Tensor factorizations have become increasingly popular approaches for various learning tasks on structured data. In this work, we extend the RESCAL tensor factorization, which has shown state-of-the-art results for multi-relational learning, to account for the binary nature of adjacency tensors. We study the improvements that can be gained via this approach on various benchmark datasets and show that the logistic extension can improve the prediction results significantly.
University of Washington（华盛顿大学）；Carnegie Mellon University（卡内基梅隆大学）
Relational learning can be used to augment one data source with other correlated sources of information, to improve predictive accuracy. We frame a large class of relational learning problems as matrix factorization problems, and propose a hierarchical Bayesian model. Training our Bayesian model using random-walk Metropolis-Hastings is impractically slow, and so we develop a block Metropolis-Hastings sampler which uses the gradient and Hessian of the likelihood to dynamically tune the proposal. We demonstrate that a predictive model of brain response to stimuli can be improved by augmenting it…
North Carolina State University（北卡罗来纳州立大学）；Fudan University（复旦大学）
With the proliferation of knowledge graphs, modeling data with complex multirelational structure has gained increasing attention in the area of statistical relational learning. One of the most important goals of statistical relational learning is link prediction, i.e., predicting whether certain relations exist in the knowledge graph. A large number of models and algorithms have been proposed to perform link prediction, among which tensor factorization method has proven to achieve state-of-the-art performance in terms of computation efficiency and prediction accuracy. However, a common drawbac…
University of Notre Dame（圣母大学）；Microsoft Research（微软研究院）
Neural collaborative filtering (NCF) and recurrent recommender systems (RRN) have been successful in modeling user-item relational data. However, they are also limited in their assumption of static or sequential modeling of relational data as they do not account for evolving users' preference over time as well as changes in the underlying factors that drive the change in user-item relationship over time. We address these limitations by proposing a Neural Tensor Factorization (NTF) model for predictive tasks on dynamic relational data. The NTF model generalizes conventional tensor factorization…
Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly (LILY)（南洋理工大学-不列颠哥伦比亚大学活跃老年生活卓越联合研究中心（LILY））；Alibaba-NTU Singapore Joint Research Institute（阿里巴巴-南洋理工大学新加坡联合研究院）；Nanyang Technological University（南洋理工大学）；ShanghaiTech University（上海科技大学）；A*Star（新加坡科技研究局）；Singapore Management University（新加坡管理大学）
Synthetic lethality (SL) is a promising concept for novel discovery of anti-cancer drug targets. However, wet-lab experiments for detecting SLs are faced with various challenges, such as high cost, low consistency across platforms or cell lines. Therefore, computational prediction methods are needed to address these issues. This paper proposes a novel SL prediction method, named SL2MF, which employs logistic matrix factorization to learn latent representations of genes from the observed SL data. The probability that two genes are likely to form SL is modeled by the linear combination of gene l…
This paper aims at the problem of link pattern prediction in collections of objects connected by multiple relation types, where each type may play a distinct role. While common link analysis models are limited to single-type link prediction, we attempt here to capture the correlations among different relation types and reveal the impact of various relation types on performance quality. For that, we define the overall relations between object pairs as a \textit{link pattern} which consists in interaction pattern and connection structure in the network, and then use tensor formalization to joint…
Heterogeneous multi-typed, multimodal relational data is increasingly available in many domains and their exploratory analysis poses several challenges. We advance the state-of-the-art in neural unsupervised learning to analyze such data. We design the first neural method for collective matrix tri-factorization of arbitrary collections of matrices to perform spectral clustering of all constituent entities and learn cluster associations. Experiments on benchmark datasets demonstrate its efficacy over previous non-neural approaches. Leveraging signals from multi-way clustering and collective mat…
Massachusetts Institute of Technology（麻省理工学院）；Istituto Italiano di Tecnologia（意大利理工学院）；Siemens AG, Corporate Technology（西门子公司企业技术部）；Google Inc.（谷歌公司）
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 fundamentally different kinds of statistical relational models, both of which can scale to massive datasets. The first is based on latent feature models such as tensor factorization and multiway neural networks. The second is based on…
Clustering on the data with multiple aspects, such as multi-view or multi-type relational data, has become popular in recent years due to their wide applicability. The approach using manifold learning with the Non-negative Matrix Factorization (NMF) framework, that learns the accurate low-rank representation of the multi-dimensional data, has shown effectiveness. We propose to include the inter-manifold in the NMF framework, utilizing the distance information of data points of different data types (or views) to learn the diverse manifold for data clustering. Empirical analysis reveals that the…
