Pre-training GNNs to extract transferable knowledge and apply it to downstream tasks has become the de facto standard of graph representation learning. Recent works focused on designing self-supervised pre-training tasks to extract useful and universal transferable knowledge from large-scale unlabeled data. However, they have to face an inevitable question: traditional pre-training strategies that aim at extracting useful information about pre-training tasks, may not extract all useful information about the downstream task. In this paper, we reexamine the pre-training process within traditional pre-training and fine-tuning frameworks from the perspective of Information Bottleneck (IB) and confirm that the forgetting phenomenon in pre-training phase may cause detrimental effects on downstream tasks. Therefore, we propose a novel \underline{D}elayed \underline{B}ottlenecking \underline{P}re-training (DBP) framework which maintains as much as possible mutual information between latent representations and training data during pre-training phase by suppressing the compression operation and delays the compression operation to fine-tuning phase to make sure the compression can be guided with labeled fine-tuning data and downstream tasks. To achieve this, we design two information control objectives that can be directly optimized and further integrate them into the actual model design. Extensive experiments on both chemistry and biology domains demonstrate the effectiveness of DBP.
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Knowledge graph embedding (KGE) is a increasingly popular technique that aims to represent entities and relations of knowledge graphs into low-dimensional semantic spaces for a wide spectrum of applications such as link prediction, knowledge reasoning and knowledge completion. In this paper, we provide a systematic review of existing KGE techniques based on representation spaces. Particularly, we build a fine-grained classification to categorise the models based on three mathematical perspectives of the representation spaces: (1) Algebraic perspective, (2) Geometric perspective, and (3) Analytical perspective. We introduce the rigorous definitions of fundamental mathematical spaces before diving into KGE models and their mathematical properties. We further discuss different KGE methods over the three categories, as well as summarise how spatial advantages work over different embedding needs. By collating the experimental results from downstream tasks, we also explore the advantages of mathematical space in different scenarios and the reasons behind them. We further state some promising research directions from a representation space perspective, with which we hope to inspire researchers to design their KGE models as well as their related applications with more consideration of their mathematical space properties.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
Knowledge graphs (KGs) capture knowledge in the form of head--relation--tail triples and are a crucial component in many AI systems. There are two important reasoning tasks on KGs: (1) single-hop knowledge graph completion, which involves predicting individual links in the KG; and (2), multi-hop reasoning, where the goal is to predict which KG entities satisfy a given logical query. Embedding-based methods solve both tasks by first computing an embedding for each entity and relation, then using them to form predictions. However, existing scalable KG embedding frameworks only support single-hop knowledge graph completion and cannot be applied to the more challenging multi-hop reasoning task. Here we present Scalable Multi-hOp REasoning (SMORE), the first general framework for both single-hop and multi-hop reasoning in KGs. Using a single machine SMORE can perform multi-hop reasoning in Freebase KG (86M entities, 338M edges), which is 1,500x larger than previously considered KGs. The key to SMORE's runtime performance is a novel bidirectional rejection sampling that achieves a square root reduction of the complexity of online training data generation. Furthermore, SMORE exploits asynchronous scheduling, overlapping CPU-based data sampling, GPU-based embedding computation, and frequent CPU--GPU IO. SMORE increases throughput (i.e., training speed) over prior multi-hop KG frameworks by 2.2x with minimal GPU memory requirements (2GB for training 400-dim embeddings on 86M-node Freebase) and achieves near linear speed-up with the number of GPUs. Moreover, on the simpler single-hop knowledge graph completion task SMORE achieves comparable or even better runtime performance to state-of-the-art frameworks on both single GPU and multi-GPU settings.
Knowledge graph embedding models learn the representations of entities and relations in the knowledge graphs for predicting missing links (relations) between entities. Their effectiveness are deeply affected by the ability of modeling and inferring different relation patterns such as symmetry, asymmetry, inversion, composition and transitivity. Although existing models are already able to model many of these relations patterns, transitivity, a very common relation pattern, is still not been fully supported. In this paper, we first theoretically show that the transitive relations can be modeled with projections. We then propose the Rot-Pro model which combines the projection and relational rotation together. We prove that Rot-Pro can infer all the above relation patterns. Experimental results show that the proposed Rot-Pro model effectively learns the transitivity pattern and achieves the state-of-the-art results on the link prediction task in the datasets containing transitive relations.
