Unmeasured or latent variables are often the cause of correlations between multivariate measurements, which are studied in a variety of fields such as psychology, ecology, and medicine. For Gaussian measurements, there are classical tools such as factor analysis or principal component analysis with a well-established theory and fast algorithms. Generalized Linear Latent Variable models (GLLVMs) generalize such factor models to non-Gaussian responses. However, current algorithms for estimating model parameters in GLLVMs require intensive computation and do not scale to large datasets with thousands of observational units or responses.
In this article, we propose a new approach for fitting GLLVMs to high-dimensional datasets, based on approximating the model using penalized quasi-likelihood and then using a Newton method and Fisher scoring to learn the model parameters. Computationally, our method is noticeably faster and more stable, enabling GLLVM fits to much larger matrices than previously possible. We apply our method on a dataset of 48,000 observational units with over 2,000 observed species in each unit and find that most of the variability can be explained with a handful of factors. We publish an easy-to-use implementation of our proposed fitting algorithm.
The Matrix Factorization models, sometimes called the latent factor models, are a family of methods in the recommender system research area to (1) generate the latent factors for the users and the items and (2) predict users' ratings on items based on their latent factors. However, current Matrix Factorization models presume that all the latent factors are equally weighted, which may not always be a reasonable assumption in practice. In this paper, we propose a new model, called Weighted-SVD, to integrate the linear regression model with the SVD model such that each latent factor accompanies w…
In this letter, we propose a new identification criterion that guarantees the recovery of the low-rank latent factors in the nonnegative matrix factorization (NMF) model, under mild conditions. Specifically, using the proposed criterion, it suffices to identify the latent factors if the rows of one factor are \emph{sufficiently scattered} over the nonnegative orthant, while no structural assumption is imposed on the other factor except being full-rank. This is by far the mildest condition under which the latent factors are provably identifiable from the NMF model.
Probabilistic approach to Boolean matrix factorization can provide solutions robustagainst noise and missing values with linear computational complexity. However,the assumption about latent factors can be problematic in real world applications.This study proposed a new probabilistic algorithm free of assumptions of latentfactors, while retaining the advantages of previous algorithms. Real data experimentshowed that our algorithm was favourably compared with current state-of-the-artprobabilistic algorithms.
Context-aware recommender systems (CARS) have gained increasing attention due to their ability to utilize contextual information. Compared to traditional recommender systems, CARS are, in general, able to generate more accurate recommendations. Latent factors approach accounts for a large proportion of CARS. Recently, a non-linear Gaussian Process (GP) based factorization method was proven to outperform the state-of-the-art methods in CARS. Despite its effectiveness, GP model-based methods can suffer from over-fitting and may not be able to determine the impact of each context automatically. I…
Text clustering is arguably one of the most important topics in modern data mining. Nevertheless, text data require tokenization which usually yields a very large and highly sparse term-document matrix, which is usually difficult to process using conventional machine learning algorithms. Methods such as Latent Semantic Analysis have helped mitigate this issue, but are nevertheless not completely stable in practice. As a result, we propose a new feature agglomeration method based on Nonnegative Matrix Factorization, which is employed to separate the terms into groups, and then each group's term…
Model-based collaborative filtering analyzes user-item interactions to infer latent factors that represent user preferences and item characteristics in order to predict future interactions. Most collaborative filtering algorithms assume that these latent factors are static, although it has been shown that user preferences and item perceptions drift over time. In this paper, we propose a conjugate and numerically stable dynamic matrix factorization (DCPF) based on compound Poisson matrix factorization that models the smoothly drifting latent factors using Gamma-Markov chains. We propose a numer…
Columbia University（哥伦比亚大学）；Princeton University（普林斯顿大学）
