Deep Learning Roles based Approach to Link Prediction in Networks

2020 ◽  
Author(s):  
Aman Gupta ◽  
Yadul Raghav
Keyword(s):  
Deep Learning ◽  
Link Prediction ◽  
Information Science ◽  
Structural Information ◽  
Structural Features ◽  
Similarity Score ◽  
Node Attribute ◽  
Depth Analysis ◽  
Real World Datasets ◽  
Better Than

The problem of predicting links has gained much attention in recent years due to its vast application in various domains such as sociology, network analysis, information science, etc. Many methods have been proposed for link prediction such as RA, AA, CCLP, etc. These methods required hand-crafted structural features to calculate the similarity scores between a pair of nodes in a network. Some methods use local structural information while others use global information of a graph. These methods do not tell which properties are better than others. With an in-depth analysis of these methods, we understand that one way to overcome this problem is to consider network structure and node attribute information to capture the discriminative features for link prediction tasks. We proposed a deep learning Autoencoder based Link Prediction (ALP) architecture for the latent representation of a graph, unified with non-negative matrix factorization to automatically determine the underlying roles in a network, after that assigning a mixed-membership of these roles to each node in the network. The idea is to transfer these roles as a feature vector for the link prediction task in the network. Further, cosine similarity is applied after getting the required features to compute the pairwise similarity score between the nodes. We present the performance of the algorithm on the real-world datasets, where it gives the competitive result compared to other algorithms.

Link prediction via layer relevance of multiplex networks

2017 ◽  
Vol 28 (08) ◽  
pp. 1750101 ◽  
Author(s):  
Yabing Yao ◽  
Ruisheng Zhang ◽  
Fan Yang ◽  
Yongna Yuan ◽  
Qingshuang Sun ◽  
...  
Keyword(s):  
Structural Properties ◽  
Link Prediction ◽  
Structural Information ◽  
Similarity Index ◽  
Single Layer ◽  
Structural Features ◽  
Prediction Performance ◽  
Multiplex Networks ◽  
Multiplex Network ◽  
Node Similarity

In complex networks, the existing link prediction methods primarily focus on the internal structural information derived from single-layer networks. However, the role of interlayer information is hardly recognized in multiplex networks, which provide more diverse structural features than single-layer networks. Actually, the structural properties and functions of one layer can affect that of other layers in multiplex networks. In this paper, the effect of interlayer structural properties on the link prediction performance is investigated in multiplex networks. By utilizing the intralayer and interlayer information, we propose a novel “Node Similarity Index” based on “Layer Relevance” (NSILR) of multiplex network for link prediction. The performance of NSILR index is validated on each layer of seven multiplex networks in real-world systems. Experimental results show that the NSILR index can significantly improve the prediction performance compared with the traditional methods, which only consider the intralayer information. Furthermore, the more relevant the layers are, the higher the performance is enhanced.

scholarly journals Unsupervised Negative Link Prediction in Signed Social Networks

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Pengfei Shen ◽  
Shufen Liu ◽  
Ying Wang ◽  
Lu Han
Keyword(s):  
Link Prediction ◽  
Nonnegative Matrix Factorization ◽  
Structural Information ◽  
Nonnegative Matrix ◽  
Sociological Study ◽  
Negative Interaction ◽  
Signed Social Networks ◽  
Real World Datasets ◽  
Negative Links ◽  
Negative Link

It has been proved in a number of applications that it is useful to predict unknown social links, and link prediction has played an important role in sociological study. Although there has been a surge of pertinent approaches to link prediction, most of them focus on positive link prediction while giving few attentions to the problem of inferring unknown negative links. The inherent characteristics of negative relations present great challenges to traditional link prediction: (1) there are very few negative interaction data; (2) negative links are much sparser than positive links; (3) social data is often noisy, incomplete, and fast-evolved. This paper intends to address this novel problem by solely leveraging structural information and further proposes the UN-PNMF framework based on the projective nonnegative matrix factorization, so as to incorporate network embedding and user’s property embedding into negative link prediction. Empirical experiments on real-world datasets corroborate their effectiveness.

