Positive Pointwise Mutual Information Research Articles

TGCN-Bert Emoji Prediction in Information Systems Using TCN and GCN Fusing Features Based on BERT

In recent studies, graph convolutional neural networks (GCNs) have been used to solve different natural language processing (NLP) tasks. However, few researches apply graph convolutional networks to short text classification. Emoji prediction, as a complex sentiment analysis task, has received even less attention. In this work, the authors propose TGCN-Bert which combines pre-trained BERT temporal convolutional networks (TCNs) and graph convolutional networks for short text classification and emoji prediction. They initialize the nodes with the help of BERT and define the edges in text graph based on the term frequency-inverse document frequency (TF-IDF) and positive point-wise mutual information (PPMI). They employ the model for emoji prediction task, and a metric based on emoji clustering is developed to better measure the validity of emoji prediction results. To validate the performance of TGCN-Bert, they compare it with other GCN variants on short text classification datasets and emoji prediction datasets; experiments show that TGCN-Bert achieves better performance.

Investigating the Extent to which Distributional Semantic Models Capture a Broad Range of Semantic Relations.

Distributional semantic models (DSMs) are a primary method for distilling semantic information from corpora. However, a key question remains: What types of semantic relations among words do DSMs detect? Prior work typically has addressed this question using limited human data that are restricted to semantic similarity and/or general semantic relatedness. We tested eight DSMs that are popular in current cognitive and psycholinguistic research (positive pointwise mutual information; global vectors; and three variations each of Skip-gram and continuous bag of words (CBOW) using word, context, and mean embeddings) on a theoretically motivated, rich set of semantic relations involving words from multiple syntactic classes and spanning the abstract-concrete continuum (19 sets of ratings). We found that, overall, the DSMs are best at capturing overall semantic similarity and also can capture verb-noun thematic role relations and noun-noun event-based relations that play important roles in sentence comprehension. Interestingly, Skip-gram and CBOW performed the best in terms of capturing similarity, whereas GloVe dominated the thematic role and event-based relations. We discuss the theoretical and practical implications of our results, make recommendations for users of these models, and demonstrate significant differences in model performance on event-based relations.

Predicting miRNA-disease associations based on PPMI and attention network

BackgroundWith the development of biotechnology and the accumulation of theories, many studies have found that microRNAs (miRNAs) play an important role in various diseases. Uncovering the potential associations between miRNAs and diseases is helpful to better understand the pathogenesis of complex diseases. However, traditional biological experiments are expensive and time-consuming. Therefore, it is necessary to develop more efficient computational methods for exploring underlying disease-related miRNAs.ResultsIn this paper, we present a new computational method based on positive point-wise mutual information (PPMI) and attention network to predict miRNA-disease associations (MDAs), called PATMDA. Firstly, we construct the heterogeneous MDA network and multiple similarity networks of miRNAs and diseases. Secondly, we respectively perform random walk with restart and PPMI on different similarity network views to get multi-order proximity features and then obtain high-order proximity representations of miRNAs and diseases by applying the convolutional neural network to fuse the learned proximity features. Then, we design an attention network with neural aggregation to integrate the representations of a node and its heterogeneous neighbor nodes according to the MDA network. Finally, an inner product decoder is adopted to calculate the relationship scores between miRNAs and diseases.ConclusionsPATMDA achieves superior performance over the six state-of-the-art methods with the area under the receiver operating characteristic curve of 0.933 and 0.946 on the HMDD v2.0 and HMDD v3.2 datasets, respectively. The case studies further demonstrate the validity of PATMDA for discovering novel disease-associated miRNAs.

Dual adaptive learning multi-task multi-view for graph network representation learning

Graph network analysis, which achieves widely application, is to explore and mine the graph structure data. However, existing graph network analysis methods with graph representation learning technique ignore the correlation between multiple graph network analysis tasks, and they need massive repeated calculation to obtain each graph network analysis results. Or they cannot adaptively balance the relative importance of multiple graph network analysis tasks, that lead to weak model fitting. Besides, most of existing methods ignore multiplex views semantic information and global graph information, which fail to learn robust node embeddings resulting in unsatisfied graph analysis results. To solve these issues, we propose a multi-task multi-view adaptive graph network representation learning model, called M2agl. The highlights of M2agl are as follows: (1) Graph convolutional network with the linear combination of the adjacency matrix and PPMI (positive point-wise mutual information) matrix is utilized as encoder to extract the local and global intra-view graph feature information of the multiplex graph network. Each intra-view graph information of the multiplex graph network can adaptively learn the parameters of graph encoder. (2) We use regularization to capture the interaction information among different graph views, and the importance of different graph views are learned by view attention mechanism for further inter-view graph network fusion. (3) The model is trained oriented by multiple graph network analysis tasks. The relative importance of multiple graph network analysis tasks are adjusted adaptively with the homoscedastic uncertainty. The regularization can be considered as an auxiliary task to further boost the performance. Experiments on real-worlds attributed multiplex graph networks demonstrate the effectiveness of M2agl in comparison with other competing approaches.

