scholarly journals An Inductive Logistic Matrix Factorization Model for Predicting Drug-Metabolite Association With Vicus Regularization

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuanyuan Ma ◽  
Lifang Liu ◽  
Qianjun Chen ◽  
Yingjun Ma
Keyword(s):  
Matrix Factorization ◽  
Large Scale ◽  
Matrix Completion ◽  
Original Data ◽  
Feature Representation ◽  
Bipartite Networks ◽  
Spectral Matrix ◽  
Drug Metabolite ◽  
Low Dimensional ◽  
Drugs And Metabolites

Metabolites are closely related to human disease. The interaction between metabolites and drugs has drawn increasing attention in the field of pharmacomicrobiomics. However, only a small portion of the drug-metabolite interactions were experimentally observed due to the fact that experimental validation is labor-intensive, costly, and time-consuming. Although a few computational approaches have been proposed to predict latent associations for various bipartite networks, such as miRNA-disease, drug-target interaction networks, and so on, to our best knowledge the associations between drugs and metabolites have not been reported on a large scale. In this study, we propose a novel algorithm, namely inductive logistic matrix factorization (ILMF) to predict the latent associations between drugs and metabolites. Specifically, the proposed ILMF integrates drug–drug interaction, metabolite–metabolite interaction, and drug-metabolite interaction into this framework, to model the probability that a drug would interact with a metabolite. Moreover, we exploit inductive matrix completion to guide the learning of projection matrices U and V that depend on the low-dimensional feature representation matrices of drugs and metabolites: Fm and Fd. These two matrices can be obtained by fusing multiple data sources. Thus, FdU and FmV can be viewed as drug-specific and metabolite-specific latent representations, different from classical LMF. Furthermore, we utilize the Vicus spectral matrix that reveals the refined local geometrical structure inherent in the original data to encode the relationships between drugs and metabolites. Extensive experiments are conducted on a manually curated “DrugMetaboliteAtlas” dataset. The experimental results show that ILMF can achieve competitive performance compared with other state-of-the-art approaches, which demonstrates its effectiveness in predicting potential drug-metabolite associations.

scholarly journals Unsupervised Text Feature Learning via Deep Variational Auto-encoder

2020 ◽  
Vol 49 (3) ◽  
pp. 421-437
Author(s):  
Genggeng Liu ◽  
Lin Xie ◽  
Chi-Hua Chen
Keyword(s):  
Dimensionality Reduction ◽  
High Dimensional Data ◽  
Image Data ◽  
Original Data ◽  
Feature Representation ◽  
High Dimensional ◽  
Learning To Learn ◽  
Text Feature ◽  
Reduction Methods ◽  
Low Dimensional

Dimensionality reduction plays an important role in the data processing of machine learning and data mining, which makes the processing of high-dimensional data more efficient. Dimensionality reduction can extract the low-dimensional feature representation of high-dimensional data, and an effective dimensionality reduction method can not only extract most of the useful information of the original data, but also realize the function of removing useless noise. The dimensionality reduction methods can be applied to all types of data, especially image data. Although the supervised learning method has achieved good results in the application of dimensionality reduction, its performance depends on the number of labeled training samples. With the growing of information from internet, marking the data requires more resources and is more difficult. Therefore, using unsupervised learning to learn the feature of data has extremely important research value. In this paper, an unsupervised multilayered variational auto-encoder model is studied in the text data, so that the high-dimensional feature to the low-dimensional feature becomes efficient and the low-dimensional feature can retain mainly information as much as possible. Low-dimensional feature obtained by different dimensionality reduction methods are used to compare with the dimensionality reduction results of variational auto-encoder (VAE), and the method can be significantly improved over other comparison methods.

