Text and data mining for human drug understanding

Publication Type:
Thesis
Issue Date:
2019
Full metadata record
This research employs text and data mining methods to gain valuable knowledge for human drugs. Specifically, computational methods are developed for three topics, namely drug-side-effect prediction, drug-target identification, and drug-drug-interaction detection. The key innovations of the proposed methods lie in the feature space construction using medical domain knowledge, generation of reliable negative samples, and successful application of machine learning algorithms. The drug-side-effect prediction problems are studied in Chapters 3-5. Side-effects are secondary phenotypic responses of human organisms to drug treatments. Side-effect prediction is an important topic for drugs especially in post-marketing surveillance because they cause significant fatality and severe morbidity. To overcome the limitations of existing computational methods such as lack of proper drug representation and reliable negative samples, this thesis presents three novel methods. The first method is to predict side-effects for single drug medication as described in Chapter 3. A comprehensive drug similarity framework is developed by integrating several types of similarities measured by representative features of drugs first. Then reliable negative samples are generated through analyzing the comprehensive drug similarities. Trained with generated reliable negatives, the prediction performance of four classical classifiers are improved significantly, outperforming those state-of-the-art methods. Chapter 4 describes the method proposed to predict side-effects for combined medication of multi-drugs. A scoring method on a drug-disease-gene tripartite network is developed to prioritize interacting drugs, paving a way to generate credible negative samples for side-effect prediction of combined medication. It creatively characterized a drug with its chemical structures, target proteins, substituents, and enriched pathways. The drug-drug pairs are represented as novel feature vectors to train binary classifiers for prediction. This novel representation and the inferred negative samples contribute to the superior performance of the proposed method in drug-drug-side-effect association prediction. Chapter 5 introduces the last method for detecting adverse drug reactions (ADRs, i.e., side-effects) from medical forums. It filters the cause-result relationship between drugs and ADRs using a self-built dictionary and detects drug-ADRs associations by information entropy. Compared with conventional co-occurrence based methods, the proposed method captures both high-frequency and low-frequency ADRs simultaneously. Besides, it returns drug-related ADRs only owing to the self-built relation dictionary. Drug-target identification plays a crucial role in drug discovery. Existing computational methods have achieved remarkable prediction accuracy, however, usually obtain poor prediction efficiency due to computational problems. Chapter 6 presents a method to improve the prediction efficiency using an advanced technique named anchor graph hashing (AGH). AGH embeds data into low-dimensional Hamming space while maintaining the neighbourship. It turns the drug-target identification problem into a binary classification task where inputs are AGH-embedded vectors of drug-target pairs, and labels are judgments of their associations. Ensemble learning with random forest and XGBoost is employed to learn a good decision boundary. The proposed method is demonstrated to be the most efficient method and achieves comparable prediction accuracy with the best literature method. Chapter 7 introduces a novel positive-unlabeled learning method named DDI-PULearn for large-scale detection of drug-drug interactions (DDIs). DDI-PULearn first generates seeds of reliable negatives via OCSVM (one-class support vector machine) under a high-recall constraint and via the cosine-similarity based KNN (k-nearest neighbors) as well. Then trained with all the labeled positives (i.e., validated DDIs) and the generated seed negatives, DDI-PULearn employs an iterative SVM to identify the set of entire reliable negatives from the unlabeled samples. The identified negatives and validated positives are represented as vectors using the bit-wise similarity of corresponding drug pairs to train random forest for prediction. Its excellent performance is confirmed by comparing with two baseline methods and five state-of-the-art methods.
Please use this identifier to cite or link to this item: