A pharmacological effect of a drug on cells, organs and systems refers to the specific biochemical interaction produced by a drug substance, which is called its mechanism of action. Drug repositioning (or drug repurposing) is a fundamental problem for the identification of new opportunities for the use of already approved or failed drugs. In this paper, we present a method based on a multi-relation unsupervised graph embedding model that learns latent representations for drugs and diseases so that the distance between these representations reveals repositioning opportunities. Once representations for drugs and diseases are obtained we learn the likelihood of new links (that is, new indications) between drugs and diseases. Known drug indications are used for learning a model that predicts potential indications. Compared with existing unsupervised graph embedding methods our method shows superior prediction performance in terms of area under the ROC curve, and we present examples of repositioning opportunities found on recent biomedical literature that were also predicted by our method.
Graph autoencoders (GAEs) are powerful tools in representation learning for graph embedding. However, the performance of GAEs is very dependent on the quality of the graph structure, i.e., of the adjacency matrix. In other words, GAEs would perform poorly when the adjacency matrix is incomplete or be disturbed. In this paper, two novel unsupervised graph embedding methods, unsupervised graph embedding via adaptive graph learning (BAGE) and unsupervised graph embedding via variational adaptive graph learning (VBAGE) are proposed. The proposed methods expand the application range of GAEs on grap…
Graph embeddings have become a key and widely used technique within the field of graph mining, proving to be successful across a broad range of domains including social, citation, transportation and biological. Graph embedding techniques aim to automatically create a low-dimensional representation of a given graph, which captures key structural elements in the resulting embedding space. However, to date, there has been little work exploring exactly which topological structures are being learned in the embeddings process. In this paper, we investigate if graph embeddings are approximating somet…
Learning unsupervised node embeddings facilitates several downstream tasks such as node classification and link prediction. A node embedding is universal if it is designed to be used by and benefit various downstream tasks. This work introduces PanRep, a graph neural network (GNN) model, for unsupervised learning of universal node representations for heterogenous graphs. PanRep consists of a GNN encoder that obtains node embeddings and four decoders, each capturing different topological and node feature properties. Abiding to these properties the novel unsupervised framework learns universal e…
SGH Warsaw School of Economics（华沙经济学院）；Ryerson University（瑞尔森大学）；Tutte Institute for Mathematics and Computing（塔特数学与计算研究所）
Graph embedding is a transformation of nodes of a network into a set of vectors. A good embedding should capture the underlying graph topology and structure, node-to-node relationship, and other relevant information about the graph, its subgraphs, and nodes themselves. If these objectives are achieved, an embedding is a meaningful, understandable, and often compressed representation of a network. Unfortunately, selecting the best embedding is a challenging task and very often requires domain experts. In this paper, we extend the framework for evaluating graph embeddings that was recently intro…
Unsupervised Framework for Evaluating and Explaining Structural Node Embeddings of Graphs
Toronto Metropolitan University（多伦多都会大学）；SGH Warsaw School of Economics（华沙经济学院）；Patagona Technologies（帕塔戈纳科技公司）；Simons Institute for the Theory of Computing（西蒙斯计算理论研究所）
SGH Warsaw School of Economics（华沙经济学院）；Ryerson University（瑞尔森大学）；Tutte Institute for Mathematics and Computing（塔特数学与计算研究所）
Graph embedding is a transformation of vertices of a graph into set of vectors. Good embeddings should capture the graph topology, vertex-to-vertex relationship, and other relevant information about graphs, subgraphs, and vertices. If these objectives are achieved, they are meaningful, understandable, and compressed representations of networks. They also provide more options and tools for data scientists as machine learning on graphs is still quite limited. Finally, vector operations are simpler and faster than comparable operations on graphs. The main challenge is that one needs to make sure …
Zhejiang University（浙江大学）；AI Lab, School of Engineering（工程学院AI实验室）；Westlake University（西湖大学）
Unsupervised attributed graph representation learning is challenging since both structural and feature information are required to be represented in the latent space. Existing methods concentrate on learning latent representation via reconstruction tasks, but cannot directly optimize representation and are prone to oversmoothing, thus limiting the applications on downstream tasks. To alleviate these issues, we propose a novel graph embedding framework named Deep Manifold Attributed Graph Embedding (DMAGE). A node-to-node geodesic similarity is proposed to compute the inter-node similarity betw…
Graph alignment, also known as network alignment, is a fundamental task in social network analysis. Many recent works have relied on partially labeled cross-graph node correspondences, i.e., anchor links. However, due to the privacy and security issue, the manual labeling of anchor links for diverse scenarios may be prohibitive. Aligning two graphs without any anchor links is a crucial and challenging task. In this paper, we propose an Unsupervised Adversarial Graph Alignment (UAGA) framework to learn a cross-graph alignment between two embedding spaces of different graphs in a fully unsupervi…
