scholarly journals WGEVIA: A Graph Level Embedding Method for Microcircuit Data

2021 ◽  
Vol 14 ◽  
Author(s):  
Xiaomin Wu ◽  
Shuvra S. Bhattacharyya ◽  
Rong Chen
Keyword(s):  
Computational Analysis ◽  
Weighted Graph ◽  
Graph Embedding ◽  
Machine Learning Algorithms ◽  
Neural Dynamics ◽  
Cognition And Emotion ◽  
Neural Activities ◽  
Low Dimensional ◽  
Embedding Methods ◽  
General Method

Functional microcircuits are useful for studying interactions among neural dynamics of neighboring neurons during cognition and emotion. A functional microcircuit is a group of neurons that are spatially close, and that exhibit synchronized neural activities. For computational analysis, functional microcircuits are represented by graphs, which pose special challenges when applied as input to machine learning algorithms. Graph embedding, which involves the conversion of graph data into low dimensional vector spaces, is a general method for addressing these challenges. In this paper, we discuss limitations of conventional graph embedding methods that make them ill-suited to the study of functional microcircuits. We then develop a novel graph embedding framework, called Weighted Graph Embedding with Vertex Identity Awareness (WGEVIA), that overcomes these limitations. Additionally, we introduce a dataset, called the five vertices dataset, that helps in assessing how well graph embedding methods are suited to functional microcircuit analysis. We demonstrate the utility of WGEVIA through extensive experiments involving real and simulated microcircuit data.

scholarly journals Graph embedding on biomedical networks: methods, applications and evaluations

2019 ◽  
Author(s):  
Xiang Yue ◽  
Zhen Wang ◽  
Jingong Huang ◽  
Srinivasan Parthasarathy ◽  
Soheil Moosavinasab ◽  
...  
Keyword(s):  
Protein Function ◽  
State Of The Art ◽  
Protein Function Prediction ◽  
Graph Embedding ◽  
Experimental Results ◽  
Supplementary Information ◽  
Protein Protein Interaction ◽  
Biological Features ◽  
Low Dimensional ◽  
Embedding Methods

Abstract Motivation Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art. Results We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug–drug interaction (DDI) prediction, protein–protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks. Availability and implementation As part of our contributions in the paper, we develop an easy-to-use Python package with detailed instructions, BioNEV, available at: https://github.com/xiangyue9607/BioNEV, including all source code and datasets, to facilitate studying various graph embedding methods on biomedical tasks. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals PolSAR Image Feature Extraction via Co-Regularized Graph Embedding

2020 ◽  
Vol 12 (11) ◽  
pp. 1738
Author(s):  
Xiayuan Huang ◽  
Xiangli Nie ◽  
Hong Qiao
Keyword(s):  
Feature Extraction ◽  
Image Classification ◽  
Weighted Graph ◽  
Graph Embedding ◽  
Image Feature ◽  
Weighted Graphs ◽  
Image Feature Extraction ◽  
Structure Information ◽  
Low Dimensional ◽  
Low Dimensional Features

Dimensionality reduction (DR) methods based on graph embedding are widely used for feature extraction. For these methods, the weighted graph plays a vital role in the process of DR because it can characterize the data’s structure information. Moreover, the similarity measurement is a crucial factor for constructing a weighted graph. Wishart distance of covariance matrices and Euclidean distance of polarimetric features are two important similarity measurements for polarimetric synthetic aperture radar (PolSAR) image classification. For obtaining a satisfactory PolSAR image classification performance, a co-regularized graph embedding (CRGE) method by combing the two distances is proposed for PolSAR image feature extraction in this paper. Firstly, two weighted graphs are constructed based on the two distances to represent the data’s local structure information. Specifically, the neighbouring samples are sought in a local patch to decrease computation cost and use spatial information. Next the DR model is constructed based on the two weighted graphs and co-regularization. The co-regularization aims to minimize the dissimilarity of low-dimensional features corresponding to two weighted graphs. We employ two types of co-regularization and the corresponding algorithms are proposed. Ultimately, the obtained low-dimensional features are used for PolSAR image classification. Experiments are implemented on three PolSAR datasets and results show that the co-regularized graph embedding can enhance the performance of PolSAR image classification.

