A Knowledge-Graph-Based Multimodal Deep Learning Framework for Identifying Drug-Drug Interactions.

The identification of drug-drug interactions (DDIs) plays a crucial role in various areas of drug development. In this study, a deep learning framework (KGCN_NFM) is presented to recognize DDIs using coupling knowledge graph convolutional networks (KGCNs) with neural factorization machines (NFMs). A KGCN is used to learn the embedding representation containing high-order structural information and semantic information in the knowledge graph (KG). The embedding and the Morgan molecular fingerprint of drugs are then used as input of NFMs to predict DDIs. The performance and effectiveness of the current method have been evaluated and confirmed based on the two real-world datasets with different sizes, and the results demonstrate that KGCN_NFM outperforms the state-of-the-art algorithms. Moreover, the identified interactions between topotecan and dantron by KGCN_NFM were validated through MTT assays, apoptosis experiments, cell cycle analysis, and molecular docking. Our study shows that the combination therapy of the two drugs exerts a synergistic anticancer effect, which provides an effective treatment strategy against lung carcinoma. These results reveal that KGCN_NFM is a valuable tool for integrating heterogeneous information to identify potential DDIs.

GAIN: A Gated Adaptive Feature Interaction Network for Click-Through Rate Prediction.

CTR (Click-Through Rate) prediction has attracted more and more attention from academia and industry for its significant contribution to revenue. In the last decade, learning feature interactions have become a mainstream research direction, and dozens of feature interaction-based models have been proposed for the CTR prediction task. The most common approach for existing models is to enumerate all possible feature interactions or to learn higher-order feature interactions by designing complex models. However, a simple enumeration will introduce meaningless and harmful interactions, and a complex model structure will bring a higher complexity. In this work, we propose a lightweight, yet effective model called the Gated Adaptive feature Interaction Network (GAIN). We devise a novel cross module to drop meaningless feature interactions and preserve informative ones. Our cross module consists of multiple gated units, each of which can independently learn an arbitrary-order feature interaction. We combine the cross module with a deep module into GAIN and conduct comparative experiments with state-of-the-art models on two public datasets to verify its validity. Our experimental results show that GAIN can achieve a comparable or even better performance compared to its competitors. Furthermore, in order to verify the effectiveness of the feature interactions learned by GAIN, we transfer learned interactions to other models, such as Logistic Regression (LR) and Factorization Machines (FM), and find out that their performance can be significantly improved.

Factorization machines and deep views-based co-training for improving answer quality prediction in online health expert question-answering services.

In online health expert question-answering (HQA) services, it is significant to automatically determine the quality of the answers. There are two prominent challenges in this task. First, the answers are usually written in short text, which makes it difficult to absorb the text semantic information. Second, it usually lacks sufficient labeled data but contains a huge amount of unlabeled data. To tackle these challenges, we propose a novel deep co-training framework based on factorization machines (FM) and deep textual views to intelligently and automatically identify the quality of HQA systems. More specifically, we exploit additional domain-specific semantic information from domain-specific word embeddings to expand the semantic space of short text and apply FM to excavate the non-independent interaction relationships among diverse features within individual views for improving the performance of the base classifier via co-training. Our learned deep textual views, the convolutional neural networks (CNN) view which focuses on extracting local features using convolution filters to locally model short text and the dependency-sensitive convolutional neural networks (DSCNN) view which focuses on capturing long-distance dependency information within the text to globally model short text, can then overcome the challenge of feature sparseness in the short text answers from the doctors. The developed co-training framework can effectively mine the highly non-linear semantic information embedded in the unlabeled data and expose the highly non-linear relationships between different views, which minimizes the labeling effort. Finally, we conduct extensive empirical evaluations and demonstrate that our proposed method can significantly improve the predictive performance of the answer quality in the context of HQA services.

Machine learning in the prediction of cancer therapy.

Resistance to therapy remains a major cause of cancer treatment failures, resulting in many cancer-related deaths. Resistance can occur at any time during the treatment, even at the beginning. The current treatment plan is dependent mainly on cancer subtypes and the presence of genetic mutations. Evidently, the presence of a genetic mutation does not always predict the therapeutic response and can vary for different cancer subtypes. Therefore, there is an unmet need for predictive models to match a cancer patient with a specific drug or drug combination. Recent advancements in predictive models using artificial intelligence have shown great promise in preclinical settings. However, despite massive improvements in computational power, building clinically useable models remains challenging due to a lack of clinically meaningful pharmacogenomic data. In this review, we provide an overview of recent advancements in therapeutic response prediction using machine learning, which is the most widely used branch of artificial intelligence. We describe the basics of machine learning algorithms, illustrate their use, and highlight the current challenges in therapy response prediction for clinical practice.

Operation-aware Neural Networks for user response prediction.

User response prediction makes a crucial contribution to the rapid development of online advertising system and recommendation system. The importance of learning feature interactions has been emphasized by many works. Many deep models are proposed to automatically learn high-order feature interactions. Since most features in advertising systems and recommendation systems are high-dimensional sparse features, deep models usually learn a low-dimensional distributed representation for each feature in the bottom layer. Besides traditional fully-connected architectures, some new operations, such as convolutional operations and product operations, are proposed to learn feature interactions better. In these models, the representation is shared among different operations. However, the best representation for each operation may be different. In this paper, we propose a new neural model named Operation-aware Neural Networks (ONN) which learns different representations for different operations. Our experimental results on two large-scale real-world ad click/conversion datasets demonstrate that ONN consistently outperforms the state-of-the-art models in both offline-training environment and online-training environment.

Synergistic drug combinations prediction by integrating pharmacological data.

There is compelling evidence that synergistic drug combinations have become promising strategies for combating complex diseases, and they have evident predominance comparing to traditional one drug - one disease approaches. In this paper, we develop a computational method, namely SyFFM, that takes pharmacological data into consideration and applies field-aware factorization machines to analyze and predict potential synergistic drug combinations. Firstly, features of drug pairs are constructed based on associations between drugs and target, and enzymes, and indication areas. Then, the synergistic scores of drug combinations are obtained by implementing field-aware factorization machines on latent vector space of these features. Finally, synergistic combinations can be predicted by introducing a threshold. We applied SyFFM to predict pairwise synergistic combinations and three-drug synergistic combinations, and the performance is good in terms of cross-validation. Besides, more than 90% combinations of the top ranked predictions are proved by literature and the analysis of parameters in model shows that our method can help to investigate and explain synergistic mechanisms underlying combinatorial therapy.