Bayesian low-rank matrix factorization techniques have become an essential tool for relational data analysis and matrix completion. A standard approach is to assign zero-mean Gaussian priors on the columns or rows of factor matrices to create a conjugate system. This choice of prior leads to simple implementations; however it also causes symmetries in the posterior distribution that can severely reduce the efficiency of Markov-chain Monte-Carlo (MCMC) sampling approaches. In this paper, we propose a simple modification to the prior choice that provably breaks these symmetries and maintains/imp…
Research in statistical relational learning has produced a number of methods for learning relational models from large-scale network data. While these methods have been successfully applied in various domains, they have been developed under the unrealistic assumption of full data access. In practice, however, the data are often collected by crawling the network, due to proprietary access, limited resources, and privacy concerns. Recently, we showed that the parameter estimates for relational Bayes classifiers computed from network samples collected by existing network crawlers can be quite ina…
Istituto Italiano di Tecnologia（意大利技术研究院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Dropout is a simple yet effective algorithm for regularizing neural networks by randomly dropping out units through Bernoulli multiplicative noise, and for some restricted problem classes, such as linear or logistic regression, several theoretical studies have demonstrated the equivalence between dropout and a fully deterministic optimization problem with data-dependent Tikhonov regularization. This work presents a theoretical analysis of dropout for matrix factorization, where Bernoulli random variables are used to drop a factor, thereby attempting to control the size of the factorization. Wh…
Multi-label network classification is a well-known task that is being used in a wide variety of web-based and non-web-based domains. It can be formalized as a multi-relational learning task for predicting nodes labels based on their relations within the network. In sparse networks, this prediction task can be very challenging when only implicit feedback information is available such as in predicting user interests in social networks. Current approaches rely on learning per-node latent representations by utilizing the network structure, however, implicit feedback relations are naturally sparse …
Matrix factorization has found incredible success and widespread application as a collaborative filtering based approach to recommendations. Unfortunately, incorporating additional sources of evidence, especially ones that are incomplete and noisy, is quite difficult to achieve in such models, however, is often crucial for obtaining further gains in accuracy. For example, additional information about businesses from reviews, categories, and attributes should be leveraged for predicting user preferences, even though this information is often inaccurate and partially-observed. Instead of creatin…
Southwest University（西南大学）；China University of Geosciences（中国地质大学）；George Mason University（乔治梅森大学）；Deakin University（迪肯大学）；Beijing University of Civil Engineering and Architecture（北京建筑大学）
Multi-view Multi-instance Multi-label Learning(M3L) deals with complex objects encompassing diverse instances, represented with different feature views, and annotated with multiple labels. Existing M3L solutions only partially explore the inter or intra relations between objects (or bags), instances, and labels, which can convey important contextual information for M3L. As such, they may have a compromised performance. In this paper, we propose a collaborative matrix factorization based solution called M3Lcmf. M3Lcmf first uses a heterogeneous network composed of nodes of bags, instances, and …
Feinberg School of Medicine Northwestern University Chicago, U.S；Weill Cornell Medicine Cornell University New York, U.S
ICU mortality risk prediction is a tough yet important task. On one hand, due to the complex temporal data collected, it is difficult to identify the effective features and interpret them easily; on the other hand, good prediction can help clinicians take timely actions to prevent the mortality. These correspond to the interpretability and accuracy problems. Most existing methods lack of the interpretability, but recently Subgraph Augmented Nonnegative Matrix Factorization (SANMF) has been successfully applied to time series data to provide a path to interpret the features well. Therefore, we …
We present a scalable Bayesian model for low-rank factorization of massive tensors with binary observations. The proposed model has the following key properties: (1) in contrast to the models based on the logistic or probit likelihood, using a zero-truncated Poisson likelihood for binary data allows our model to scale up in the number of \emph{ones} in the tensor, which is especially appealing for massive but sparse binary tensors; (2) side-information in form of binary pairwise relationships (e.g., an adjacency network) between objects in any tensor mode can also be leveraged, which can be es…
Indiana University, Bloomington（印第安纳大学伯明顿分校）；The University of Texas at Dallas（德克萨斯大学达拉斯分校）；Allen Institute for Artificial Intelligence（艾伦人工智能研究所）；University of British Columbia（不列颠哥伦比亚大学）；TU Darmstadt University（达姆施塔特工业大学）