FREDE

2021 ◽  
Vol 14 (6) ◽  
pp. 1102-1110
Author(s):  
Anton Tsitsulin ◽  
Marina Munkhoeva ◽  
Davide Mottin ◽  
Panagiotis Karras ◽  
Ivan Oseledets ◽  
...  
Keyword(s):  
Data Science ◽  
State Of The Art ◽  
Graph Embedding ◽  
Space Complexity ◽  
Similarity Matrix ◽  
Data Engineering ◽  
Matrix Sketching ◽  
Low Dimensional ◽  
Diverse Data ◽  
Embedding Methods

Low-dimensional representations, or embeddings , of a graph's nodes facilitate several practical data science and data engineering tasks. As such embeddings rely, explicitly or implicitly, on a similarity measure among nodes, they require the computation of a quadratic similarity matrix, inducing a tradeoff between space complexity and embedding quality. To date, no graph embedding work combines (i) linear space complexity, (ii) a nonlinear transform as its basis, and (iii) nontrivial quality guarantees. In this paper we introduce FREDE ( FREquent Directions Embedding ), a graph embedding based on matrix sketching that combines those three desiderata. Starting out from the observation that embedding methods aim to preserve the covariance among the rows of a similarity matrix, FREDE iteratively improves on quality while individually processing rows of a nonlinearly transformed PPR similarity matrix derived from a state-of-the-art graph embedding method and provides, at any iteration , column-covariance approximation guarantees in due course almost indistinguishable from those of the optimal approximation by SVD. Our experimental evaluation on variably sized networks shows that FREDE performs almost as well as SVD and competitively against state-of-the-art embedding methods in diverse data science tasks, even when it is based on as little as 10% of node similarities.

scholarly journals Classification of Brainwaves for Sleep Stages by High-Dimensional FFT Features from EEG Signals

2020 ◽  
Vol 10 (5) ◽  
pp. 1797 ◽  
Author(s):  
Mera Kartika Delimayanti ◽  
Bedy Purnama ◽  
Ngoc Giang Nguyen ◽  
Mohammad Reza Faisal ◽  
Kunti Robiatul Mahmudah ◽  
...  
Keyword(s):  
Machine Learning ◽  
Sleep Stage ◽  
Machine Learning Algorithms ◽  
High Dimensional ◽  
Sleep Stages ◽  
Eeg Signals ◽  
Stage Classification ◽  
Sleep Stage Classification ◽  
Low Dimensional

Manual classification of sleep stage is a time-consuming but necessary step in the diagnosis and treatment of sleep disorders, and its automation has been an area of active study. The previous works have shown that low dimensional fast Fourier transform (FFT) features and many machine learning algorithms have been applied. In this paper, we demonstrate utilization of features extracted from EEG signals via FFT to improve the performance of automated sleep stage classification through machine learning methods. Unlike previous works using FFT, we incorporated thousands of FFT features in order to classify the sleep stages into 2–6 classes. Using the expanded version of Sleep-EDF dataset with 61 recordings, our method outperformed other state-of-the art methods. This result indicates that high dimensional FFT features in combination with a simple feature selection is effective for the improvement of automated sleep stage classification.

scholarly journals Graph Learning for Combinatorial Optimization: A Survey of State-of-the-Art

2021 ◽  
Author(s):  
Yun Peng ◽  
Byron Choi ◽  
Jianliang Xu
Keyword(s):  
Machine Learning ◽  
Combinatorial Optimization ◽  
Graph Embedding ◽  
Partial Solution ◽  
Complex Data ◽  
Learning Methods ◽  
Graph Learning ◽  
Second Stage ◽  
End To End ◽  
Embedding Methods

AbstractGraphs have been widely used to represent complex data in many applications, such as e-commerce, social networks, and bioinformatics. Efficient and effective analysis of graph data is important for graph-based applications. However, most graph analysis tasks are combinatorial optimization (CO) problems, which are NP-hard. Recent studies have focused a lot on the potential of using machine learning (ML) to solve graph-based CO problems. Most recent methods follow the two-stage framework. The first stage is graph representation learning, which embeds the graphs into low-dimension vectors. The second stage uses machine learning to solve the CO problems using the embeddings of the graphs learned in the first stage. The works for the first stage can be classified into two categories, graph embedding methods and end-to-end learning methods. For graph embedding methods, the learning of the the embeddings of the graphs has its own objective, which may not rely on the CO problems to be solved. The CO problems are solved by independent downstream tasks. For end-to-end learning methods, the learning of the embeddings of the graphs does not have its own objective and is an intermediate step of the learning procedure of solving the CO problems. The works for the second stage can also be classified into two categories, non-autoregressive methods and autoregressive methods. Non-autoregressive methods predict a solution for a CO problem in one shot. A non-autoregressive method predicts a matrix that denotes the probability of each node/edge being a part of a solution of the CO problem. The solution can be computed from the matrix using search heuristics such as beam search. Autoregressive methods iteratively extend a partial solution step by step. At each step, an autoregressive method predicts a node/edge conditioned to current partial solution, which is used to its extension. In this survey, we provide a thorough overview of recent studies of the graph learning-based CO methods. The survey ends with several remarks on future research directions.

