A Review of Relational Machine Learning for Knowledge Graphs

Relational machine learning studies methods for the statistical analysis of relational, or graph-structured, data. In this paper, we provide a review of how such statistical models can be “trained” on large knowledge graphs, and then used to predict new facts about the world (which is equivalent to predicting new edges in the graph). In particular, we discuss two different kinds of statistical relational models, both of which can scale to massive datasets. The first is based on tensor factorization methods and related latent variable models. The second is based on mining observable patterns in the graph. We also show how to combine these latent and observable models to get improved modeling power at decreased computational cost. Finally, we discuss how such statistical models of graphs can be combined with text-based information extraction methods for automatically constructing knowledge graphs from the Web. In particular, we discuss Google’s Knowledge Vault project.This work was supported by the Center for Brains, Minds and Machines (CBMM), funded by NSF STC award CCF - 1231216

Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Models

Machine learning has recently entered into the mainstream of coarse-grained (CG) molecular modeling and simulation. While a variety of methods for incorporating deep learning into these models exist, many of them involve training neural networks to act directly as the CG force field. This has several benefits, the most significant of which is accuracy. Neural networks can inherently incorporate multi-body effects during the calculation of CG forces, and a well-trained neural network force field outperforms pairwise basis sets generated from essentially any methodology. However, this comes at a significant cost. First, these models are typically slower than pairwise force fields even when accounting for specialized hardware which accelerates the training and integration of such networks. The second, and the focus of this paper, is the need for the considerable amount of data needed to train such force fields. It is common to use tens of microseconds of molecular dynamics data to train a single CG model, which approaches the point of eliminating the CG models usefulness in the first place. As we investigate in this work, it is apparent that this data-hunger trap from neural networks for predicting molecular energies and forces is caused in large part by the difficulty in learning force equivariance, i.e., the fact that force vectors should rotate while maintaining their magnitude in response to an equivalent rotation of the system. We demonstrate that for CG water, networks that inherently incorporate this equivariance into their embedding can produce functional models using datasets as small as a single frame of reference data, which networks without inherent symmetry equivariance cannot

Predicting Pair Correlation Functions of Glasses using Machine Learning

Glasses offer a broad range of tunable thermophysical properties that are linked to their compositions. However, it is challenging to establish a universal composition-property relation of glasses due to their enormous composition and chemical space. Here, we address this problem and develop a metamodel of composition-atomistic structure relation of a class of glassy material via a machine learning (ML) approach. Within this ML framework, an unsupervised deep learning technique, viz. convolutional neural network (CNN) autoencoder, and a regression algorithm, viz. random forest (RF), are integrated into a fully automated pipeline to predict the spatial distribution of atoms in a glass. The RF regression model predicts the pair correlation function of a glass in a latent space. Subsequently, the decoder of the CNN converts the latent space representation to the actual pair correlation function of the given glass. The atomistic structures of silicate (SiO2) and sodium borosilicate (NBS) based glasses with varying compositions and dopants are collected from molecular dynamics (MD) simulations to establish and validate this ML pipeline. The model is found to predict the atom pair correlation function for many unknown glasses very accurately. This method is very generic and can accelerate the design, discovery, and fundamental understanding of composition-atomistic structure relations of glasses and other materials

A Survey on Knowledge Graphs: Representation, Acquisition and Applications

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions

How to Retrain Recommender System? A Sequential Meta-Learning Method

Practical recommender systems need be periodically retrained to refresh the model with new interaction data. To pursue high model fidelity, it is usually desirable to retrain the model on both historical and new data, since it can account for both long-term and short-term user preference. However, a full model retraining could be very time-consuming and memory-costly, especially when the scale of historical data is large. In this work, we study the model retraining mechanism for recommender systems, a topic of high practical values but has been relatively little explored in the research community. Our first belief is that retraining the model on historical data is unnecessary, since the model has been trained on it before. Nevertheless, normal training on new data only may easily cause overfitting and forgetting issues, since the new data is of a smaller scale and contains fewer information on long-term user preference. To address this dilemma, we propose a new training method, aiming to abandon the historical data during retraining through learning to transfer the past training experience. Specifically, we design a neural network-based transfer component, which transforms the old model to a new model that is tailored for future recommendations. To learn the transfer component well, we optimize the "future performance" -- i.e., the recommendation accuracy evaluated in the next time period. Our Sequential Meta-Learning(SML) method offers a general training paradigm that is applicable to any differentiable model. We demonstrate SML on matrix factorization and conduct experiments on two real-world datasets. Empirical results show that SML not only achieves significant speed-up, but also outperforms the full model retraining in recommendation accuracy, validating the effectiveness of our proposals. We release our codes at: https://github.com/zyang1580/SML.Comment: Appear in SIGIR 202

Predicting Drug-Drug Interactions Using Knowledge Graphs

In the last decades, people have been consuming and combining more drugs than before, increasing the number of Drug-Drug Interactions (DDIs). To predict unknown DDIs, recently, studies started incorporating Knowledge Graphs (KGs) since they are able to capture the relationships among entities providing better drug representations than using a single drug property. In this paper, we propose the medicX end-to-end framework that integrates several drug features from public drug repositories into a KG and embeds the nodes in the graph using various translation, factorisation and Neural Network (NN) based KG Embedding (KGE) methods. Ultimately, we use a Machine Learning (ML) algorithm that predicts unknown DDIs. Among the different translation and factorisation-based KGE models, we found that the best performing combination was the ComplEx embedding method with a Long Short-Term Memory (LSTM) network, which obtained an F1-score of 95.19% on a dataset based on the DDIs found in DrugBank version 5.1.8. This score is 5.61% better than the state-of-the-art model DeepDDI. Additionally, we also developed a graph auto-encoder model that uses a Graph Neural Network (GNN), which achieved an F1-score of 91.94%. Consequently, GNNs have demonstrated a stronger ability to mine the underlying semantics of the KG than the ComplEx model, and thus using higher dimension embeddings within the GNN can lead to state-of-the-art performance