We consider the problem of learning Relational Logistic Regression (RLR). Unlike standard logistic regression, the features of RLRs are first-order formulae with associated weight vectors instead of scalar weights. We turn the problem of learning RLR to learning these vector-weighted formulae and develop a learning algorithm based on the recently successful functional-gradient boosting methods for probabilistic logic models. We derive the functional gradients and show how weights can be learned simultaneously in an efficient manner. Our empirical evaluation on standard and novel data sets demo…
Relational logistic regression (RLR) is a representation of conditional probability in terms of weighted formulae for modelling multi-relational data. In this paper, we develop a learning algorithm for RLR models. Learning an RLR model from data consists of two steps: 1- learning the set of formulae to be used in the model (a.k.a. structure learning) and learning the weight of each formula (a.k.a. parameter learning). For structure learning, we deploy Schmidt and Murphy's hierarchical assumption: first we learn a model with simple formulae, then more complex formulae are added iteratively only…
Georgia Institute of Technology（佐治亚理工学院）；Health at Scale；INOVA；Sutter Health（萨特医疗）；Emory University（埃默里大学）
Phenotyping electronic health records (EHR) focuses on defining meaningful patient groups (e.g., heart failure group and diabetes group) and identifying the temporal evolution of patients in those groups. Tensor factorization has been an effective tool for phenotyping. Most of the existing works assume either a static patient representation with aggregate data or only model temporal data. However, real EHR data contain both temporal (e.g., longitudinal clinical visits) and static information (e.g., patient demographics), which are difficult to model simultaneously. In this paper, we propose Te…
Cross-graph Relational Learning (CGRL) refers to the problem of predicting the strengths or labels of multi-relational tuples of heterogeneous object types, through the joint inference over multiple graphs which specify the internal connections among each type of objects. CGRL is an open challenge in machine learning due to the daunting number of all possible tuples to deal with when the numbers of nodes in multiple graphs are large, and because the labeled training instances are extremely sparse as typical. Existing methods such as tensor factorization or tensor-kernel machines do not work we…
Matrix Factorization for Inferring Associations and Missing Links
Los Alamos National Laboratory（洛斯阿拉莫斯国家实验室）；University of Maryland, Baltimore County（马里兰大学巴尔的摩县分校）；Institute for Clarity in Documentation（文献清晰度研究所）；Inria Paris-Rocquencourt（法国国家信息与自动化研究所巴黎-罗康校区）；Rajiv Gandhi University（拉吉夫·甘地大学）；Tsinghua University（清华大学）；Palmer Research Laboratories（帕尔默研究实验室）
This paper proposes a method to guide tensor factorization, using class labels. Furthermore, it shows the advantages of using the proposed method in identifying nodes that play a special role in multi-relational networks, e.g. spammers. Most complex systems involve multiple types of relationships and interactions among entities. Combining information from different relationships may be crucial for various prediction tasks. Instead of creating distinct prediction models for each type of relationship, in this paper we present a tensor factorization approach based on RESCAL, which collectively ex…
Univ. Grenoble Alpes（格勒诺布尔阿尔卑斯大学）；NAVER LABS Europe（NAVER LABS 欧洲实验室）；University College London（伦敦大学学院）；Bloomsbury AI
In statistical relational learning, knowledge graph completion deals with automatically understanding the structure of large knowledge graphs---labeled directed graphs---and predicting missing relationships---labeled edges. State-of-the-art embedding models propose different trade-offs between modeling expressiveness, and time and space complexity. We reconcile both expressiveness and complexity through the use of complex-valued embeddings and explore the link between such complex-valued embeddings and unitary diagonalization. We corroborate our approach theoretically and show that all real sq…
We propose Macau, a powerful and flexible Bayesian factorization method for heterogeneous data. Our model can factorize any set of entities and relations that can be represented by a relational model, including tensors and also multiple relations for each entity. Macau can also incorporate side information, specifically entity and relation features, which are crucial for predicting sparsely observed relations. Macau scales to millions of entity instances, hundred millions of observations, and sparse entity features with millions of dimensions. To achieve the scale up, we specially designed sam…
RIKEN Center for Advanced Intelligence Project（理化学研究所先进智能项目中心）；Graduate School of Informatics, Kyoto University（京都大学信息学研究科）
A collection of $U \: (\in \mathbb{N})$ data vectors is called a $U$-tuple, and the association strength among the vectors of a tuple is termed as the \emph{hyperlink weight}, that is assumed to be symmetric with respect to permutation of the entries in the index. We herein propose Bregman hyperlink regression (BHLR), which learns a user-specified symmetric similarity function such that it predicts the tuple's hyperlink weight from data vectors stored in the $U$-tuple. BHLR is a simple and general framework for hyper-relational learning, that minimizes Bregman-divergence (BD) between the hyper…
