In recent years, numerous machine learning models which attempt to solve polypharmacy side effect identification, drug-drug interaction prediction and combination therapy design tasks have been proposed. Here, we present a unified theoretical view of relational machine learning models which can address these tasks. We provide fundamental definitions, compare existing model architectures and discuss performance metrics, datasets and evaluation protocols. In addition, we emphasize possible high impact applications and important future research directions in this domain.
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With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.
Model complexity is a fundamental problem in deep learning. In this paper we conduct a systematic overview of the latest studies on model complexity in deep learning. Model complexity of deep learning can be categorized into expressive capacity and effective model complexity. We review the existing studies on those two categories along four important factors, including model framework, model size, optimization process and data complexity. We also discuss the applications of deep learning model complexity including understanding model generalization capability, model optimization, and model selection and design. We conclude by proposing several interesting future directions.
Deep models trained in supervised mode have achieved remarkable success on a variety of tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a new paradigm for making use of large amounts of unlabeled samples. SSL has achieved promising performance on natural language and image learning tasks. Recently, there is a trend to extend such success to graph data using graph neural networks (GNNs). In this survey, we provide a unified review of different ways of training GNNs using SSL. Specifically, we categorize SSL methods into contrastive and predictive models. In either category, we provide a unified framework for methods as well as how these methods differ in each component under the framework. Our unified treatment of SSL methods for GNNs sheds light on the similarities and differences of various methods, setting the stage for developing new methods and algorithms. We also summarize different SSL settings and the corresponding datasets used in each setting. To facilitate methodological development and empirical comparison, we develop a standardized testbed for SSL in GNNs, including implementations of common baseline methods, datasets, and evaluation metrics.
Distance based knowledge graph embedding methods show promising results on link prediction task, on which two topics have been widely studied: one is the ability to handle complex relations, such as N-to-1, 1-to-N and N-to-N, the other is to encode various relation patterns, such as symmetry/antisymmetry. However, the existing methods fail to solve these two problems at the same time, which leads to unsatisfactory results. To mitigate this problem, we propose PairRE, a model with paired vectors for each relation representation. The paired vectors enable an adaptive adjustment of the margin in loss function to fit for complex relations. Besides, PairRE is capable of encoding three important relation patterns, symmetry/antisymmetry, inverse and composition. Given simple constraints on relation representations, PairRE can encode subrelation further. Experiments on link prediction benchmarks demonstrate the proposed key capabilities of PairRE. Moreover, We set a new state-of-the-art on two knowledge graph datasets of the challenging Open Graph Benchmark.
Knowledge is a formal way of understanding the world, providing a human-level cognition and intelligence for the next-generation artificial intelligence (AI). One of the representations of knowledge is the structural relations between entities. An effective way to automatically acquire this important knowledge, called Relation Extraction (RE), a sub-task of information extraction, plays a vital role in Natural Language Processing (NLP). Its purpose is to identify semantic relations between entities from natural language text. To date, there are several studies for RE in previous works, which have documented these techniques based on Deep Neural Networks (DNNs) become a prevailing technique in this research. Especially, the supervised and distant supervision methods based on DNNs are the most popular and reliable solutions for RE. This article 1)introduces some general concepts, and further 2)gives a comprehensive overview of DNNs in RE from two points of view: supervised RE, which attempts to improve the standard RE systems, and distant supervision RE, which adopts DNNs to design the sentence encoder and the de-noise method. We further 3)cover some novel methods and describe some recent trends and discuss possible future research directions for this task.
Deep learning models on graphs have achieved remarkable performance in various graph analysis tasks, e.g., node classification, link prediction and graph clustering. However, they expose uncertainty and unreliability against the well-designed inputs, i.e., adversarial examples. Accordingly, various studies have emerged for both attack and defense addressed in different graph analysis tasks, leading to the arms race in graph adversarial learning. For instance, the attacker has poisoning and evasion attack, and the defense group correspondingly has preprocessing- and adversarial- based methods. Despite the booming works, there still lacks a unified problem definition and a comprehensive review. To bridge this gap, we investigate and summarize the existing works on graph adversarial learning tasks systemically. Specifically, we survey and unify the existing works w.r.t. attack and defense in graph analysis tasks, and give proper definitions and taxonomies at the same time. Besides, we emphasize the importance of related evaluation metrics, and investigate and summarize them comprehensively. Hopefully, our works can serve as a reference for the relevant researchers, thus providing assistance for their studies. More details of our works are available at //github.com/gitgiter/Graph-Adversarial-Learning.
The Visual Question Answering (VQA) task combines challenges for processing data with both Visual and Linguistic processing, to answer basic `common sense' questions about given images. Given an image and a question in natural language, the VQA system tries to find the correct answer to it using visual elements of the image and inference gathered from textual questions. In this survey, we cover and discuss the recent datasets released in the VQA domain dealing with various types of question-formats and enabling robustness of the machine-learning models. Next, we discuss about new deep learning models that have shown promising results over the VQA datasets. At the end, we present and discuss some of the results computed by us over the vanilla VQA models, Stacked Attention Network and the VQA Challenge 2017 winner model. We also provide the detailed analysis along with the challenges and future research directions.
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with arbitrary depth. Although the primitive GNNs have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on variants of graph neural networks such as graph convolutional network (GCN), graph attention network (GAT), gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.
The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.
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