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Abstract Due to the high heterogeneity of cancers, it is rather essential to explore driver modules with the help of gene mutation data as well as known interactions between genes/proteins. Unfortunately, latent false positive interactions are inevitable in the Protein-Protein Interaction (PPI) network. Hence in the presented method, a new weight evaluation index, based on the gene-microRNA network as well as somatic mutation profile, is introduced for weighting the PPI network first. Subsequently, the vertices in the weighted PPI network are hierarchically clustered by measuring the Mahalanobis distance of their feature vectors, extracted with the graph embedding method Node2vec. Finally, a heuristic process with dropping and extracting is conducted on the gene clusters to produce a group of gene modules. Numerous experiment results demonstrate that the proposed method exhibits superior performance to four cutting-edge identification methods in most cases regarding the capability of recognizing the acknowledged cancer-related genes, generating modules having relatively high coverage and mutual exclusivity, and are significantly enriched for specific types of cancers. The majority of the genes in the identified modules are involved in cancer-related signaling pathways, or have been reported to be carcinogenic in the literature. Furthermore, many cancer related genes detected by the proposed method are actually omitted by the four comparison methods, which has been verified in the experiments.

Abstract Background Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments. It is an urgent problem to generate high quality gene expression data with computational methods. WGAN-GP, a generative adversarial network-based method, has been successfully applied in augmenting gene expression data. However, mode collapse or over-fitting may take place for small training samples due to just one discriminator is adopted in the method. Results In this study, an improved data augmentation approach MDWGAN-GP, a generative adversarial network model with multiple discriminators, is proposed. In addition, a novel method is devised for enriching training samples based on linear graph convolutional network. Extensive experiments were implemented on real biological data. Conclusions The experimental results have demonstrated that compared with other state-of-the-art methods, the MDWGAN-GP method can produce higher quality generated gene expression data in most cases.

Abstract Background Tremendous amounts of omics data accumulated have made it possible to identify cancer driver pathways through computational methods, which is believed to be able to offer critical information in such downstream research as ascertaining cancer pathogenesis, developing anti-cancer drugs, and so on. It is a challenging problem to identify cancer driver pathways by integrating multiple omics data. Results In this study, a parameter-free identification model SMCMN, incorporating both pathway features and gene associations in Protein–Protein Interaction (PPI) network, is proposed. A novel measurement of mutual exclusivity is devised to exclude some gene sets with “inclusion” relationship. By introducing gene clustering based operators, a partheno-genetic algorithm CPGA is put forward for solving the SMCMN model. Experiments were implemented on three real cancer datasets to compare the identification performance of models and methods. The comparisons of models demonstrate that the SMCMN model does eliminate the “inclusion” relationship, and produces gene sets with better enrichment performance compared with the classical model MWSM in most cases. Conclusions The gene sets recognized by the proposed CPGA-SMCMN method possess more genes engaging in known cancer related pathways, as well as stronger connectivity in PPI network. All of which have been demonstrated through extensive contrast experiments among the CPGA-SMCMN method and six state-of-the-art ones.

A thermodynamic study on a toluene chemical looping reforming process with six metal oxides was conducted to evaluate the product distribution for selecting an appropriate oxygen carrier with thermodynamic favorability towards high syngas yield. The results show that a suitable operation temperature for most oxygen carriers is 900 °C considering syngas selectivity and solid C formation whether the toluene is fed alone or together with fuel gas. The syngas selectivity of all oxygen carriers decreases with the increasing equivalence ratio, but the decrease degrees are quite different due to their different thermodynamic natures. With the increasing amounts of H2 and CO, the syngas selectivity for various oxygen carriers correspondingly decreases. The addition of CO2 and H2O(g) benefits reducing the solid C formation, whereas the addition of CH4 leads to more solid C being produced. Under the simulated gasification gas atmosphere, a synergetic elimination of solid C and water–gas shift reactions are observed. In terms of syngas selectivity, Mn2O3 possesses the best performance, followed by CaFe2O4 and Fe2O3, but NiO and CuO exhibit the lowest performance. BaFe2O4 presents a high H2 selectivity but a very poor CO selectivity due to the formation of BaCO3, which has a high thermodynamic stability below 1200 °C. Nevertheless, Mn2O3 is more likely to form solid C than feeding toluene alone and has a lower melting point. Considering syngas selectivity, carbon deposit and melting point, CaFe2O4 exhibits the highest performance concerning the tar chemical looping.

Abstract Background Haplotype assembly, reconstructing haplotypes from sequence data, is one of the major computational problems in bioinformatics. Most of the current methodologies for haplotype assembly are designed for diploid individuals. In recent years, genomes having more than two sets of homologous chromosomes have attracted many research groups that are interested in the genomics of disease, phylogenetics, botany and evolution. However, there is still a lack of methods for reconstructing polyploid haplotypes. Results In this work, the minimum error correction with genotype information (MEC/GI) model, an important combinatorial model for haplotyping a single individual, is used to study the triploid individual haplotype reconstruction problem. A fast and accurate enumeration-based algorithm enumeration haplotyping triploid with least difference (EHTLD) is proposed for solving the MEC/GI model. The EHTLD algorithm tries to reconstruct the three haplotypes according to the order of single nucleotide polymorphism (SNP) loci along them. When reconstructing a given SNP site, the EHTLD algorithm enumerates three kinds of SNP values in terms of the corresponding site’s genotype value, and chooses the one, which leads to the minimum difference between the reconstructed haplotypes and the sequenced fragments covering that SNP site, to fill the SNP loci being reconstructed. Conclusion Extensive experimental comparisons were performed between the EHTLD algorithm and the well known HapCompass and HapTree. Compared with algorithms HapCompass and HapTree, the EHTLD algorithm can reconstruct more accurate haplotypes, which were proven by a number of experiments.

Nowadays, more and more applications are dependent on storage and management of semi-structured information. For scientific research and knowledge-based decision-making, such data often needs to be published, e.g., medical data is released to implement a computer-assisted clinical decision support system. Since this data contains individuals’ privacy, they must be appropriately anonymized before to be released. However, the existing anonymization method based on l-diversity for hierarchical data may cause serious similarity attacks, and cannot protect data privacy very well. In this paper, we utilize fuzzy sets to divide levels for sensitive numerical and categorical attribute values uniformly (a categorical attribute value can be converted into a numerical attribute value according to its frequency of occurrences), and then transform the value levels to sensitivity levels. The privacy model ( α l e v h , k)-anonymity for hierarchical data with multi-level sensitivity is proposed. Furthermore, we design a privacy-preserving approach to achieve this privacy model. Experiment results demonstrate that our approach is obviously superior to existing anonymous approach in hierarchical data in terms of utility and security.