A variety of machine learning tasks---e.g., matrix factorization, topic modelling, and feature allocation---can be viewed as learning the parameters of a probability distribution over bipartite graphs. Recently, a new class of models for networks, the sparse exchangeable graphs, have been introduced to resolve some important pathologies of traditional approaches to statistical network modelling; most notably, the inability to model sparsity (in the asymptotic sense). The present paper explains some practical insights arising from this work. We first show how to check if sparsity is relevant fo…
We present the first deep learning based architecture for collective matrix tri-factorization (DCMTF) of arbitrary collections of matrices, also known as augmented multi-view data. DCMTF can be used for multi-way spectral clustering of heterogeneous collections of relational data matrices to discover latent clusters in each input matrix, across both dimensions, as well as the strengths of association across clusters. The source code for DCMTF is available on our public repository: https://bitbucket.org/cdal/dcmtf_generic
Predicting the novel effects of drugs based on information about approved drugs can be regarded as a recommendation system. Matrix factorization is one of the most used recommendation systems and various algorithms have been devised for it. A literature survey and summary of existing algorithms for predicting drug effects demonstrated that most such methods, including neighborhood regularized logistic matrix factorization, which was the best performer in benchmark tests, used a binary matrix that considers only the presence or absence of interactions. However, drug effects are known to have tw…
We present a discriminative nonparametric latent feature relational model (LFRM) for link prediction to automatically infer the dimensionality of latent features. Under the generic RegBayes (regularized Bayesian inference) framework, we handily incorporate the prediction loss with probabilistic inference of a Bayesian model; set distinct regularization parameters for different types of links to handle the imbalance issue in real networks; and unify the analysis of both the smooth logistic log-loss and the piecewise linear hinge loss. For the nonconjugate posterior inference, we present a simpl…
Boolean tensor has been broadly utilized in representing high dimensional logical data collected on spatial, temporal and/or other relational domains. Boolean Tensor Decomposition (BTD) factorizes a binary tensor into the Boolean sum of multiple rank-1 tensors, which is an NP-hard problem. Existing BTD methods have been limited by their high computational cost, in applications to large scale or higher order tensors. In this work, we presented a computationally efficient BTD algorithm, namely \textit{Geometric Expansion for all-order Tensor Factorization} (GETF), that sequentially identifies th…
Symmetric binary matrices representing relations among entities are commonly collected in many areas. Our focus is on dynamically evolving binary relational matrices, with interest being in inference on the relationship structure and prediction. We propose a nonparametric Bayesian dynamic model, which reduces dimensionality in characterizing the binary matrix through a lower-dimensional latent space representation, with the latent coordinates evolving in continuous time via Gaussian processes. By using a logistic mapping function from the probability matrix space to the latent relational space…
Scientists increasingly rely on Python tools to perform scalable distributed memory array operations using rich, NumPy-like expressions. However, many of these tools rely on dynamic schedulers optimized for abstract task graphs, which often encounter memory and network bandwidth-related bottlenecks due to sub-optimal data and operator placement decisions. Tools built on the message passing interface (MPI), such as ScaLAPACK and SLATE, have better scaling properties, but these solutions require specialized knowledge to use. In this work, we present NumS, an array programming library which optim…
IQIVA Inc.（艾昆纬公司）；University of Minnesota（明尼苏达大学）；University of Chicago（芝加哥大学）
Models have been proposed to extract temporal patterns from longitudinal electronic health records (EHR) for clinical predictive models. However, the common relations among patients (e.g., receiving the same medical treatments) were rarely considered. In this paper, we propose to learn patient similarity features as phenotypes from the aggregated patient-medical service matrix using non-negative matrix factorization. On real-world medical claim data, we show that the learned phenotypes are coherent within each group, and also explanatory and indicative of targeted diseases. We conducted experi…
Topic Modeling and Link-Prediction for Material Property Discovery
Theoretical Division, Los Alamos National Laboratory Los Alamos New Mexico USA；CSEE, University of Maryland, Baltimore County Baltimore Maryland USA；Modeling, Los Alamos National Laboratory Los Alamos New Mexico USA；Department of Material Science \& Engineering, University of Maryland College Park Maryland USA；Theoretical Division, Los Alamos National Laboratory；CSEE, University of Maryland, Baltimore County；Modeling, Los Alamos National Laboratory；Department of Material Science \& Engineering, University of Maryland