Models for recommender systems use latent factors to explain the preferences and behaviors of users with respect to a set of items (e.g., movies, books, academic papers). Typically, the latent factors are assumed to be static and, given these factors, the observed preferences and behaviors of users are assumed to be generated without order. These assumptions limit the explorative and predictive capabilities of such models, since users' interests and item popularity may evolve over time. To address this, we propose dPF, a dynamic matrix factorization model based on the recent Poisson factorizat…
Matrix factorization techniques have been widely used as a method for collaborative filtering for recommender systems. In recent times, different variants of deep learning algorithms have been explored in this setting to improve the task of making a personalized recommendation with user-item interaction data. The idea that the mapping between the latent user or item factors and the original features is highly nonlinear suggest that classical matrix factorization techniques are no longer sufficient. In this paper, we propose a multilayer nonlinear semi-nonnegative matrix factorization method, w…
University of Cambridge（剑桥大学）；University of Toronto（多伦多大学）
Data often comes in the form of an array or matrix. Matrix factorization techniques attempt to recover missing or corrupted entries by assuming that the matrix can be written as the product of two low-rank matrices. In other words, matrix factorization approximates the entries of the matrix by a simple, fixed function---namely, the inner product---acting on the latent feature vectors for the corresponding row and column. Here we consider replacing the inner product by an arbitrary function that we learn from the data at the same time as we learn the latent feature vectors. In particular, we re…
Non-negative Matrix Factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy data sets with applications in data mining, text recognition, dimension reduction, face recognition, anomaly detection, blind source separation, and many other fields. An important input for NMF is the latent dimensionality of the data, that is, the number of hidden features, K, present in the explored data set. Unfortunately, this quantity is rarely known a priori. We utilize a supervised machine learning approach in combination with a recent met…
We introduce Polytopic Matrix Factorization (PMF) as a novel data decomposition approach. In this new framework, we model input data as unknown linear transformations of some latent vectors drawn from a polytope. In this sense, the article considers a semi-structured data model, in which the input matrix is modeled as the product of a full column rank matrix and a matrix containing samples from a polytope as its column vectors. The choice of polytope reflects the presumed features of the latent components and their mutual relationships. As the factorization criterion, we propose the determinan…
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…
Non-negative tensor factorization models enable predictive analysis on count data. Among them, Bayesian Poisson-Gamma models can derive full posterior distributions of latent factors and are less sensitive to sparse count data. However, current inference methods for these Bayesian models adopt restricted update rules for the posterior parameters. They also fail to share the update information to better cope with the data sparsity. Moreover, these models are not endowed with a component that handles the imbalance in count data values. In this paper, we propose a novel variational auto-encoder f…
The University of Texas at Austin（德克萨斯大学奥斯汀分校）；New York University（纽约大学）
This work proposes a new algorithm for automated and simultaneous phenotyping of multiple co-occurring medical conditions, also referred as comorbidities, using clinical notes from the electronic health records (EHRs). A basic latent factor estimation technique of non-negative matrix factorization (NMF) is augmented with domain specific constraints to obtain sparse latent factors that are anchored to a fixed set of chronic conditions. The proposed anchoring mechanism ensures a one-to-one identifiable and interpretable mapping between the latent factors and the target comorbidities. Qualitative…
University of Minnesota（明尼苏达大学）；IQVIA（艾昆纬）；University of Virginia（弗吉尼亚大学）；Temple University（天普大学）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Accurate prediction of the transmission of epidemic diseases such as COVID-19 is crucial for implementing effective mitigation measures. In this work, we develop a tensor method to predict the evolution of epidemic trends for many regions simultaneously. We construct a 3-way spatio-temporal tensor (location, attribute, time) of case counts and propose a nonnegative tensor factorization with latent epidemiological model regularization named STELAR. Unlike standard tensor factorization methods which cannot predict slabs ahead, STELAR enables long-term prediction by incorporating latent temporal …
Department of Mathematics, UC Santa Barbara（加州大学圣巴巴拉分校数学系）；Department of ECE, UC Santa Barbara（加州大学圣巴巴拉分校电气工程与计算机科学系）