A Place Recommendation Approach Using Word Embeddings in Conceptual Spaces

The way that computing systems digest geographic space is fundamentally different from people’s understanding of space. In human discourse, a geographic space is referred to by a place name, and the reasoning about a place are based on its characteristics. This is in contrast with computing systems where geographical spaces are handled by the definition of coordinate systems. Hence, when recommending places, a recommendation method that leverages textual content, as a medium of communication among people, can be better understood. In this paper, we use elements of Natural Language Processing (NLP), such as Positive Point-wise Mutual Information (PPMI), Term Frequency - Inverse Document Frequency (TF-IDF), and Multi-Dimensional Scaling (MDS), to infer a conceptual space of the items of a place-based recommender system. By applying a Support Vector Machine (SVM) classifier on the resulting conceptual space, some meaningful directions are extracted. Shannon entropy is used as a measure to identify the directions that imply a valid geographic region. We apply the method on a dataset of advertisement descriptions of rental properties and a dataset of Persian Wikipedia articles. The results showed the proposed method is able to measure the similarity of items in the inferred conceptual space with 88% of accuracy. A comparison with BERT algorithm demonstrates the superiority of the proposed method over the baseline models.

Deciphering the Diversity of Mental Models in Neurodevelopmental Disorders: Knowledge Graph Representation of Public Data Using Natural Language Processing.

BackgroundUnderstanding how individuals think about a topic, known as the mental model, can significantly improve communication, especially in the medical domain where emotions and implications are high. Neurodevelopmental disorders (NDDs) represent a group of diagnoses, affecting up to 18% of the global population, involving differences in the development of cognitive or social functions. In this study, we focus on 2 NDDs, attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD), which involve multiple symptoms and interventions requiring interactions between 2 important stakeholders: parents and health professionals. There is a gap in our understanding of differences between mental models for each stakeholder, making communication between stakeholders more difficult than it could be.ObjectiveWe aim to build knowledge graphs (KGs) from web-based information relevant to each stakeholder as proxies of mental models. These KGs will accelerate the identification of shared and divergent concerns between stakeholders. The developed KGs can help improve knowledge mobilization, communication, and care for individuals with ADHD and ASD.MethodsWe created 2 data sets by collecting the posts from web-based forums and PubMed abstracts related to ADHD and ASD. We utilized the Unified Medical Language System (UMLS) to detect biomedical concepts and applied Positive Pointwise Mutual Information followed by truncated Singular Value Decomposition to obtain corpus-based concept embeddings for each data set. Each data set is represented as a KG using a property graph model. Semantic relatedness between concepts is calculated to rank the relation strength of concepts and stored in the KG as relation weights. UMLS disorder-relevant semantic types are used to provide additional categorical information about each concept’s domain.ResultsThe developed KGs contain concepts from both data sets, with node sizes representing the co-occurrence frequency of concepts and edge sizes representing relevance between concepts. ADHD- and ASD-related concepts from different semantic types shows diverse areas of concerns and complex needs of the conditions. KG identifies converging and diverging concepts between health professionals literature (PubMed) and parental concerns (web-based forums), which may correspond to the differences between mental models for each stakeholder.ConclusionsWe show for the first time that generating KGs from web-based data can capture the complex needs of families dealing with ADHD or ASD. Moreover, we showed points of convergence between families and health professionals’ KGs. Natural language processing–based KG provides access to a large sample size, which is often a limiting factor for traditional in-person mental model mapping. Our work offers a high throughput access to mental model maps, which could be used for further in-person validation, knowledge mobilization projects, and basis for communication about potential blind spots from stakeholders in interactions about NDDs. Future research will be needed to identify how concepts could interact together differently for each stakeholder.