A Meta-Algorithm for Improving Top-N Prediction Efficiency of Matrix Factorization Models in Collaborative Filtering

2019 ◽  
Vol 34 (03) ◽  
pp. 2059007
Author(s):  
A. Murat Yagci ◽  
Tevfik Aytekin ◽  
Fikret S. Gurgen
Keyword(s):  
Collaborative Filtering ◽  
Matrix Factorization ◽  
Large Scale ◽  
Nearest Neighbor ◽  
Nearest Neighbor Search ◽  
Space Efficiency ◽  
Neighbor Search ◽  
Prediction Time ◽  
Low Dimensional ◽  
Prediction Efficiency

Matrix factorization models often reveal the low-dimensional latent structure in high-dimensional spaces while bringing space efficiency to large-scale collaborative filtering problems. Improving training and prediction time efficiencies of these models are also important since an accurate model may raise practical concerns if it is slow to capture the changing dynamics of the system. For the training task, powerful improvements have been proposed especially using SGD, ALS, and their parallel versions. In this paper, we focus on the prediction task and combine matrix factorization with approximate nearest neighbor search methods to improve the efficiency of top-N prediction queries. Our efforts result in a meta-algorithm, MMFNN, which can employ various common matrix factorization models, drastically improve their prediction efficiency, and still perform comparably to standard prediction approaches or sometimes even better in terms of predictive power. Using various batch, online, and incremental matrix factorization models, we present detailed empirical analysis results on many large implicit feedback datasets from different application domains.

scholarly journals Adaptive-Weighted Multiview Deep Basis Matrix Factorization for Multimedia Data Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Shicheng Li ◽  
Qinghua Liu ◽  
Jiangyan Dai ◽  
Wenle Wang ◽  
Xiaolin Gui ◽  
...  
Keyword(s):  
Data Analysis ◽  
Matrix Factorization ◽  
Feature Learning ◽  
Representation Learning ◽  
Feature Representation ◽  
Multimedia Data ◽  
Basis Matrix ◽  
Rich Information ◽  
Low Dimensional ◽  
Better Than

Feature representation learning is a key issue in artificial intelligence research. Multiview multimedia data can provide rich information, which makes feature representation become one of the current research hotspots in data analysis. Recently, a large number of multiview data feature representation methods have been proposed, among which matrix factorization shows the excellent performance. Therefore, we propose an adaptive-weighted multiview deep basis matrix factorization (AMDBMF) method that integrates matrix factorization, deep learning, and view fusion together. Specifically, we first perform deep basis matrix factorization on data of each view. Then, all views are integrated to complete the procedure of multiview feature learning. Finally, we propose an adaptive weighting strategy to fuse the low-dimensional features of each view so that a unified feature representation can be obtained for multiview multimedia data. We also design an iterative update algorithm to optimize the objective function and justify the convergence of the optimization algorithm through numerical experiments. We conducted clustering experiments on five multiview multimedia datasets and compare the proposed method with several excellent current methods. The experimental results demonstrate that the clustering performance of the proposed method is better than those of the other comparison methods.

scholarly journals Finding Potential Propagators and Customers in Location-Based Social Networks: An Embedding-Based Approach

2020 ◽  
Vol 10 (22) ◽  
pp. 8003
Author(s):  
Yi-Chun Chen ◽  
Cheng-Te Li
Keyword(s):  
Social Networks ◽  
Large Scale ◽  
Main Idea ◽  
Feature Representation ◽  
Specific Point ◽  
Point Of Interest ◽  
The Future ◽  
Location Based Social Networks ◽  
Low Dimensional ◽  
Embedding Methods

In the scenarios of location-based social networks (LBSN), the goal of location promotion is to find information propagators to promote a specific point-of-interest (POI). While existing studies mainly focus on accurately recommending POIs for users, less effort is made for identifying propagators in LBSN. In this work, we propose and tackle two novel tasks, Targeted Propagator Discovery (TPD) and Targeted Customer Discovery (TCD), in the context of Location Promotion. Given a target POI l to be promoted, TPD aims at finding a set of influential users, who can generate more users to visit l in the future, and TCD is to find a set of potential users, who will visit l in the future. To deal with TPD and TCD, we propose a novel graph embedding method, LBSN2vec. The main idea is to jointly learn a low dimensional feature representation for each user and each location in an LBSN. Equipped with learned embedding vectors, we propose two similarity-based measures, Influential and Visiting scores, to find potential targeted propagators and customers. Experiments conducted on a large-scale Instagram LBSN dataset exhibit that LBSN2vec and its variant can significantly outperform well-known network embedding methods in both tasks.