We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at //bit.ly/2EPbrJs.
Existing few-shot learning (FSL) methods assume that there exist sufficient training samples from source classes for knowledge transfer to target classes with few training samples. However, this assumption is often invalid, especially when it comes to fine-grained recognition. In this work, we define a new FSL setting termed few-shot fewshot learning (FSFSL), under which both the source and target classes have limited training samples. To overcome the source class data scarcity problem, a natural option is to crawl images from the web with class names as search keywords. However, the crawled images are inevitably corrupted by large amount of noise (irrelevant images) and thus may harm the performance. To address this problem, we propose a graph convolutional network (GCN)-based label denoising (LDN) method to remove the irrelevant images. Further, with the cleaned web images as well as the original clean training images, we propose a GCN-based FSL method. For both the LDN and FSL tasks, a novel adaptive aggregation GCN (AdarGCN) model is proposed, which differs from existing GCN models in that adaptive aggregation is performed based on a multi-head multi-level aggregation module. With AdarGCN, how much and how far information carried by each graph node is propagated in the graph structure can be determined automatically, therefore alleviating the effects of both noisy and outlying training samples. Extensive experiments show the superior performance of our AdarGCN under both the new FSFSL and the conventional FSL settings.
InteractE: Improving Convolution-based Knowledge Graph Embeddings by Increasing Feature Interactions
Most existing knowledge graphs suffer from incompleteness, which can be alleviated by inferring missing links based on known facts. One popular way to accomplish this is to generate low-dimensional embeddings of entities and relations, and use these to make inferences. ConvE, a recently proposed approach, applies convolutional filters on 2D reshapings of entity and relation embeddings in order to capture rich interactions between their components. However, the number of interactions that ConvE can capture is limited. In this paper, we analyze how increasing the number of these interactions affects link prediction performance, and utilize our observations to propose InteractE. InteractE is based on three key ideas -- feature permutation, a novel feature reshaping, and circular convolution. Through extensive experiments, we find that InteractE outperforms state-of-the-art convolutional link prediction baselines on FB15k-237. Further, InteractE achieves an MRR score that is 9%, 7.5%, and 23% better than ConvE on the FB15k-237, WN18RR and YAGO3-10 datasets respectively. The results validate our central hypothesis -- that increasing feature interaction is beneficial to link prediction performance. We make the source code of InteractE available to encourage reproducible research.
Language model pre-training, such as BERT, has significantly improved the performances of many natural language processing tasks. However, pre-trained language models are usually computationally expensive and memory intensive, so it is difficult to effectively execute them on some resource-restricted devices. To accelerate inference and reduce model size while maintaining accuracy, we firstly propose a novel transformer distillation method that is a specially designed knowledge distillation (KD) method for transformer-based models. By leveraging this new KD method, the plenty of knowledge encoded in a large teacher BERT can be well transferred to a small student TinyBERT. Moreover, we introduce a new two-stage learning framework for TinyBERT, which performs transformer distillation at both the pre-training and task-specific learning stages. This framework ensures that TinyBERT can capture both the general-domain and task-specific knowledge of the teacher BERT. TinyBERT is empirically effective and achieves comparable results with BERT in GLUE datasets, while being 7.5x smaller and 9.4x faster on inference. TinyBERT is also significantly better than state-of-the-art baselines, even with only about 28% parameters and 31% inference time of baselines.
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.
State-of-the-art Convolutional Neural Network (CNN) benefits a lot from multi-task learning (MTL), which learns multiple related tasks simultaneously to obtain shared or mutually related representations for different tasks. The most widely-used MTL CNN structure is based on an empirical or heuristic split on a specific layer (e.g., the last convolutional layer) to minimize different task-specific losses. However, this heuristic sharing/splitting strategy may be harmful to the final performance of one or multiple tasks. In this paper, we propose a novel CNN structure for MTL, which enables automatic feature fusing at every layer. Specifically, we first concatenate features from different tasks according to their channel dimension, and then formulate the feature fusing problem as discriminative dimensionality reduction. We show that this discriminative dimensionality reduction can be done by 1x1 Convolution, Batch Normalization, and Weight Decay in one CNN, which we refer to as Neural Discriminative Dimensionality Reduction (NDDR). We perform ablation analysis in details for different configurations in training the network. The experiments carried out on different network structures and different task sets demonstrate the promising performance and desirable generalizability of our proposed method.
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