Streaming tensor factorization is a powerful tool for processing high-volume and multi-way temporal data in Internet networks, recommender systems and image/video data analysis. Existing streaming tensor factorization algorithms rely on least-squares data fitting and they do not possess a mechanism for tensor rank determination. This leaves them susceptible to outliers and vulnerable to over-fitting. This paper presents a Bayesian robust streaming tensor factorization model to identify sparse outliers, automatically determine the underlying tensor rank and accurately fit low-rank structure. We…
Faculty of Computer Science and Information Systems, University of Technology Malaysia（马来西亚理工大学计算机科学与信息系统学院）
This paper provides a theoretical support for clustering aspect of the nonnegative matrix factorization (NMF). By utilizing the Karush-Kuhn-Tucker optimality conditions, we show that NMF objective is equivalent to graph clustering objective, so clustering aspect of the NMF has a solid justification. Different from previous approaches which usually discard the nonnegativity constraints, our approach guarantees the stationary point being used in deriving the equivalence is located on the feasible region in the nonnegative orthant. Additionally, since clustering capability of a matrix decompositi…
In the context of time series forecasting, it is a common practice to evaluate multiple methods and choose one of these methods or an ensemble for producing the best forecasts. However, choosing among different ensembles over multiple methods remains a challenging task that undergoes a combinatorial explosion as the number of methods increases. In the context of demand forecasting or revenue forecasting, this challenge is further exacerbated by a large number of time series as well as limited historical data points available due to changing business context. Although deep learning forecasting …
Columbia University（哥伦比亚大学）；Adobe Research（Adobe研究院）；Adobe Systems Incorporated（奥多比系统公司）
Beta process is the standard nonparametric Bayesian prior for latent factor model. In this paper, we derive a structured mean-field variational inference algorithm for a beta process non-negative matrix factorization (NMF) model with Poisson likelihood. Unlike the linear Gaussian model, which is well-studied in the nonparametric Bayesian literature, NMF model with beta process prior does not enjoy the conjugacy. We leverage the recently developed stochastic structured mean-field variational inference to relax the conjugacy constraint and restore the dependencies among the latent variables in t…
NTT DATA Mathematical Systems Inc.（NTT数据数学系统株式会社）；Tokyo Institute of Technology（东京工业大学）
Latent Dirichlet allocation (LDA) is useful in document analysis, image processing, and many information systems; however, its generalization performance has been left unknown because it is a singular learning machine to which regular statistical theory can not be applied. Stochastic matrix factorization (SMF) is a restricted matrix factorization in which matrix factors are stochastic; the column of the matrix is in a simplex. SMF is being applied to image recognition and text mining. We can understand SMF as a statistical model by which a stochastic matrix of given data is represented by a pr…
This work explores non-negative low-rank matrix factorization based on regularized Poisson models (PF or "Poisson factorization" for short) for recommender systems with implicit-feedback data. The properties of Poisson likelihood allow a shortcut for very fast computations over zero-valued inputs, and oftentimes results in very sparse factors for both users and items. Compared to HPF (a popular Bayesian formulation of the problem with hierarchical priors), the frequentist optimization-based approach presented here tends to produce better top-N recommendations with significantly shorter fitting…
Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）；University of Bath（巴斯大学）
Nonnegative matrix factorization (NMF) is one of the most frequently-used matrix factorization models in data analysis. A significant reason to the popularity of NMF is its interpretability and the `parts of whole' interpretation of its components. Recently, max-times, or subtropical, matrix factorization (SMF) has been introduced as an alternative model with equally interpretable `winner takes it all' interpretation. In this paper we propose a new mixed linear--tropical model, and a new algorithm, called Latitude, that combines NMF and SMF, being able to smoothly alternate between the two. In…
In this paper, we introduce a probabilistic model for learning nonnegative matrix factorization (NMF) that is commonly used for predicting missing values and finding hidden patterns in the data, in which the matrix factors are latent variables associated with each data dimension. The nonnegativity constraint for the latent factors is handled by choosing priors with support on the nonnegative subspace. Bayesian inference procedure based on Gibbs sampling is employed. We evaluate the model on several real-world datasets including MovieLens 100K and MovieLens 1M with different sizes and dimension…
