Mohamed Khamis — Page 2

arXiv2018

DialPlate: Enhancing the Detection of Smooth Pursuits Eye Movements Using Linear Regression

We introduce and evaluate a novel approach for detecting smooth pursuit eye movements that increases the number of distinguishable targets and is more robust against false positives. Being natural and calibration-free, Pursuits has been gaining popularity in the past years. At the same time, current implementations show poor performance when more than eight on-screen targets are being used, thus limiting its applicability. Our approach (1) leverages the slope of a regression line, and (2) introduces a minimum signal duration that improves both the new and the traditional detection method. After introducing the approach as well as the implementation, we compare it to the traditional correlation-based Pursuits detection method. We tested the approach up to 24 targets and show that, if accepting a similar error rate, nearly twice as many targets can be distinguished compared to state of the art. For fewer targets, accuracy increases significantly. We believe our approach will enable more robust pursuit-based user interfaces, thus making it valuable for both researchers and practitioners.

cs.HC↗

arXiv2016

Deep learning is competing random forest in computational docking

Computational docking is the core process of computer-aided drug design; it aims at predicting the best orientation and conformation of a small drug molecule when bound to a target large protein receptor. The docking quality is typically measured by a scoring function: a mathematical predictive model that produces a score representing the binding free energy and hence the stability of the resulting complex molecule. We analyze the performance of both learning techniques on the scoring power, the ranking power, docking power, and screening power using the PDBbind 2013 database. For the scoring and ranking powers, the proposed learning scoring functions depend on a wide range of features (energy terms, pharmacophore, intermolecular) that entirely characterize the protein-ligand complexes. For the docking and screening powers, the proposed learning scoring functions depend on the intermolecular features of the RF-Score to utilize a larger number of training complexes. For the scoring power, the DL\_RF scoring function achieves Pearson's correlation coefficient between the predicted and experimentally measured binding affinities of 0.799 versus 0.758 of the RF scoring function. For the ranking power, the DL scoring function ranks the ligands bound to fixed target protein with accuracy 54% for the high-level ranking and with accuracy 78% for the low-level ranking while the RF scoring function achieves (46% and 62%) respectively. For the docking power, the DL\_RF scoring function has a success rate when the three best-scored ligand binding poses are considered within 2 Å root-mean-square-deviation from the native pose of 36.0% versus 30.2% of the RF scoring function. For the screening power, the DL scoring function has an average enrichment factor and success rate at the top 1% level of (2.69 and 6.45%) respectively versus (1.61 and 4.84%) respectively of the RF scoring function.

q-bio.BM↗