In this paper we consider the binary similarity problem that consists in determining if two binary functions are similar only considering their compiled form. This problem is know to be crucial in several application scenarios, such as copyright disputes, malware analysis, vulnerability detection, etc. The current state-of-the-art solutions in this field work by creating an embedding model that maps binary functions into vectors in $\mathbb{R}^{n}$. Such embedding model captures syntactic and semantic similarity between binaries, i.e., similar binary functions are mapped to points that are clo…
National Physical Laboratory（英国国家物理实验室）；Université de Bourgogne Franche-Comté（勃艮第-弗朗什-孔泰大学）；Digital Surf（Digital Surf公司）
This paper proposes a variant of the method of Guédon and Verhynin for estimating the cluster matrix in the Mixture of Gaussians framework via Semi-Definite Programming. A clustering oriented embedding is deduced from this estimate. The procedure is suitable for very high dimensional data because it is based on pairwise distances only. Theoretical garantees are provided and an eigenvalue optimisation approach is proposed for computing the embedding. The performance of the method is illustrated via Monte Carlo experiements and comparisons with other embeddings from the literature.
Recent progress on unsupervised learning of cross-lingual embeddings in bilingual setting has given impetus to learning a shared embedding space for several languages without any supervision. A popular framework to solve the latter problem is to jointly solve the following two sub-problems: 1) learning unsupervised word alignment between several pairs of languages, and 2) learning how to map the monolingual embeddings of every language to a shared multilingual space. In contrast, we propose a simple, two-stage framework in which we decouple the above two sub-problems and solve them separately …
University of California, San Diego（加利福尼亚大学圣地亚哥分校）
Deep embedding methods have influenced many areas of unsupervised learning. However, the best methods for learning hierarchical structure use non-Euclidean representations, whereas Euclidean geometry underlies the theory behind many hierarchical clustering algorithms. To bridge the gap between these two areas, we consider learning a non-linear embedding of data into Euclidean space as a way to improve the hierarchical clustering produced by agglomerative algorithms. To learn the embedding, we revisit using a variational autoencoder with a Gaussian mixture prior, and we show that rescaling the …
KAIST（韩国科学技术院）；National Cheng Kung University（国立成功大学）；Institute for Basic Science（基础科学研究所）
Unsupervised embedding learning aims to extract good representation from data without the need for any manual labels, which has been a critical challenge in many supervised learning tasks. This paper proposes a new unsupervised embedding approach, called Super-AND, which extends the current state-of-the-art model. Super-AND has its unique set of losses that can gather similar samples nearby within a low-density space while keeping invariant features intact against data augmentation. Super-AND outperforms all existing approaches and achieves an accuracy of 89.2% on the image classification task…
We present a novel event embedding algorithm for crime data that can jointly capture time, location, and the complex free-text component of each event. The embedding is achieved by regularized Restricted Boltzmann Machines (RBMs), and we introduce a new way to regularize by imposing a $\ell_1$ penalty on the conditional distributions of the observed variables of RBMs. This choice of regularization performs feature selection and it also leads to efficient computation since the gradient can be computed in a closed form. The feature selection forces embedding to be based on the most important key…
We propose a new model for unsupervised document embedding. Leading existing approaches either require complex inference or use recurrent neural networks (RNN) that are difficult to parallelize. We take a different route and develop a convolutional neural network (CNN) embedding model. Our CNN architecture is fully parallelizable resulting in over 10x speedup in inference time over RNN models. Parallelizable architecture enables to train deeper models where each successive layer has increasingly larger receptive field and models longer range semantic structure within the document. We additiona…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Yahoo! Research（雅虎研究院）；Pohang University of Science and Technology（浦项科技大学）
Nodes in a multiplex network are connected by multiple types of relations. However, most existing network embedding methods assume that only a single type of relation exists between nodes. Even for those that consider the multiplexity of a network, they overlook node attributes, resort to node labels for training, and fail to model the global properties of a graph. We present a simple yet effective unsupervised network embedding method for attributed multiplex network called DMGI, inspired by Deep Graph Infomax (DGI) that maximizes the mutual information between local patches of a graph, and t…
Topic segmentation of meetings is the task of dividing multi-person meeting transcripts into topic blocks. Supervised approaches to the problem have proven intractable due to the difficulties in collecting and accurately annotating large datasets. In this paper we show how previous unsupervised topic segmentation methods can be improved using pre-trained neural architectures. We introduce an unsupervised approach based on BERT embeddings that achieves a 15.5% reduction in error rate over existing unsupervised approaches applied to two popular datasets for meeting transcripts.