Understanding the effects of negative (and positive) pointwise mutual information on word vectors

ABSTRACT Despite the recent popularity of contextual word embeddings, static word embeddings still dominate lexical semantic tasks, making their study of continued relevance. A widely adopted family of such static word embeddings is derived by explicitly factorising the Pointwise Mutual Information (PMI) weighting of the co-occurrence matrix. As unobserved co-occurrences lead PMI to negative infinity, a common workaround is to clip negative PMI at 0. However, it is unclear what information is lost by collapsing negative PMI values to 0. To answer this question, we isolate and study the effects of negative (and positive) PMI on the semantics and geometry of models adopting factorisation of different PMI matrices. Word and sentence-level evaluations show that only accounting for positive PMI in the factorisation strongly captures both semantics and syntax, whereas using only negative PMI captures little of semantics but a surprising amount of syntactic information. Results also reveal that incorporating negative PMI induces stronger rank invariance of vector norms and directions, as well as improved rare word representations.

Prediction of the Drug-Drug Interaction Types with the Unified Embedding Features from Drug Similarity Networks.

Drug combination therapies are a promising strategy to overcome drug resistance and improve the efficacy of monotherapy in cancer, and it has been shown to lead to a decrease in dose-related toxicities. Except the synergistic reaction between drugs, some antagonistic drug–drug interactions (DDIs) exist, which is the main cause of adverse drug events. Precisely predicting the type of DDI is important for both drug development and more effective drug combination therapy applications. Recently, numerous text mining– and machine learning–based methods have been developed for predicting DDIs. All these methods implicitly utilize the feature of drugs from diverse drug-related properties. However, how to integrate these features more efficiently and improve the accuracy of classification is still a challenge. In this paper, we proposed a novel method (called NMDADNN) to predict the DDI types by integrating five drug-related heterogeneous information sources to extract the unified drug mapping features. NMDADNN first constructs the similarity networks by using the Jaccard coefficient and then implements random walk with restart algorithm and positive pointwise mutual information for extracting the topological similarities. After that, five network-based similarities are unified by using a multimodel deep autoencoder. Finally, NMDADNN implements the deep neural network (DNN) on the unified drug feature to infer the types of DDIs. In comparison with other recent state-of-the-art DNN-based methods, NMDADNN achieves the best results in terms of accuracy, area under the precision-recall curve, area under the ROC curve, F1 score, precision and recall. In addition, many of the promising types of drug–drug pairs predicted by NMDADNN are also confirmed by using the interactions checker tool. These results demonstrate the effectiveness of our NMDADNN method, indicating that NMDADNN has the great potential for predicting DDI types.

Intelligent Recognition and Teaching of English Fuzzy Texts Based on Fuzzy Computing and Big Data

In this paper, we conduct in-depth research and analysis on the intelligent recognition and teaching of English fuzzy text through parallel projection and region expansion. Multisense Soft Cluster Vector (MSCVec), a multisense word vector model based on nonnegative matrix decomposition and sparse soft clustering, is constructed. The MSCVec model is a monolingual word vector model, which uses nonnegative matrix decomposition of positive point mutual information between words and contexts to extract low-rank expressions of mixed semantics of multisense words and then uses sparse. It uses the nonnegative matrix decomposition of the positive pointwise mutual information between words and contexts to extract the low-rank expressions of the mixed semantics of the polysemous words and then uses the sparse soft clustering algorithm to partition the multiple word senses of the polysemous words and also obtains the global sense of the polysemous word affiliation distribution; the specific polysemous word cluster classes are determined based on the negative mean log-likelihood of the global affiliation between the contextual semantics and the polysemous words, and finally, the polysemous word vectors are learned using the Fast text model under the extended dictionary word set. The advantage of the MSCVec model is that it is an unsupervised learning process without any knowledge base, and the substring representation in the model ensures the generation of unregistered word vectors; in addition, the global affiliation of the MSCVec model can also expect polysemantic word vectors to single word vectors. Compared with the traditional static word vectors, MSCVec shows excellent results in both word similarity and downstream text classification task experiments. The two sets of features are then fused and extended into new semantic features, and similarity classification experiments and stack generalization experiments are designed for comparison. In the cross-lingual sentence-level similarity detection task, SCLVec cross-lingual word vector lexical-level features outperform MSCVec multisense word vector features as the input embedding layer; deep semantic sentence-level features trained by twin recurrent neural networks outperform the semantic features of twin convolutional neural networks; extensions of traditional statistical features can effectively improve cross-lingual similarity detection performance, especially cross-lingual topic model (BL-LDA); the stack generalization integration approach maximizes the error rate of the underlying classifier and improves the detection accuracy.

Linear functional organization of the omic embedding space.

