = 0.87 (Figure S1, five-fold ROC 0.87, leave out 50% × 100 cross-validation ROC = 0.86) and MLSMR dose–response model three-fold cross-validation ROC = 0.75 (leave out 50% × 100 cross-validation ROC = 0.73), M. tuberculosis efficacy in mouse three-fold ROC = 0.73 (five-fold ROC = 0.73), and Ames mutagenicity three-fold ROC = 0.83 (five-fold ROC = 0.84).…”
Section: Resultsmentioning
confidence: 71%
Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets
J. Chem. Inf. Model.
Self Cite
Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD).
Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD.
The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC).
Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.
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