University of Memphis（孟菲斯大学）；Adobe Research（奥多比研究院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Clinical notes in Electronic Health Records (EHR) present rich documented information of patients to inference phenotype for disease diagnosis and study patient characteristics for cohort selection. Unsupervised user embedding aims to encode patients into fixed-length vectors without human supervisions. Medical concepts extracted from the clinical notes contain rich connections between patients and their clinical categories. However, existing unsupervised approaches of user embeddings from clinical notes do not explicitly incorporate medical concepts. In this study, we propose a concept-aware …
We propose a novel manifold based geometric approach for learning unsupervised alignment of word embeddings between the source and the target languages. Our approach formulates the alignment learning problem as a domain adaptation problem over the manifold of doubly stochastic matrices. This viewpoint arises from the aim to align the second order information of the two language spaces. The rich geometry of the doubly stochastic manifold allows to employ efficient Riemannian conjugate gradient algorithm for the proposed formulation. Empirically, the proposed approach outperforms state-of-the-ar…
In this paper, we reproduce the experiments of Artetxe et al. (2018b) regarding the robust self-learning method for fully unsupervised cross-lingual mappings of word embeddings. We show that the reproduction of their method is indeed feasible with some minor assumptions. We further investigate the robustness of their model by introducing four new languages that are less similar to English than the ones proposed by the original paper. In order to assess the stability of their model, we also conduct a grid search over sensible hyperparameters. We then propose key recommendations applicable to an…
Stanford University（斯坦福大学）；University of Pennsylvania（宾夕法尼亚大学）；HRL Laboratories, LLC（HRL实验室有限责任公司）
We address the problem of unsupervised domain adaptation (UDA) by learning a cross-domain agnostic embedding space, where the distance between the probability distributions of the two source and target visual domains is minimized. We use the output space of a shared cross-domain deep encoder to model the embedding space anduse the Sliced-Wasserstein Distance (SWD) to measure and minimize the distance between the embedded distributions of two source and target domains to enforce the embedding to be domain-agnostic.Additionally, we use the source domain labeled data to train a deep classifier fr…
Given multiple source word embeddings learnt using diverse algorithms and lexical resources, meta word embedding learning methods attempt to learn more accurate and wide-coverage word embeddings. Prior work on meta-embedding has repeatedly discovered that simple vector concatenation of the source embeddings to be a competitive baseline. However, it remains unclear as to why and when simple vector concatenation can produce accurate meta-embeddings. We show that weighted concatenation can be seen as a spectrum matching operation between each source embedding and the meta-embedding, minimising th…
School of Interactive Computing（交互计算学院）；Georgia Institute of Technology（佐治亚理工学院）
Representation learning is the dominant technique for unsupervised domain adaptation, but existing approaches often require the specification of "pivot features" that generalize across domains, which are selected by task-specific heuristics. We show that a novel but simple feature embedding approach provides better performance, by exploiting the feature template structure common in NLP problems.