MotivationWe are increasingly accumulating complex omics data that capture different aspects of cellular functioning. A key challenge is to untangle their complexity and effectively mine them for new biomedical information. To decipher this new information, we introduce algorithms based on network embeddings. Such algorithms represent biological macromolecules as vectors in d-dimensional space, in which topologically similar molecules are embedded close in space and knowledge is extracted directly by vector operations. Recently, it has been shown that neural networks used to obtain vectorial representations (embeddings) are implicitly factorizing a mutual information matrix, called Positive Pointwise Mutual Information (PPMI) matrix. Thus, we propose the use of the PPMI matrix to represent the human protein–protein interaction (PPI) network and also introduce the graphlet degree vector PPMI matrix of the PPI network to capture different topological (structural) similarities of the nodes in the molecular network.ResultsWe generate the embeddings by decomposing these matrices with Nonnegative Matrix Tri-Factorization. We demonstrate that genes that are embedded close in these spaces have similar biological functions, so we can extract new biomedical knowledge directly by doing linear operations on their embedding vector representations. We exploit this property to predict new genes participating in protein complexes and to identify new cancer-related genes based on the cosine similarities between the vector representations of the genes. We validate 80% of our novel cancer-related gene predictions in the literature and also by patient survival curves that demonstrating that 93.3% of them have a potential clinical relevance as biomarkers of cancer.Availability and implementationCode and data are available online at https://gitlab.bsc.es/axenos/embedded-omics-data-geometry/.Supplementary information Supplementary data are available at Bioinformatics online.

Temporal network embedding using graph attention network

Graph convolutional network (GCN) has made remarkable progress in learning good representations from graph-structured data. The layer-wise propagation rule of conventional GCN is designed in such a way that the feature aggregation at each node depends on the features of the one-hop neighbouring nodes. Adding an attention layer over the GCN can allow the network to provide different importance within various one-hop neighbours. These methods can capture the properties of static network, but is not well suited to capture the temporal patterns in time-varying networks. In this work, we propose a temporal graph attention network (TempGAN), where the aim is to learn representations from continuous-time temporal network by preserving the temporal proximity between nodes of the network. First, we perform a temporal walk over the network to generate a positive pointwise mutual information matrix (PPMI) which denote the temporal correlation between the nodes. Furthermore, we design a TempGAN architecture which uses both adjacency and PPMI information to generate node embeddings from temporal network. Finally, we conduct link prediction experiments by designing a TempGAN autoencoder to evaluate the quality of the embedding generated, and the results are compared with other state-of-the-art methods.

Relation Representation Learning via Signed Graph Mutual Information Maximization for Trust Prediction

Trust prediction is essential to enhancing reliability and reducing risk from the unreliable node, especially for online applications in open network environments. An essential fact in trust prediction is to measure the relation of both the interacting entities accurately. However, most of the existing methods infer the trust relation between interacting entities usually rely on modeling the similarity between nodes on a graph and ignore semantic relation and the influence of negative links (e.g., distrust relation). In this paper, we proposed a relation representation learning via signed graph mutual information maximization (called SGMIM). In SGMIM, we incorporate a translation model and positive point-wise mutual information to enhance the relation representations and adopt Mutual Information Maximization to align the entity and relation semantic spaces. Moreover, we further develop a sign prediction model for making accurate trust predictions. We conduct link sign prediction in trust networks based on learned the relation representation. Extensive experimental results in four real-world datasets on trust prediction task show that SGMIM significantly outperforms state-of-the-art baseline methods.

AENEA: A novel autoencoder-based network embedding algorithm

Network embedding aims to represent vertices in the network with low-dimensional dense real number vectors, so that the attained vertices can acquire the ability of representation and inference in vector space. With the expansion of the scale of complex networks, how to make the high-dimensional network represented in low-dimensional vector space through network becomes an important issue. The typical algorithms of current autoencoder-based network embedding methods include DNGR and SDNE. DNGR method trains the Positive Pointwise Mutual Information (PPMI) matrix with the Stacked Denosing Autoencoder (SDAE), which is lacking in depth thereby attaining less satisfactory representation of network. Besides, SDNE used a semi-supervised autoencoder for embedding the adjacency matrix, whose sparsity may generate more cost in the learning process. In order to solve these problems, we propose a novel Autoencoder-based Network Embedding Algorithm (AENEA). AENEA is mainly divided into three steps. First, the random surfing model is used to process the original network to obtain the Probabilistic Co-occurrence (PCO) matrix between the nodes. Secondly, the Probabilistic Co-occurrence (PCO) matrix is processed to generate the corresponding Positive Pointwise Mutual Information (PPMI) matrix. Finally, the PPMI matrix is used to learn the representation of vertices in the network by using a semi-supervised autoencoder. We implemented a series of experiments to test the performance of AENEA, DNGR, SDNE and so on, on the standardized datasets 20-NewsGroup and Wine. The experimental results show that the performance of AENEA is obviously superior to the existing algorithms in clustering, classification and visualization tasks.