In recent years, the rapid growth in technology has increased the opportunity for longitudinal human behavioral studies. Rich multimodal data, from wearables like Fitbit, online social networks, mobile phones etc. can be collected in natural environments. Uncovering the underlying low-dimensional structure of noisy multi-way data in an unsupervised setting is a challenging problem. Tensor factorization has been successful in extracting the interconnected low-dimensional descriptions of multi-way data. In this paper, we apply non-negative tensor factorization on a real-word wearable sensor data…
Dimensionality reduction techniques play an essential role in data analytics, signal processing and machine learning. Dimensionality reduction is usually performed in a preprocessing stage that is separate from subsequent data analysis, such as clustering or classification. Finding reduced-dimension representations that are well-suited for the intended task is more appealing. This paper proposes a joint factor analysis and latent clustering framework, which aims at learning cluster-aware low-dimensional representations of matrix and tensor data. The proposed approach leverages matrix and tenso…
Urban areas provide us with a treasure trove of available data capturing almost every aspect of a population's life. This work focuses on mobility data and how it will help improve our understanding of urban mobility patterns. Readily available and sizable farecard data captures trips in a public transportation network. However, such data typically lacks temporal modalities and as such the task of inferring trip semantic, station function, and user profile is quite challenging. As existing approaches either focus on station-level or user-level signals, they are prone to overfitting and generat…
Computational drug repositioning aims to discover new therapeutic diseases for marketed drugs and has the advantages of low cost, short development cycle, and high controllability compared to traditional drug development. The matrix factorization model has become the cornerstone technique for computational drug repositioning due to its ease of implementation and excellent scalability. However, the matrix factorization model uses the inner product to represent the association between drugs and diseases, which is lacking in expressive ability. Moreover, the degree of similarity of drugs or disea…
University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；Columbia University（哥伦比亚大学）；Microsoft Research（微软研究院）
We present a Bayesian tensor factorization model for inferring latent group structures from dynamic pairwise interaction patterns. For decades, political scientists have collected and analyzed records of the form "country $i$ took action $a$ toward country $j$ at time $t$"---known as dyadic events---in order to form and test theories of international relations. We represent these event data as a tensor of counts and develop Bayesian Poisson tensor factorization to infer a low-dimensional, interpretable representation of their salient patterns. We demonstrate that our model's predictive perform…
Chinese Academy of Sciences（中国科学院）；University of Science and Technology of China（中国科学技术大学）；Alibaba Group（阿里巴巴集团）
Rating Prediction is a basic problem in Recommender System, and one of the most widely used method is Factorization Machines(FM). However, traditional matrix factorization methods fail to utilize the benefit of implicit feedback, which has been proved to be important in Rating Prediction problem. In this work, we consider a specific situation, movie rating prediction, where we assume that watching history has a big influence on his/her rating behavior on an item. We introduce two models, Latent Dirichlet Allocation(LDA) and word2vec, both of which perform state-of-the-art results in training l…
Carnegie Mellon University（卡内基梅隆大学）；University of Minnesota（明尼苏达大学）
How can we correlate neural activity in the human brain as it responds to words, with behavioral data expressed as answers to questions about these same words? In short, we want to find latent variables, that explain both the brain activity, as well as the behavioral responses. We show that this is an instance of the Coupled Matrix-Tensor Factorization (CMTF) problem. We propose Scoup-SMT, a novel, fast, and parallel algorithm that solves the CMTF problem and produces a sparse latent low-rank subspace of the data. In our experiments, we find that Scoup-SMT is 50-100 times faster than a state-o…
CANDECOMP/PARAFAC (CP) tensor factorization of incomplete data is a powerful technique for tensor completion through explicitly capturing the multilinear latent factors. The existing CP algorithms require the tensor rank to be manually specified, however, the determination of tensor rank remains a challenging problem especially for CP rank. In addition, existing approaches do not take into account uncertainty information of latent factors, as well as missing entries. To address these issues, we formulate CP factorization using a hierarchical probabilistic model and employ a fully Bayesian trea…