CICS, University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校信息与计算机科学学院）
Most unsupervised NLP models represent each word with a single point or single region in semantic space, while the existing multi-sense word embeddings cannot represent longer word sequences like phrases or sentences. We propose a novel embedding method for a text sequence (a phrase or a sentence) where each sequence is represented by a distinct set of multi-mode codebook embeddings to capture different semantic facets of its meaning. The codebook embeddings can be viewed as the cluster centers which summarize the distribution of possibly co-occurring words in a pre-trained word embedding spac…
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；Purdue University（普渡大学）
We introduce a novel approach to graph-level representation learning, which is to embed an entire graph into a vector space where the embeddings of two graphs preserve their graph-graph proximity. Our approach, UGRAPHEMB, is a general framework that provides a novel means to performing graph-level embedding in a completely unsupervised and inductive manner. The learned neural network can be considered as a function that receives any graph as input, either seen or unseen in the training set, and transforms it into an embedding. A novel graph-level embedding generation mechanism called Multi-Sca…
Facebook AI Research（脸书人工智能研究院）；University of Cambridge（剑桥大学）；Statistical Laboratory（统计实验室）
We consider the task of aligning two sets of points in high dimension, which has many applications in natural language processing and computer vision. As an example, it was recently shown that it is possible to infer a bilingual lexicon, without supervised data, by aligning word embeddings trained on monolingual data. These recent advances are based on adversarial training to learn the mapping between the two embeddings. In this paper, we propose to use an alternative formulation, based on the joint estimation of an orthogonal matrix and a permutation matrix. While this problem is not convex, …
Because of the rich dynamical structure of videos and their ubiquity in everyday life, it is a natural idea that video data could serve as a powerful unsupervised learning signal for training visual representations in deep neural networks. However, instantiating this idea, especially at large scale, has remained a significant artificial intelligence challenge. Here we present the Video Instance Embedding (VIE) framework, which extends powerful recent unsupervised loss functions for learning deep nonlinear embeddings to multi-stream temporal processing architectures on large-scale video dataset…
We investigate unsupervised models that can map a variable-duration speech segment to a fixed-dimensional representation. In settings where unlabelled speech is the only available resource, such acoustic word embeddings can form the basis for "zero-resource" speech search, discovery and indexing systems. Most existing unsupervised embedding methods still use some supervision, such as word or phoneme boundaries. Here we propose the encoder-decoder correspondence autoencoder (EncDec-CAE), which, instead of true word segments, uses automatically discovered segments: an unsupervised term discovery…
Nara Institute of Science and Technology（奈良先端科学技术大学院大学）；NTT Communication Science Laboratories（NTT通信科学实验室）
We propose an unsupervised method to obtain cross-lingual embeddings without any parallel data or pre-trained word embeddings. The proposed model, which we call multilingual neural language models, takes sentences of multiple languages as an input. The proposed model contains bidirectional LSTMs that perform as forward and backward language models, and these networks are shared among all the languages. The other parameters, i.e. word embeddings and linear transformation between hidden states and outputs, are specific to each language. The shared LSTMs can capture the common sentence structure …
Amazon（亚马逊）；University of Washington（华盛顿大学）；Allen Institute for AI（艾伦人工智能研究所）
We describe an unsupervised method to create pseudo-parallel corpora for machine translation (MT) from unaligned text. We use multilingual BERT to create source and target sentence embeddings for nearest-neighbor search and adapt the model via self-training. We validate our technique by extracting parallel sentence pairs on the BUCC 2017 bitext mining task and observe up to a 24.5 point increase (absolute) in F1 scores over previous unsupervised methods. We then improve an XLM-based unsupervised neural MT system pre-trained on Wikipedia by supplementing it with pseudo-parallel text mined from …
Cross-dataset transfer learning is an important problem in person re-identification (Re-ID). Unfortunately, not too many deep transfer Re-ID models exist for realistic settings of practical Re-ID systems. We propose a purely deep transfer Re-ID model consisting of a deep convolutional neural network and an autoencoder. The latent code is divided into metric embedding and nuisance variables. We then utilize an unsupervised training method that does not rely on co-training with non-deep models. Our experiments show improvements over both the baseline and competitors' transfer learning models.