University of Hildesheim（希尔德斯海姆大学）；IBM Research（IBM研究院）
Learning from multiple-relational data which contains noise, ambiguities, or duplicate entities is essential to a wide range of applications such as statistical inference based on Web Linked Data, recommender systems, computational biology, and natural language processing. These tasks usually require working with very large and complex datasets - e.g., the Web graph - however, current approaches to multi-relational learning are not practical for such scenarios due to their high computational complexity and poor scalability on large data. In this paper, we propose a novel and scalable approach …
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；University of British Columbia（英属哥伦比亚大学）
Performance of distributed optimization and learning systems is bottlenecked by "straggler" nodes and slow communication links, which significantly delay computation. We propose a distributed optimization framework where the dataset is "encoded" to have an over-complete representation with built-in redundancy, and the straggling nodes in the system are dynamically left out of the computation at every iteration, whose loss is compensated by the embedded redundancy. We show that oblivious application of several popular optimization algorithms on encoded data, including gradient descent, L-BFGS, …
Networks have been a general tool for representing, analyzing, and modeling relational data arising in several domains. One of the most important aspect of network analysis is community detection or network clustering. Until recently, the major focus have been on discovering community structure in single (i.e., monoplex) networks. However, with the advent of relational data with multiple modalities, multiplex networks, i.e., networks composed of multiple layers representing different aspects of relations, have emerged. Consequently, community detection in multiplex network, i.e., detecting clu…
University of Amsterdam（阿姆斯特丹大学）；VU Amsterdam（阿姆斯特丹自由大学）；CIFAR（加拿大高等研究院）
Knowledge graphs enable a wide variety of applications, including question answering and information retrieval. Despite the great effort invested in their creation and maintenance, even the largest (e.g., Yago, DBPedia or Wikidata) remain incomplete. We introduce Relational Graph Convolutional Networks (R-GCNs) and apply them to two standard knowledge base completion tasks: Link prediction (recovery of missing facts, i.e. subject-predicate-object triples) and entity classification (recovery of missing entity attributes). R-GCNs are related to a recent class of neural networks operating on grap…
Many scientific and engineering fields involve analyzing network data. For document networks, relational topic models (RTMs) provide a probabilistic generative process to describe both the link structure and document contents, and they have shown promise on predicting network structures and discovering latent topic representations. However, existing RTMs have limitations in both the restricted model expressiveness and incapability of dealing with imbalanced network data. To expand the scope and improve the inference accuracy of RTMs, this paper presents three extensions: 1) unlike the common l…
We introduce deep switching auto-regressive factorization (DSARF), a deep generative model for spatio-temporal data with the capability to unravel recurring patterns in the data and perform robust short- and long-term predictions. Similar to other factor analysis methods, DSARF approximates high dimensional data by a product between time dependent weights and spatially dependent factors. These weights and factors are in turn represented in terms of lower dimensional latent variables that are inferred using stochastic variational inference. DSARF is different from the state-of-the-art technique…
Principal component analysis (PCA) for binary data, known as logistic PCA, has become a popular alternative to dimensionality reduction of binary data. It is motivated as an extension of ordinary PCA by means of a matrix factorization, akin to the singular value decomposition, that maximizes the Bernoulli log-likelihood. We propose a new formulation of logistic PCA which extends Pearson's formulation of a low dimensional data representation with minimum error to binary data. Our formulation does not require a matrix factorization, as previous methods do, but instead looks for projections of th…
University of British Columbia（不列颠哥伦比亚大学）；McGill University（麦吉尔大学）；Mila（米拉研究所）
The relational model is a ubiquitous representation of big-data, in part due to its extensive use in databases. In this paper, we propose the Equivariant Entity-Relationship Network (EERN), which is a Multilayer Perceptron equivariant to the symmetry transformations of the Entity-Relationship model. To this end, we identify the most expressive family of linear maps that are exactly equivariant to entity relationship symmetries, and further show that they subsume recently introduced equivariant maps for sets, exchangeable tensors, and graphs. The proposed feed-forward layer has linear complexit…
Gradient-Based Spectral Embeddings of Random Dot Product Graphs
Facultad de Ingeniería, Universidad de la República（乌拉圭共和国大学工程学院）；Centro Interdisciplinario en Ciencia de Datos y Aprendizaje Automático (CICADA), Universidad de la República（乌拉圭共和国大学数据科学与机器学习跨学科中心（CICADA））；University of Rochester（罗切斯特大学）