scholarly journals Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aparna R. Rajpurkar ◽  
Leslie J. Mateo ◽  
Sedona E. Murphy ◽  
Alistair N. Boettiger
Keyword(s):  
Deep Learning ◽  
Structural Information ◽  
Single Cells ◽  
3D Structure ◽  
Super Resolution ◽  
Structural Features ◽  
Complex Data ◽  
Chromatin Architecture ◽  
Complex Data Sets ◽  
A Minor

AbstractChromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these complex data sets with a computationally unbiased method has been challenging. Here, we present a deep learning-based approach to better understand to what degree chromatin structure relates to transcriptional state of individual cells. Furthermore, we explore methods to “unpack the black box” to determine in an unbiased manner which structural features of chromatin regulation are most important for gene expression state. We apply this approach to an Optical Reconstruction of Chromatin Architecture dataset of the Bithorax gene cluster in Drosophila and show it outperforms previous contact-focused methods in predicting expression state from 3D structure. We find the structural information is distributed across the domain, overlapping and extending beyond domains identified by prior genetic analyses. Individual enhancer-promoter interactions are a minor contributor to predictions of activity.

scholarly journals A Novel Sequence-to-Subgraph Framework for Diagnosis Classification

2021 ◽  
Author(s):  
Jun Chen ◽  
Quan Yuan ◽  
Chao Lu ◽  
Haifeng Huang
Keyword(s):  
Deep Learning ◽  
Structural Information ◽  
Diagnostic Errors ◽  
Structural Features ◽  
Classification Model ◽  
New Classification ◽  
Convolutional Network ◽  
Clinical Notes ◽  
World English ◽  
Diagnosis Classification

Text-based diagnosis classification is a critical problem in AI-enabled healthcare studies, which assists clinicians in making correct decision and lowering the rate of diagnostic errors. Previous studies follow the routine of sequence based deep learning models in NLP literature to deal with clinical notes. However, recent studies find that structural information is important in clinical contents that greatly impacts the predictions. In this paper, a novel sequence-to-subgraph framework is introduced to process clinical texts for classification, which changes the paradigm of managing texts. Moreover, a new classification model under the framework is proposed that incorporates subgraph convolutional network and hierarchical diagnostic attentive network to extract the layered structural features of clinical texts. The evaluation conducted on both the real-world English and Chinese datasets shows that the proposed method outperforms the state-of-the-art deep learning based diagnosis classification models.

scholarly journals DeepLink: A novel link prediction framework based on deep learning

2019 ◽  
pp. 016555151989134 ◽  
Author(s):  
Mohammad Mehdi Keikha ◽  
Maseud Rahgozar ◽  
Masoud Asadpour
Keyword(s):  
Deep Learning ◽  
Structural Feature ◽  
Network Topology ◽  
Link Prediction ◽  
Feature Learning ◽  
Structural Features ◽  
Feature Engineering ◽  
Hybrid Approaches ◽  
Learning Techniques ◽  
Content Information

Recently, link prediction has attracted more attention from various disciplines such as computer science, bioinformatics and economics. In link prediction, numerous information such as network topology, profile information and user-generated contents are considered to discover missing links between nodes. Whereas numerous previous researches had focused on the structural features of the networks for link prediction, recent studies have shown more interest in profile and content information, too. So, some of these researches combine structural and content information. However, some issues such as scalability and feature engineering need to be investigated to solve a few remaining problems. Moreover, most of the previous researches are presented only for undirected and unweighted networks. In this article, a novel link prediction framework named ‘DeepLink’ is presented, which is based on deep learning techniques. While deep learning has the advantage of extracting automatically the best features for link prediction, many other link prediction algorithms need manual feature engineering. Moreover, in the proposed framework, both structural and content information are employed. The framework is capable of using different structural feature vectors that are prepared by various link prediction methods. It learns all proximity orders that are presented on a network during the structural feature learning. We have evaluated the effectiveness of DeepLink on two real social network datasets, Telegram and irBlogs. On both datasets, the proposed framework outperforms several other structural and hybrid approaches for link prediction.

scholarly journals Topological and Attribute Link Prediction using Firefly algorithm

2020 ◽  
Vol 10 (1) ◽  
pp. 33-41
Author(s):  
Srilatha Pulipati ◽  
Manjula Ramakrishnan
Keyword(s):  
Link Prediction ◽  
Area Under The Curve ◽  
Similarity Score ◽  
Data Sets ◽  
Prediction Problem ◽  
Recent Past ◽  
Common Neighbor ◽  
Standard Data ◽  
Node Attribute ◽  
Swarm Intelligence Algorithm

