Studying the similarity of diseases can help us to explore the pathological characteristics of complex diseases, and help provide reliable reference information for inferring the relationship between new diseases and known diseases, so as to develop effective treatment plans. To obtain the similarity of the disease, most previous methods either use a single similarity metric such as semantic score, functional score from single data source, or utilize weighting coefficients to simply combine multiple metrics with different dimensions. In this paper, we proposes a method to predict the similarity of diseases by node representation learning. We first integrate the semantic score and topological score between diseases by combining multiple data sources. Then for each disease, its integrated scores with all other diseases are utilized to map it into a vector of the same spatial dimension, and the vectors are used to measure and comprehensively analyze the similarity between diseases. Lastly, we conduct comparative experiment based on benchmark set and other disease nodes outside the benchmark set. Using the statistics such as average, variance, and coefficient of variation in the benchmark set to evaluate multiple methods demonstrates the effectiveness of our approach in the prediction of similar diseases.

Similar Disease Prediction With Heterogeneous Disease Information Networks

Exponential growth of genome-wide assays of gene expressions and their public access open new horizons for machine learning methodologies to effectively perform genetic analysis. In this work, domain specific pre-train k-mer embeddings of DNA sequences are generated by utilising FastText approach. Sequence co-expression pattern information is embedded into 200 dimensional vectors by training Fasttext model on 317,151 samples of DNA sequences (with k-mers representation). We propose a novel idea to utilize the information of various codons present in amino acids for the evaluation of learned sequence vectors. We employ two diverse techniques to compare the performance of generated task-specific k-mer embeddings with state-of-the-art publicly available generic k-mer embeddings of genome. Firstly, we utilize a dimensionality reduction approach namely PCA to alleviate the dimensions of DNA sequences upto 50 features by preserving almost 85% of sequence features information. Afterwards, TSNE algorithms is used to visualize k-mer embeddings and to make sure whether different codons representing the same amino acid are more closer to each other than the ones representing different amino acids. Secondly, to assess the analogy of k-mer embeddings, generated domain specific k-mer embeddings are compared with state-of-the-art k-mer embeddings by estimating the cosine similarity among those codons vectors which represent same amino acid. Overall, we believe that task-specific distributed representation of k-mers would be useful for DNA methylation and Histone occupancy prediction tasks.

K-mer Neural Embedding Performance Analysis Using Amino Acid Codons

Network alignment (NA) that identifies equivalent nodes across networks is an effective tool for integrating knowledge from multiple networks. The state-of-the-art NA methods learn inter-network node similarities based on labeled anchor links, which are costly, time-consuming, and difficult to acquire. Therefore, a few unsupervised network alignment (UNA) methods propose solving NA problems without anchor links. However, most existing UNA methods rely on discriminative attributes to capture nodes’ similarities and are hard to obtain optimal one-to-one alignments. Toward these issues, this article proposes a novel method named HackGAN to solve the UNA problem solely based on the structural information. Specifically, HackGAN represents nodes with embeddings based on an unsupervised graph neural network (GNN) to capture their global and local structural features. After that, it initializes mapping functions to transform the embedding spaces of different networks into the same vector space by iteratively solving the Wasserstein–Procrustes problem. The mapping functions are then refined by an adversarial model with cycle-consistency and Sinkhorn distance losses to obtain optimized one-to-one mappings. Based on the distances between mapped embeddings, accurate and robust results are obtained with a collective alignment algorithm. Experimental comparisons on both synthetic and real-world datasets demonstrate the superiority of HackGAN. 

HackGAN: Harmonious Cross-Network Mapping Using CycleGAN With Wasserstein–Procrustes Learning for Unsupervised Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.

/pdf/an-extensive-assessment-of-network-embedding-in-ppi-network-u1mlqgwm.pdf

An Extensive Assessment of Network Embedding in PPI Network Alignment

Names make up a large portion of queries in search engines, while the name ambiguity problem brings negative effect to the service quality of search engines. In digital academic systems, this problem refers to a large number of publications containing ambiguous author names. Name ambiguity derives from many people sharing identical names, or names may be abbreviated. Although some methods have been proposed in the decade, this problem is still not completely solved and there are many subproblems needing to be studied. Due to lack of information, it is a nontrivial task to distinguish ambiguous authors accurately relying on limited internal information only. In this paper, we focus on the cold-start disambiguation task with homonymous author names, i.e., distinguishing publications written by authors with identical names. We present a supervised framework named DND (abbreviation for Distributed Framework for Name Disambiguation) to solve the author disambiguation problem efficiently. DND utilizes accessible information and trains a robust function to measure similarities between publications, and then determines whether they belong to the same author. In traditional clustering-based approaches for author disambiguation, the number of clusters which is the amount of authors sharing the same name is hard to predict in advance, while DND transforms the clustering task to a linkage prediction task to avoid specifying the number of clusters. We validate the effectiveness of DND on two real-world datasets. The experimental results indicate that DND achieves a competitive performance compared with the baselines.

A supervised and distributed framework for cold-start author disambiguation in large-scale publications

Research of Protein-Protein Interaction (PPI) Network Alignment is playing an important role in understanding the crucial underlying biological knowledge such as functionally homologous proteins and conserved evolutionary pathways across different species. Existing methods of PPI network alignment often try to improve the coverage ratio of the alignment result by aligning all proteins from different species. However, there is a fundamental biological premise that needs to be considered carefully: not every protein in a species can, nor should, find its homologous proteins in other species. In this work, we propose a novel alignment method to map only those proteins with the most similarity throughout the PPI networks of multiple species. For the similarity features of the protein in the networks, we integrate both topological features with biological characteristics to provide enhanced supports for the alignment procedures. For topological features, we apply a representation learning method on the networks and generate a low dimensional vector embedding with its surrounding structural features for each protein. The topological similarity of proteins from different PPI networks can thus be transferred as the similarity of their corresponding vector representations, which provides a new way to comprehensively quantify the topological similarities between proteins. We also propose a new measure for the topological evaluation of the alignment results which better uncover the structural quality of the alignment across multiple networks. Both biological and topological evaluations on the alignment results of real datasets demonstrate our approach is promising and preferable against previous multiple alignment methods.

Protein2Vec: Aligning Multiple PPI Networks with Representation Learning

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Protein2Vec: Aligning Multiple PPI Networks with Representation Learning