Finding the Number of Latent Topics With Semantic Non-Negative Matrix Factorization

Topic modeling, or identifying the set of topics that occur in a collection of articles, is one of the primary objectives of text mining. One of the big challenges in topic modeling is determining the correct number of topics: underestimating the number of topics results in a loss of information, i.e., omission of topics, underfitting, while overestimating leads to noisy and unexplainable topics and overfitting. In this paper, we consider a semantic-assisted non-negative matrix factorization (NMF) topics model, which we call SeNMFk, based on Kullback-Leibler(KL) divergence and integrated with a method for determining the number of latent topics. SeNMFk involves (i) creating a random ensemble of pairs of matrices whose mean is equal to the initial words-by-documents matrix representing the text corpus and the Shifted Positive Pointwise Mutual Information (SPPMI) matrix, which encodes the context information, respectively, and (ii) jointly factorizing each of these pairs with different number of topics to acquire sets of latent topics that are stable to noise. We demonstrate the performance of our method by identifying the number of topics in several benchmark text corpora, when compared to other state-of-the-art techniques. We also show that the number of document classes in the input text corpus may differ from the number of the extracted latent topics, but these classes can be retrieved by clustering the column-vectors of one of the factor matrices. Additionally, we introduce a software called pyDNMFk to estimate the number of topics. We demonstrate that our unsupervised method, SeNMFk, not only determines the correct number of topics, but also extracts topics with a high coherence and accurately classifies the documents of the corpus.

A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder.

Drug targets are biomacromolecules or biomolecular structures that bind to specific drugs and produce therapeutic effects. Therefore, the prediction of drug-target interactions (DTIs) is important for disease therapy. Incorporating multiple similarity measures for drugs and targets is of essence for improving the accuracy of prediction of DTIs. However, existing studies with multiple similarity measures ignored the global structure information of similarity measures, and required manual extraction features of drug-target pairs, ignoring the non-linear relationship among features. In this paper, we proposed a novel approach MDADTI for DTIs prediction based on MDA. MDADTI applied random walk with restart method and positive pointwise mutual information to calculate the topological similarity matrices of drugs and targets, capturing the global structure information of similarity measures. Then, MDADTI applied multimodal deep autoencoder to fuse multiple topological similarity matrices of drugs and targets, automatically learned the low-dimensional features of drugs and targets, and applied deep neural network to predict DTIs. The results of 5-repeats of 10-fold cross-validation under three different cross-validation settings indicated that MDADTI is superior to the other four baseline methods. In addition, we validated the predictions of the MDADTI in six drug-target interactions reference databases, and the results showed that MDADTI can effectively identify unknown DTIs.

Unsupervised Learning of Multi-Sense Embedding with Matrix Factorization and Sparse Soft Clustering

In the natural language environment, accurately inferring the meaning of a token according to its context is crucial to understanding a sophisticated expression. However, this is not easy for a machine. The traditional language models used to train distributed word vectors are often restricted by single-sense embedding. In this paper, we develop a model called MSCvec (Multi-sense Soft Clustering Vector) for word sense disambiguation of polysemy in context. We extract the features of individual words by the co-occurrence PPMI (Positive Pointwise Mutual Information) matrix, and decompose the matrix by NMF (Nonnegative Matrix Factorization) into low-rank representations of target words, which are used as the input of an unsupervised sparse soft clustering method called Sparse Fuzzy C-means (SFCM). We use SFCM to determine the global semantic space of words, and partition the subspaces of multiple senses of a polysemous word. We relabel candidate words by the negative average log likelihood, and train multi-sense embedding with extensional vocabulary by the fastText model. Compared with the traditional static embeddings, the result shows that NMF and SFCM design can improve the performance in word similarity and relatedness tasks as well as in text classification tasks of different types of text. Accurate semantic representation of MSCvec would be necessary to produce outstanding results.

