25 papers · ranked by Valyu relevance
Walter Nelson, Marinka Zitnik, Bo Wang, Jure Leskovec + 2 more
'Anna Goldenberg' 'Roded Sharan'] Current technology is producing high throughput biomedical data at an ever-growing rate. A common approach to interpreting such data is through network-based analyses. Since biological networks are notoriously complex and hard to decipher, a growing body of work applies graph embedding…
Haochen Chen, Bryan Perozzi, Rami Al‐Rfou, Steven Skiena
Network embedding methods aim at learning low-dimensional latent representation of nodes in a network. These representations can be used as features for a wide range of tasks on graphs such as classification, clustering, link prediction, and visualization. In this survey, we give an overview of network embeddings by…
Anthony Baptista, Rubén J. Sánchez-García, Anaı̈s Baudot, Ginestra Bianconi
'Ginestra Bianconi'] 1School of Mathematical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom; 2The Alan Turing Institute, The British Library, London, NW1 2DB, United Kingdom; 3School of Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom; 4 Institute for…
Bo Kang, Jefrey Lijffijt, Tijl De Bie
Network Embeddings (NEs) map the nodes of a given network into d-dimensional Euclidean space R d . Ideally, this mapping is such that 'similar' nodes are mapped onto nearby points, such that the NE can be used for purposes such as link prediction (if 'similar' means being 'more likely to be connected') or…
Weiwei Gu, Aditya Tandon, Yong-Yeol Ahn, Filippo Radicchi
Network embedding is a general-purpose machine learning technique that encodes network structure in vector spaces with tunable dimension. Choosing an appropriate embedding dimension - small enough to be efficient and large enough to be effective - is challenging but necessary to generate embeddings applicable to a…
Peng Cui, Xiao Wang, Jian Pei, Wenwu Zhu
Network embedding assigns nodes in a network to lowdimensional representations and effectively preserves the network structure. Recently, a significant amount of progresses have been made toward this emerging network analysis paradigm. In this survey, we focus on categorizing and then reviewing the current development…
Jianshu Zhao, Jean Pierre Both, Rob Knight
Graph/network representation learning (or graph/network embedding) is a widely used machine learning technique in industry recommending systems and has recently been applied in computational biology. Popular network representation learning algorithms include random walk and matrix factorization methods, but they do not…
Ilya Makarov, Dmitrii Kiselev, Nikita Nikitinsky, Lovro Subelj + 1 more
Dealing with relational data always required significant computational resources, domain expertise and task-dependent feature engineering to incorporate structural information into a predictive model. Nowadays, a family of automated graph feature engineering techniques has been proposed in different streams of…
Poorya Parvizi, Francisco Azuaje, Evropi Theodoratou, Saturnino Luz
A network embedding approach reduces the analysis complexity of large biological networks by converting them to lowdimensional vector representations (features/embeddings). These lower-dimensional vectors can then be used in machine learning prediction tasks with a wide range of applications in computational biology…
Boaz Shmueli
In this tutorial I cover a few recent papers in the field of network embedding. Network embedding is a collective term for techniques for mapping graph nodes to vectors of real numbers in a multidimensional space. To be useful, a good embedding should preserve the structure of the graph. The vectors can then be used as…
Mustafa Coşkun, Mehmet Koyutürk
Link prediction is an important and well-studied problem in computational biology, with a broad range of applications including disease gene prioritization, drug-disease associations, and drug response in cancer. The general principle in link prediction is to use the topological characteristics and the attributes–if…
Amina Amara, Mohamed Ali Hadj Taieb, Mohamed Ben Aouicha
Real-world information networks are increasingly occurring across various disciplines including online social networks and citation networks. These network data are generally characterized by sparseness, nonlinearity and heterogeneity bringing different challenges to the network analytics task to capture inherent…
Gamal Crichton, Yufan Guo, Sampo Pyysalo, Anna Korhonen
Background Link prediction in biomedical graphs has several important applications including predicting Drug-Target Interactions (DTI), Protein-Protein Interaction (PPI) prediction and Literature-Based Discovery (LBD). It can be done using a classifier to output the probability of link formation between nodes. Recently…
Farzaneh Heidari, Manos Papagelis
Large-scale network mining and analysis is key to revealing the underlying dynamics of networks, not easily observable before. Lately, there is a fast-growing interest in learning low-dimensional continuous representations of networks that can be utilized to perform highly accurate and scalable graph mining tasks. A…
Ilya Makarov, Olga Gerasimova, Pavel Sulimov, Leonid E. Zhukov + 1 more
'Diego Amancio'] We present a study on co-authorship network representation based on network embedding together with additional information on topic modeling of research papers and new edge embedding operator. We use the link prediction (LP) model for constructing a recommender system for searching collaborators with…
Qiaoyu Tan, Ninghao Liu, Xia Hu
Social network analysis is an important problem in data mining. A fundamental step for analyzing social networks is to encode network data into low-dimensional representations, i.e., network embeddings, so that the network topology structure and other attribute information can be effectively preserved. Network…
Renming Liu, Matthew Hirn, Arjun Krishnan
Accurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased random walks. However, while many networks, including functional gene interaction…
Joshua Levy, Carly Bobak, Brock Christensen, Louis Vaickus + 1 more
Network analysis methods are useful to better understand and contextualize relationships between entities. While statistical and machine learning prediction models generally assume independence between actors, network-based statistical methods for social network data allow for dyadic dependence between actors. While…
Alejandro A. Edera, Georgina Stegmayer, Diego H. Milone
Unsupervised learning of node representations from knowledge graphs is critical for numerous downstream tasks, ranging from large-scale graph analysis to measuring semantic similarity between nodes. This study presents gGN as a novel representation that defines graph nodes as Gaussian distributions. Unlike existing…
Amer El-Samman, Stijn De Baerdemacker
In deep learning methods, especially in the context of chemistry, there is an increasing urgency to uncover the hidden learning mechanisms often dubbed as ``black box." In this work, we show that graph models built on computational chemical data behave similar to natural language processing (NLP) models built on text…
Authors not listed
Chemical reactions typically follow mechanistic templates and hence fall into a manageable number of clearly distinguishable classes that usually labeled by names of chemists who discovered or explored them. These ``named reactions'' form the core of reaction ontologies and are associated with specific synthetic…
David Buterez, Jon Paul Janet, Steven Kiddle, Pietro Liò
We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property ofinterest. This problem arises in discovery processes…
Nathan Frey, Ryan Soklaski, Simon Axelrod, Siddharth Samsi + 3 more
Massive scale, both in terms of data availability and computation, enables significant breakthroughs in key application areas of deep learning such as natural language processing (NLP) and computer vision. There is emerging evidence that scale may be a key ingredient in scientific deep learning, but the importance of…
Authors not listed
Real-world datasets in chemical engineering and bioengineering processes--such as those from catalytic reactors, multiphase flows, polymerization reactors, bioreactors, and clinical trials--can often be unlabelled or disorganized, rendering the training of existing supervised learning models ineffective at learning the…
Authors not listed
Compound similarity is fundamental to various cheminformatics analyses, particularly in the drug discovery industry, where the structure-activity principle is central to medicinal chemistry. Historically, binary fingerprints combined with Tanimoto and “Tanimoto-related metrics” (such as Dice, Sørensen–Dice, and…