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Full-Text Articles in Computer Engineering
On Resource-Efficiency And Performance Optimization In Big Data Computing And Networking Using Machine Learning, Wuji Liu
Dissertations
Due to the rapid transition from traditional experiment-based approaches to large-scale, computational intensive simulations, next-generation scientific applications typically involve complex numerical modeling and extreme-scale simulations. Such model-based simulations oftentimes generate colossal amounts of data, which must be transferred over high-performance network (HPN) infrastructures to remote sites and analyzed against experimental or observation data on high-performance computing (HPC) facility. Optimizing the performance of both data transfer in HPN and simulation-based model development on HPC is critical to enabling and accelerating knowledge discovery and scientific innovation. However, such processes generally involve an enormous set of attributes including domain-specific model parameters, network transport …
Benchmarking Small-Dataset Structure-Activity-Relationship Models For Prediction Of Wnt Signaling Inhibition, Mahtab Kokabi
Benchmarking Small-Dataset Structure-Activity-Relationship Models For Prediction Of Wnt Signaling Inhibition, Mahtab Kokabi
Masters Theses
Quantitative structure-activity relationship (QSAR) models based on machine learning algorithms are powerful tools to expedite drug discovery processes and therapeutics development. Given the cost in acquiring large-sized training datasets, it is useful to examine if QSAR analysis can reasonably predict drug activity with only a small-sized dataset (size < 100) and benchmark these small-dataset QSAR models in application-specific studies. To this end, here we present a systematic benchmarking study on small-dataset QSAR models built for prediction of effective Wnt signaling inhibitors, which are essential to therapeutics development in prevalent human diseases (e.g., cancer). Specifically, we examined a total of 72 two-dimensional (2D) QSAR models based on 4 best-performing algorithms, 6 commonly used molecular fingerprints, and 3 typical fingerprint lengths. We trained these models using a training dataset (56 compounds), benchmarked their performance on 4 figures-of-merit (FOMs), and examined their prediction accuracy using an external validation dataset (14 compounds). Our data show that the model performance is maximized when: 1) molecular fingerprints are selected to provide sufficient, unique, and not overly detailed representations of the chemical structures of drug compounds; 2) algorithms are selected to reduce the number of false predictions due to class imbalance in the dataset; and 3) models are selected to reach balanced performance on all 4 FOMs. These results may provide general guidelines in developing high-performance small-dataset QSAR models for drug activity prediction.