For latent class models where the class weights depend on individual covariates, we derive a simple expression for computing the score vector and a convenient hybrid between the observed and the expected information matrices which is always positive defnite. These ingredients, combined with a maximization algorithm based on line search, provides an efficient tool for maximum likelihood estimation. In particular, the proposed algorithm is such that the log-likelihood never decreases from one step to the next and the choice of starting values is not crucial for reaching a local maximum. We show …
Newsroom in online ecosystem is difficult to untangle. With prevalence of social media, interactions between journalists and individuals become visible, but lack of understanding to inner processing of information feedback loop in public sphere leave most journalists baffled. Can we provide an organized view to characterize journalist behaviors on individual level to know better of the ecosystem? To this end, I propose Poisson Factorization Machine (PFM), a Bayesian analogue to matrix factorization that assumes Poisson distribution for generative process. The model generalizes recent studies o…
Dyadic Data Prediction (DDP) is an important problem in many research areas. This paper develops a novel fully Bayesian nonparametric framework which integrates two popular and complementary approaches, discrete mixed membership modeling and continuous latent factor modeling into a unified Heterogeneous Matrix Factorization~(HeMF) model, which can predict the unobserved dyadics accurately. The HeMF can determine the number of communities automatically and exploit the latent linear structure for each bicluster efficiently. We propose a Variational Bayesian method to estimate the parameters and …
Learning by integrating multiple heterogeneous data sources is a common requirement in many tasks. Collective Matrix Factorization (CMF) is a technique to learn shared latent representations from arbitrary collections of matrices. It can be used to simultaneously complete one or more matrices, for predicting the unknown entries. Classical CMF methods assume linearity in the interaction of latent factors which can be restrictive and fails to capture complex non-linear interactions. In this paper, we develop the first deep-learning based method, called dCMF, for unsupervised learning of multiple…
Coordinated Science Laboratory, University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校协调科学实验室）
Revealed preference theory studies the possibility of modeling an agent's revealed preferences and the construction of a consistent utility function. However, modeling agent's choices over preference orderings is not always practical and demands strong assumptions on human rationality and data-acquisition abilities. Therefore, we propose a simple generative choice model where agents are assumed to generate the choice probabilities based on latent factor matrices that capture their choice evaluation across multiple attributes. Since the multi-attribute evaluation is typically hidden within the …
Tensor factorization arises in many machine learning applications, such knowledge base modeling and parameter estimation in latent variable models. However, numerical methods for tensor factorization have not reached the level of maturity of matrix factorization methods. In this paper, we propose a new method for CP tensor factorization that uses random projections to reduce the problem to simultaneous matrix diagonalization. Our method is conceptually simple and also applies to non-orthogonal and asymmetric tensors of arbitrary order. We prove that a small number random projections essentiall…
Interpretable factorization of clinical questionnaires to identify latent factors of psychopathology
Machine Learning Core, National Institute of Mental Health, National Institutes of Health（机器学习核心，国家心理健康研究所，国立卫生研究院）；Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, National Institutes of Health（发育神经基因组学部门，人类遗传学分支，国家心理健康研究所，国立卫生研究院）；National Institute of Mental Health, National Institutes of Health（国家心理健康研究所，国立卫生研究院）
Matrix factorization is one of the best approaches for collaborative filtering, because of its high accuracy in presenting users and items latent factors. The main disadvantages of matrix factorization are its complexity, and being very hard to be parallelized, specially with very large matrices. In this paper, we introduce a new method for collaborative filtering based on Matrix Factorization by combining simulated annealing with levy distribution. By using this method, good solutions are achieved in acceptable time with low computations, compared to other methods like stochastic gradient des…
Ege University（埃杰大学）；Yildiz Technical University（耶尔德兹技术大学）；Walmart Global Tech（沃尔玛全球科技）