scholarly journals Robust Matrix Completion By Exploiting Dynamic Low-Dimensional Structures

2021 ◽  
Author(s):  
Ren Wang ◽  
Pengzhi Gao ◽  
Meng Wang
Keyword(s):  
Matrix Completion ◽  
Synthetic Data ◽  
Original Data ◽  
Low Rank ◽  
Temporal Correlations ◽  
Completion Problem ◽  
Reconstruction Performance ◽  
Matrix Completion Problem ◽  
Recovery Error ◽  
Low Dimensional

Abstract This paper studies the robust matrix completion problem for time-varying models. Leveraging the low-rank property and the temporal information of the data, we develop novel methods to recover the original data from partially observed and corrupted measurements. We show that the reconstruction performance can be improved if one further leverages the information of the sparse corruptions in addition to the temporal correlations among a sequence of matrices. The dynamic robust matrix completion problem is formulated as a nonconvex optimization problem, and the recovery error is quantified analytically and proved to decay in the same order as that of the state-of-the-art method when there is no corruption. A fast iterative algorithm with convergence guarantee to the stationary point is proposed to solve the nonconvex problem. Experiments on synthetic data and real video dataset demonstrate the effectiveness of our method.

scholarly journals Small-variance asymptotics for non-parametric online robot learning

2018 ◽  
Vol 38 (1) ◽  
pp. 3-22 ◽  
Author(s):  
Ajay Kumar Tanwani ◽  
Sylvain Calinon
Keyword(s):  
Mixture Models ◽  
Dirichlet Process ◽  
Large Scale ◽  
Principal Component ◽  
Small Variance ◽  
Remote Manipulation ◽  
State Duration ◽  
Duration Information ◽  
Low Dimensional ◽  
Non Parametric

Small-variance asymptotics is emerging as a useful technique for inference in large-scale Bayesian non-parametric mixture models. This paper analyzes the online learning of robot manipulation tasks with Bayesian non-parametric mixture models under small-variance asymptotics. The analysis yields a scalable online sequence clustering (SOSC) algorithm that is non-parametric in the number of clusters and the subspace dimension of each cluster. SOSC groups the new datapoint in low-dimensional subspaces by online inference in a non-parametric mixture of probabilistic principal component analyzers (MPPCA) based on a Dirichlet process, and captures the state transition and state duration information online in a hidden semi-Markov model (HSMM) based on a hierarchical Dirichlet process. A task-parameterized formulation of our approach autonomously adapts the model to changing environmental situations during manipulation. We apply the algorithm in a teleoperation setting to recognize the intention of the operator and remotely adjust the movement of the robot using the learned model. The generative model is used to synthesize both time-independent and time-dependent behaviors by relying on the principles of shared and autonomous control. Experiments with the Baxter robot yield parsimonious clusters that adapt online with new demonstrations and assist the operator in performing remote manipulation tasks.

scholarly journals Introduction to Matrix Factorization for Recommender Systems

2021 ◽  
Author(s):  
Shalin Shah
Keyword(s):  
Singular Value Decomposition ◽  
Online Education ◽  
Recommender Systems ◽  
Matrix Factorization ◽  
Gradient Descent ◽  
Large Scale ◽  
Singular Value ◽  
Factorization Algorithms ◽  
Value Decomposition ◽  
Interaction History

Recommender systems aim to personalize the experience of user by suggesting items to the user based on the preferences of a user. The preferences are learned from the user’s interaction history or through explicit ratings that the user has given to the items. The system could be part of a retail website, an online bookstore, a movie rental service or an online education portal and so on. In this paper, I will focus on matrix factorization algorithms as applied to recommender systems and discuss the singular value decomposition, gradient descent-based matrix factorization and parallelizing matrix factorization for large scale applications.

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