scholarly journals TransET: Knowledge Graph Embedding with Entity Types

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1407
Author(s):  
Peng Wang ◽  
Jing Zhou ◽  
Yuzhang Liu ◽  
Xingchen Zhou
Keyword(s):  
Link Prediction ◽  
State Of The Art ◽  
Score Function ◽  
Graph Embedding ◽  
Vector Spaces ◽  
Knowledge Graph ◽  
Semantic Features ◽  
Knowledge Graphs ◽  
Real World Datasets ◽  
Low Dimensional

Knowledge graph embedding aims to embed entities and relations into low-dimensional vector spaces. Most existing methods only focus on triple facts in knowledge graphs. In addition, models based on translation or distance measurement cannot fully represent complex relations. As well-constructed prior knowledge, entity types can be employed to learn the representations of entities and relations. In this paper, we propose a novel knowledge graph embedding model named TransET, which takes advantage of entity types to learn more semantic features. More specifically, circle convolution based on the embeddings of entity and entity types is utilized to map head entity and tail entity to type-specific representations, then translation-based score function is used to learn the presentation triples. We evaluated our model on real-world datasets with two benchmark tasks of link prediction and triple classification. Experimental results demonstrate that it outperforms state-of-the-art models in most cases.

scholarly journals Multiscale low-dimensional motor cortical state dynamics predict naturalistic reach-and-grasp behavior

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hamidreza Abbaspourazad ◽  
Mahdi Choudhury ◽  
Yan T. Wong ◽  
Bijan Pesaran ◽  
Maryam M. Shanechi
Keyword(s):  
Neural Control ◽  
Multiple Scales ◽  
Network Activity ◽  
Neural Dynamics ◽  
Population Activity ◽  
Reach And Grasp ◽  
Spatiotemporal Scales ◽  
Motor Cortical ◽  
Low Dimensional ◽  
Low Dimensional Dynamics

AbstractMotor function depends on neural dynamics spanning multiple spatiotemporal scales of population activity, from spiking of neurons to larger-scale local field potentials (LFP). How multiple scales of low-dimensional population dynamics are related in control of movements remains unknown. Multiscale neural dynamics are especially important to study in naturalistic reach-and-grasp movements, which are relatively under-explored. We learn novel multiscale dynamical models for spike-LFP network activity in monkeys performing naturalistic reach-and-grasps. We show low-dimensional dynamics of spiking and LFP activity exhibited several principal modes, each with a unique decay-frequency characteristic. One principal mode dominantly predicted movements. Despite distinct principal modes existing at the two scales, this predictive mode was multiscale and shared between scales, and was shared across sessions and monkeys, yet did not simply replicate behavioral modes. Further, this multiscale mode’s decay-frequency explained behavior. We propose that multiscale, low-dimensional motor cortical state dynamics reflect the neural control of naturalistic reach-and-grasp behaviors.

scholarly journals Exploiting node metadata to predict interactions in large networks using graph embedding and neural networks

2021 ◽  
Author(s):  
Rogini Runghen ◽  
Daniel B Stouffer ◽  
Giulio Valentino Dalla Riva
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Link Prediction ◽  
Graph Embedding ◽  
Feature Space ◽  
Machine Learning Techniques ◽  
Large Networks ◽  
Data Set ◽  
Learning Techniques ◽  
Low Dimensional