IBM Research（IBM研究院）；Indian Institute of Science（印度科学学院）
Network representation learning has traditionally been used to find lower dimensional vector representations of the nodes in a network. However, there are very important edge driven mining tasks of interest to the classical network analysis community, which have mostly been unexplored in the network embedding space. For applications such as link prediction in homogeneous networks, vector representation (i.e., embedding) of an edge is derived heuristically just by using simple aggregations of the embeddings of the end vertices of the edge. Clearly, this method of deriving edge embedding is subo…
Graph-based extractive document summarization relies on the quality of the sentence similarity graph. Bag-of-words or tf-idf based sentence similarity uses exact word matching, but fails to measure the semantic similarity between individual words or to consider the semantic structure of sentences. In order to improve the similarity measure between sentences, we employ off-the-shelf deep embedding features and tf-idf features, and introduce a new text similarity metric. An improved sentence similarity graph is built and used in a submodular objective function for extractive summarization, which…
IXA NLP Group（IXA 自然语言处理研究组）；University of the Basque Country (UPV/EHU)（巴斯克大学（UPV/EHU））
Recent work has managed to learn cross-lingual word embeddings without parallel data by mapping monolingual embeddings to a shared space through adversarial training. However, their evaluation has focused on favorable conditions, using comparable corpora or closely-related languages, and we show that they often fail in more realistic scenarios. This work proposes an alternative approach based on a fully unsupervised initialization that explicitly exploits the structural similarity of the embeddings, and a robust self-learning algorithm that iteratively improves this solution. Our method succee…
Cross-lingual word embeddings aim to bridge the gap between high-resource and low-resource languages by allowing to learn multilingual word representations even without using any direct bilingual signal. The lion's share of the methods are projection-based approaches that map pre-trained embeddings into a shared latent space. These methods are mostly based on the orthogonal transformation, which assumes language vector spaces to be isomorphic. However, this criterion does not necessarily hold, especially for morphologically-rich languages. In this paper, we propose a self-supervised method to …
University of Chinese Academy of Sciences（中国科学院大学）；Chinese Academy of Sciences（中国科学院）；Shanghai Advanced Research Institute（上海高等研究院）；Shanghai Carbon Data Research Center（上海碳数据研究中心）；Centre for Excellence in Brain Science and Intelligence Technology（脑科学与智能技术卓越创新中心）
Recent work on segmentation-free word embedding(sembei) developed a new pipeline of word embedding for unsegmentated language while avoiding segmentation as a preprocessing step. However, too many noisy n-grams existing in the embedding vocabulary that do not have strong association strength between characters would limit the quality of learned word embedding. To deal with this problem, a new version of segmentation-free word embedding model is proposed by collecting n-grams vocabulary via a novel unsupervised association measure called pointwise association with times information(PATI). Compa…
Sun Yat-Sen University（中山大学）；JiaYing University（嘉应学院）；Guangzhou University（广州大学）
Unsupervised domain adaptation is effective in leveraging the rich information from the source domain to the unsupervised target domain. Though deep learning and adversarial strategy make an important breakthrough in the adaptability of features, there are two issues to be further explored. First, the hard-assigned pseudo labels on the target domain are risky to the intrinsic data structure. Second, the batch-wise training manner in deep learning limits the description of the global structure. In this paper, a Riemannian manifold learning framework is proposed to achieve transferability and di…
In this paper, we develop an unsupervised generative clustering framework that combines the Variational Information Bottleneck and the Gaussian Mixture Model. Specifically, in our approach, we use the Variational Information Bottleneck method and model the latent space as a mixture of Gaussians. We derive a bound on the cost function of our model that generalizes the Evidence Lower Bound (ELBO) and provide a variational inference type algorithm that allows computing it. In the algorithm, the coders' mappings are parametrized using neural networks, and the bound is approximated by Monte Carlo s…
Unite Network SE（Unite Network SE公司）；TU Munich（慕尼黑工业大学）
Network embedding has emerged as a promising research field for network analysis. Recently, an approach, named Barlow Twins, has been proposed for self-supervised learning in computer vision by applying the redundancy-reduction principle to the embedding vectors corresponding to two distorted versions of the image samples. Motivated by this, we propose Barlow Graph Auto-Encoder, a simple yet effective architecture for learning network embedding. It aims to maximize the similarity between the embedding vectors of immediate and larger neighborhoods of a node, while minimizing the redundancy betw…