Fast PMI-Based Word Embedding with Efficient Use of Unobserved Patterns

Continuous word representations that can capture the semantic information in the corpus are the building blocks of many natural language processing tasks. Pre-trained word embeddings are being used for sentiment analysis, text classification, question answering and so on. In this paper, we propose a new word embedding algorithm that works on a smoothed Positive Pointwise Mutual Information (PPMI) matrix which is obtained from the word-word co-occurrence counts. One of our major contributions is to propose an objective function and an optimization framework that exploits the full capacity of “negative examples”, the unobserved or insignificant wordword co-occurrences, in order to push unrelated words away from each other which improves the distribution of words in the latent space. We also propose a kernel similarity measure for the latent space that can effectively calculate the similarities in high dimensions. Moreover, we propose an approximate alternative to our algorithm using a modified Vantage Point tree and reduce the computational complexity of the algorithm to |V |log|V | with respect to the number of words in the vocabulary. We have trained various word embedding algorithms on articles of Wikipedia with 2.1 billion tokens and show that our method outperforms the state-of-the-art in most word similarity tasks by a good margin.

Learning deep neural networks for node classification

Deep Neural Network (DNN) has made great leaps in image classification and speech recognition in recent years. However, employing DNN for node classification such as in social network remains to be a non-trivial problem. Moreover, the current advanced method of implementing node classification tasks usually takes two steps, i.e. firstly, the embedding vector of the node is obtained through network embedding and then the classifier such as SVM is leveraged to do the task. Distinctly, this may only get the suboptimal solution of the problem. To settle the above issues, a novel Deep Neural Network method for node classification named DNNNC is proposed in the framework of Deep Learning. Specifically, we first get the positive pointwise mutual information (PPMI) matrix from the given adjacency matrix. Then, the data is fed to deep neural network composed of deep stacked sparse autoencoders and softmax layer, which could learn the node representation while encoding the rich nonlinear structural and semantic information and could be well trained for node classification under the DNN framework. Extensive experiments are conducted on real-world network datasets for node classification task and have shown that the proposed model DNNNC outperforms the state-of-the-art method in the view of superior performance.

Time-sensitive clinical concept embeddings learned from large electronic health records

BackgroundLearning distributional representation of clinical concepts (e.g., diseases, drugs, and labs) is an important research area of deep learning in the medical domain. However, many existing relevant methods do not consider temporal dependencies along the longitudinal sequence of a patient’s records, which may lead to incorrect selection of contexts.MethodsTo address this issue, we extended three popular concept embedding learning methods: word2vec, positive pointwise mutual information (PPMI) and FastText, to consider time-sensitive information. We then trained them on a large electronic health records (EHR) database containing about 50 million patients to generate concept embeddings and evaluated them for both intrinsic evaluations focusing on concept similarity measure and an extrinsic evaluation to assess the use of generated concept embeddings in the task of predicting disease onset.ResultsOur experiments show that embeddings learned from information within one visit (time window zero) improve performance on the concept similarity measure and the FastText algorithm usually had better performance than the other two algorithms. For the predictive modeling task, the optimal result was achieved by word2vec embeddings with a 30-day sliding window.ConclusionsConsidering time constraints are important in training clinical concept embeddings. We expect they can benefit a series of downstream applications.

Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information

BackgroundLong non-coding RNAs play an important role in human complex diseases. Identification of lncRNA-disease associations will gain insight into disease-related lncRNAs and benefit disease diagnoses and treatment. However, using experiments to explore the lncRNA-disease associations is expensive and time consuming.ResultsIn this study, we developed a novel method to identify potential lncRNA-disease associations by Integrating Diverse Heterogeneous Information sources with positive pointwise Mutual Information and Random Walk with restart algorithm (namely IDHI-MIRW). IDHI-MIRW first constructs multiple lncRNA similarity networks and disease similarity networks from diverse lncRNA-related and disease-related datasets, then implements the random walk with restart algorithm on these similarity networks for extracting the topological similarities which are fused with positive pointwise mutual information to build a large-scale lncRNA-disease heterogeneous network. Finally, IDHI-MIRW implemented random walk with restart algorithm on the lncRNA-disease heterogeneous network to infer potential lncRNA-disease associations.ConclusionsCompared with other state-of-the-art methods, IDHI-MIRW achieves the best prediction performance. In case studies of breast cancer, stomach cancer, and colorectal cancer, 36/45 (80%) novel lncRNA-disease associations predicted by IDHI-MIRW are supported by recent literatures. Furthermore, we found lncRNA LINC01816 is associated with the survival of colorectal cancer patients. IDHI-MIRW is freely available at https://github.com/NWPU-903PR/IDHI-MIRW.