Collecting network interaction data is difficult. Non-exhaustive sampling and complex hidden processes often result in an incomplete data set. Thus, identifying potentially present but unobserved interactions is crucial both in understanding the structure of large scale data, and in predicting how previously unseen elements will interact. Recent studies in network analysis have shown that accounting for metadata (such as node attributes) can improve both our understanding of how nodes interact with one another, and the accuracy of link prediction. However, the dimension of the object we need to learn to predict interactions in a network grows quickly with the number of nodes. Therefore, it becomes computationally and conceptually challenging for large networks. Here, we present a new predictive procedure combining a graph embedding method with machine learning techniques to predict interactions on the base of nodes' metadata. Graph embedding methods project the nodes of a network onto a---low dimensional---latent feature space. The position of the nodes in the latent feature space can then be used to predict interactions between nodes. Learning a mapping of the nodes' metadata to their position in a latent feature space corresponds to a classic---and low dimensional---machine learning problem. In our current study we used the Random Dot Product Graph model to estimate the embedding of an observed network, and we tested different neural networks architectures to predict the position of nodes in the latent feature space. Flexible machine learning techniques to map the nodes onto their latent positions allow to account for multivariate and possibly complex nodes' metadata. To illustrate the utility of the proposed procedure, we apply it to a large dataset of tourist visits to destinations across New Zealand. We found that our procedure accurately predicts interactions for both existing nodes and nodes newly added to the network, while being computationally feasible even for very large networks. Overall, our study highlights that by exploiting the properties of a well understood statistical model for complex networks and combining it with standard machine learning techniques, we can simplify the link prediction problem when incorporating multivariate node metadata. Our procedure can be immediately applied to different types of networks, and to a wide variety of data from different systems. As such, both from a network science and data science perspective, our work offers a flexible and generalisable procedure for link prediction.

scholarly journals Predicting partially observed processes on temporal networks by Dynamics-Aware Node Embeddings (DyANE)

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Koya Sato ◽  
Mizuki Oka ◽  
Alain Barrat ◽  
Ciro Cattuto
Keyword(s):  
Network Structure ◽  
Machine Learning Algorithms ◽  
Temporal Networks ◽  
Dynamical Processes ◽  
Network Nodes ◽  
Partially Observed ◽  
Low Dimensional ◽  
Vector Representations ◽  
Infectious Disease Dynamics ◽  
Random Times

AbstractLow-dimensional vector representations of network nodes have proven successful to feed graph data to machine learning algorithms and to improve performance across diverse tasks. Most of the embedding techniques, however, have been developed with the goal of achieving dense, low-dimensional encoding of network structure and patterns. Here, we present a node embedding technique aimed at providing low-dimensional feature vectors that are informative of dynamical processes occurring over temporal networks – rather than of the network structure itself – with the goal of enabling prediction tasks related to the evolution and outcome of these processes. We achieve this by using a lossless modified supra-adjacency representation of temporal networks and building on standard embedding techniques for static graphs based on random walks. We show that the resulting embedding vectors are useful for prediction tasks related to paradigmatic dynamical processes, namely epidemic spreading over empirical temporal networks. In particular, we illustrate the performance of our approach for the prediction of nodes’ epidemic states in single instances of a spreading process. We show how framing this task as a supervised multi-label classification task on the embedding vectors allows us to estimate the temporal evolution of the entire system from a partial sampling of nodes at random times, with potential impact for nowcasting infectious disease dynamics.

scholarly journals Semisupervised Community Preserving Network Embedding with Pairwise Constraints

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Dong Liu ◽  
Yan Ru ◽  
Qinpeng Li ◽  
Shibin Wang ◽  
Jianwei Niu
Keyword(s):  
Community Structure ◽  
Link Prediction ◽  
Learning Algorithms ◽  
Nonnegative Matrix ◽  
Machine Learning Algorithms ◽  
Network Visualization ◽  
Network Embedding ◽  
Pairwise Constraints ◽  
Node Clustering ◽  
Low Dimensional

Network embedding aims to learn the low-dimensional representations of nodes in networks. It preserves the structure and internal attributes of the networks while representing nodes as low-dimensional dense real-valued vectors. These vectors are used as inputs of machine learning algorithms for network analysis tasks such as node clustering, classification, link prediction, and network visualization. The network embedding algorithms, which considered the community structure, impose a higher level of constraint on the similarity of nodes, and they make the learned node embedding results more discriminative. However, the existing network representation learning algorithms are mostly unsupervised models; the pairwise constraint information, which represents community membership, is not effectively utilized to obtain node embedding results that are more consistent with prior knowledge. This paper proposes a semisupervised modularized nonnegative matrix factorization model, SMNMF, while preserving the community structure for network embedding; the pairwise constraints (must-link and cannot-link) information are effectively fused with the adjacency matrix and node similarity matrix of the network so that the node representations learned by the model are more interpretable. Experimental results on eight real network datasets show that, comparing with the representative network embedding methods, the node representations learned after incorporating the pairwise constraints can obtain higher accuracy in node clustering task and the results of link prediction, and network visualization tasks indicate that the semisupervised model SMNMF is more discriminative than unsupervised ones.

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