We present the efficiency of semi-orthogonal embedding for unsupervised anomaly segmentation. The multi-scale features from pre-trained CNNs are recently used for the localized Mahalanobis distances with significant performance. However, the increased feature size is problematic to scale up to the bigger CNNs, since it requires the batch-inverse of multi-dimensional covariance tensor. Here, we generalize an ad-hoc method, random feature selection, into semi-orthogonal embedding for robust approximation, cubically reducing the computational cost for the inverse of multi-dimensional covariance t…
Methods that learn representations of nodes in a graph play a critical role in network analysis since they enable many downstream learning tasks. We propose Graph2Gauss - an approach that can efficiently learn versatile node embeddings on large scale (attributed) graphs that show strong performance on tasks such as link prediction and node classification. Unlike most approaches that represent nodes as point vectors in a low-dimensional continuous space, we embed each node as a Gaussian distribution, allowing us to capture uncertainty about the representation. Furthermore, we propose an unsuper…
Tsinghua University（清华大学）；Mila（米拉研究所）；HEC Montreal（蒙特利尔高等商学院）；UIUC（伊利诺伊大学厄巴纳-香槟分校）；University of Michigan（密歇根大学）；University of California, Berkeley（加州大学伯克利分校）
Unsupervised node embedding methods (e.g., DeepWalk, LINE, and node2vec) have attracted growing interests given their simplicity and effectiveness. However, although these methods have been proved effective in a variety of applications, none of the existing work has analyzed the robustness of them. This could be very risky if these methods are attacked by an adversarial party. In this paper, we take the task of link prediction as an example, which is one of the most fundamental problems for graph analysis, and introduce a data positioning attack to node embedding methods. We give a complete ch…
University of Toronto（多伦多大学）；Vector Institute for Artificial Intelligence（向量人工智能研究所）；University Health Network（大学健康网络）
Sentence embeddings are an important component of many natural language processing (NLP) systems. Like word embeddings, sentence embeddings are typically learned on large text corpora and then transferred to various downstream tasks, such as clustering and retrieval. Unlike word embeddings, the highest performing solutions for learning sentence embeddings require labelled data, limiting their usefulness to languages and domains where labelled data is abundant. In this paper, we present DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations. Inspired by recent advances in d…
University of Florida（佛罗里达大学）；National Renewable Energy Lab（美国国家可再生能源实验室）
We present a new approach to unsupervised shape correspondence learning between pairs of point clouds. We make the first attempt to adapt the classical locally linear embedding algorithm (LLE) -- originally designed for nonlinear dimensionality reduction -- for shape correspondence. The key idea is to find dense correspondences between shapes by first obtaining high-dimensional neighborhood-preserving embeddings of low-dimensional point clouds and subsequently aligning the source and target embeddings using locally linear transformations. We demonstrate that learning the embedding using a new …
Technical University of Munich（慕尼黑工业大学）；Mercateo AG（Mercateo公司）
Heterogeneous Information Network (HIN) embedding refers to the low-dimensional projections of the HIN nodes that preserve the HIN structure and semantics. HIN embedding has emerged as a promising research field for network analysis as it enables downstream tasks such as clustering and node classification. In this work, we propose \ours for joint learning of cluster embeddings as well as cluster-aware HIN embedding. We assume that the connected nodes are highly likely to fall in the same cluster, and adopt a variational approach to preserve the information in the pairwise relations in a cluste…
University of Washington（华盛顿大学）；Facebook AI Research (FAIR)（脸书人工智能研究院）
Clustering is central to many data-driven application domains and has been studied extensively in terms of distance functions and grouping algorithms. Relatively little work has focused on learning representations for clustering. In this paper, we propose Deep Embedded Clustering (DEC), a method that simultaneously learns feature representations and cluster assignments using deep neural networks. DEC learns a mapping from the data space to a lower-dimensional feature space in which it iteratively optimizes a clustering objective. Our experimental evaluations on image and text corpora show sign…
Transfer Learning from Foundational Optimization Embeddings to Unsupervised SAT Representations
AI Center of Excellence, Fidelity Investments, USA（Fidelity Investments人工智能卓越中心，美国）；Khoury College of Computer Sciences, Northeastern University, USA（东北大学科里学院计算机科学系，美国）；Department of Computer Science, Brown University, USA（布朗大学计算机科学系，美国）