AbstractLink prediction problem has received remarkable interest in recent past. In this paper, firefly swarm intelligence algorithm is used to perform link prediction exploiting the topological and node attribute features of social network. Fireflies will be made to traverse on nodes and edges of social networks and the brightness of fireflies will play a major role in their movement. Common neighbor method of link prediction is used to compute similarity score upon each iteration. Performance of the proposed algorithm were analyzed over standard data sets using validation method called ten-fold method. The accuracy of proposed work is measured in terms of Area Under the Curve Characteristics (AUC), Recall and Precision. Experimental results showed that the proposed work outperforms the methods proposed in the literature.

Measurement and Reduction of Radiation Damage in Frozen Hydrated Crystalline Specimens

1978 ◽  
Vol 36 (3) ◽  
pp. 70-77 ◽  
Author(s):  
R.M. Glaeser ◽  
S.B. Hayward
Keyword(s):  
Diffraction Pattern ◽  
Structural Information ◽  
Structural Disorder ◽  
Structural Features ◽  
Biological Macromolecules ◽  
Diffraction Intensity ◽  
Object Structure ◽  
Specimen Material ◽  
Unit Cells ◽  
Identical Unit

Highly ordered or crystalline biological macromolecules become severely damaged and structurally disordered after a brief electron exposure. Evidence that damage and structural disorder are occurring is clearly given by the fading and eventual disappearance of the specimen's electron diffraction pattern. The fading and disappearance of sharp diffraction spots implies a corresponding disappearance of periodic structural features in the specimen. By the same token, there is a oneto- one correspondence between the disappearance of the crystalline diffraction pattern and the disappearance of reproducible structural information that can be observed in the images of identical unit cells of the object structure. The electron exposures that result in a significant decrease in the diffraction intensity will depend somewhat upon the resolution (Bragg spacing) involved, and can vary considerably with the chemical makeup and composition of the specimen material.

HAZARD: An Expert System for Risk Assessment of Environmental Chemicals

1987 ◽  
Vol 26 (01) ◽  
pp. 13-23 ◽  
Author(s):  
H. W. Gottinger
Keyword(s):  
Expert System ◽  
Structural Information ◽  
Chemical Carcinogenesis ◽  
Structural Features ◽  
Environmental Chemicals ◽  
Chemical Carcinogens ◽  
Carcinogenic Activity ◽  
Current State ◽  
Structure Activity ◽  
Carcinogenic Potential

AbstractThe purpose of this paper is to report on an expert system in design that screens for potential hazards from environmental chemicals on the basis of structure-activity relationships in the study of chemical carcinogenesis, particularly with respect to analyzing the current state of known structural information about chemical carcinogens and predicting the possible carcinogenicity of untested chemicals. The structure-activity tree serves as an index of known chemical structure features associated with carcinogenic activity. The basic units of the tree are the principal recognized classes of chemical carcinogens that are subdivided into subclasses known as nodes according to specific structural features that may reflect differences in carcinogenic potential among chemicals in the class. An analysis of a computerized data base of known carcinogens (knowledge base) is proposed using the structure-activity tree in order to test the validity of the tree as a classification scheme (inference engine).

Rapid Online Buffer Exchange: A Method for Screening of Proteins, Protein Complexes, and Cell Lysates by Native Mass Spectrometry

2019 ◽  
Author(s):  
Zachary VanAernum ◽  
Florian Busch ◽  
Benjamin J. Jones ◽  
Mengxuan Jia ◽  
Zibo Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Speed ◽  
Structural Information ◽  
Protein Complexes ◽  
High Sensitivity ◽  
Native Mass Spectrometry ◽  
Structural Features ◽  
Consumer Products ◽  
Cell Lysates ◽  
Protein Expression And Purification

It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes, and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is timeconsuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes, or clarified cell lysates. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization.

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

2020 ◽  
Vol 27 (37) ◽  
pp. 6306-6355 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Drug Discovery ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Structural Features ◽  
Protein Protein Interactions ◽  
Modular Architecture ◽  
Post Translational Modifications ◽  
Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

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