With the development of technology, the use of social media has become quite common. Analyzing comments on social media in areas such as media and advertising plays an important role today. For this reason, new and traditional natural language processing methods are used to detect the emotion of these shares. In this paper, the Latent Dirichlet Allocation, namely LDA, and Non-Negative Matrix Factorization methods in topic modeling were used to determine which emotion the Turkish tweets posted via Twitter. In addition, the accuracy of a proposed n-level method based on LDA was analyzed. Dataset…
We introduce a probabilistic model with implicit norm regularization for learning nonnegative matrix factorization (NMF) that is commonly used for predicting missing values and finding hidden patterns in the data, in which the matrix factors are latent variables associated with each data dimension. The nonnegativity constraint for the latent factors is handled by choosing priors with support on the nonnegative subspace, e.g., exponential density or distribution based on exponential function. Bayesian inference procedure based on Gibbs sampling is employed. We evaluate the model on several real…
The Ohio State University（俄亥俄州立大学）；The University of Hong Kong（香港大学）；Carnegie Mellon University（卡内基梅隆大学）
Low-rank matrix completion has achieved great success in many real-world data applications. A matrix factorization model that learns latent features is usually employed and, to improve prediction performance, the similarities between latent variables can be exploited by pairwise learning using the graph regularized matrix factorization (GRMF) method. However, existing GRMF approaches often use the squared loss to measure the pairwise differences, which may be overly influenced by dissimilar pairs and lead to inferior prediction. To fully empower pairwise learning for matrix completion, we prop…
We present the Infinite Latent Events Model, a nonparametric hierarchical Bayesian distribution over infinite dimensional Dynamic Bayesian Networks with binary state representations and noisy-OR-like transitions. The distribution can be used to learn structure in discrete timeseries data by simultaneously inferring a set of latent events, which events fired at each timestep, and how those events are causally linked. We illustrate the model on a sound factorization task, a network topology identification task, and a video game task.
Columbia University（哥伦比亚大学）；University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；Microsoft（微软）
We present a new non-negative matrix factorization model for $(0,1)$ bounded-support data based on the doubly non-central beta (DNCB) distribution, a generalization of the beta distribution. The expressiveness of the DNCB distribution is particularly useful for modeling DNA methylation datasets, which are typically highly dispersed and multi-modal; however, the model structure is sufficiently general that it can be adapted to many other domains where latent representations of $(0,1)$ bounded-support data are of interest. Although the DNCB distribution lacks a closed-form conjugate prior, sever…
Queensland University of Technology（昆士兰科技大学）；Singapore University of Technology and Design（新加坡科技设计大学）
Coupled Matrix Tensor Factorization (CMTF) facilitates the integration and analysis of multiple data sources and helps discover meaningful information. Nonnegative CMTF (N-CMTF) has been employed in many applications for identifying latent patterns, prediction, and recommendation. However, due to the added complexity with coupling between tensor and matrix data, existing N-CMTF algorithms exhibit poor computation efficiency. In this paper, a computationally efficient N-CMTF factorization algorithm is presented based on the column-wise element selection, preventing frequent gradient updates. Th…
Georgia Institute of Technology（佐治亚理工学院）；Georgia Tech Research Institute（佐治亚理工研究所）
We present a hybrid method for latent information discovery on the data sets containing both text content and connection structure based on constrained low rank approximation. The new method jointly optimizes the Nonnegative Matrix Factorization (NMF) objective function for text clustering and the Symmetric NMF (SymNMF) objective function for graph clustering. We propose an effective algorithm for the joint NMF objective function, based on a block coordinate descent (BCD) framework. The proposed hybrid method discovers content associations via latent connections found using SymNMF. The method …
We introduce a new method based on nonnegative matrix factorization, Neural NMF, for detecting latent hierarchical structure in data. Datasets with hierarchical structure arise in a wide variety of fields, such as document classification, image processing, and bioinformatics. Neural NMF recursively applies NMF in layers to discover overarching topics encompassing the lower-level features. We derive a backpropagation optimization scheme that allows us to frame hierarchical NMF as a neural network. We test Neural NMF on a synthetic hierarchical dataset, the 20 Newsgroups dataset, and the MyLymeD…
