Reconstructing gene regulatory networks with a memetic-neural hybrid based on fuzzy cognitive maps

Reconstructing gene regulatory networks (GRNs) plays an important role in identifying the complicated regulatory relationships, uncovering regulatory patterns in cells, and gaining a systematic view for biological processes. In order to reconstruct large-scale GRNs accurately, in this paper, we first use fuzzy cognitive maps (FCMs), which are a kind of cognition fuzzy influence graphs based on fuzzy logic and neural networks, to model GRNs. Then, a novel hybrid method is proposed to reconstruct GRNs from time series expression profiles using memetic algorithm (MA) combined with neural network (NN), which is labeled as MANN_FCM-GRN. In MANN_FCM-GRN, the MA is used to determine regulatory connections in GRNs and the NN is used to determine the interaction strength of the regulatory connections. In the experiments, the performance of MANN_FCM-GRN is validated on both synthetic data and the benchmark dataset DREAM3 and DREAM4. The experimental results demonstrate the efficacy of MANN_FCM-GRN and show that MANN_FCM-GRN can reconstruct GRNs with high accuracy without expert knowledge. The comparison with existing algorithms also shows that MANN_FCM-GRN outperforms ant colony optimization, non-linear Hebbian learning, and real-coded genetic algorithms.

     

MPE: a mobility pattern embedding model for predicting next locations

World Wide Web - The wide spread use of positioning and photographing devices gives rise to a deluge of traffic trajectory data (e.g., vehicle passage records and taxi trajectory data), with each...     

Quality enhancement of the abundant under‐valued crustacean,lobster krill (Munida spp.), during its chilled storage

Lobster krill (Munida genus) represents an under‐valued crustacean frequently caught on European fishing banks. In this work, its sensory, microbiological and biochemical qualities were evaluated during chilled storage. Additionally, the effects of a prestorage antimelanosic treatment consisting of soaking in sodium metabisulphite (SMB) solutions at two different concentrations (0.25% and 0.75%) were also studied. SMB prestorage treatment provided lobster specimens that still exhibited acceptable sensory quality after 10 days of storage, while control specimens were unacceptable at that time. SMB treatment also resulted in a significant (P < 0.05) inhibition of microbial growth, mainly of Enterobacteriaceae, psychrotrophes and proteolytic bacteria. Low lipid oxidation levels were observed for all batches; however, a significantly higher (P < 0.05) retention of polyunsaturated fatty acids was found in SMB‐treated lobster, especially in the 0.75% SMB batch. The results presented here open the way to the potential commercialisation of currently under‐utilised lobster krill as a chilled product.     

Blocked crystallization in capped ultrathin polymer films studied by molecular simulations

The crystallization of capped ultrathin polymer films is closely dependent on film thickness and interfacial interaction. Using dynamic Monte Carlo simulations, the crystallization behaviors of polymer films confined between two substrates were investigated. The crystallization rate of confined polymers is reduced with high interfacial interactions. Above a critical strength of interfacial interaction, polymer crystallization in the thin film is inhibited within the simulation time scales. An increase in film thickness leads to a rise in critical interfacial interaction. In thicker films, the chains have more space to change conformation to form crystal stems. In addition, there are fewer absorbed segments in confined chains for the thicker films, and thus the chains have stronger ability to adjust their conformation. Therefore an increase in film thickness can cause a reduction in the entropic barrier required for the formation of crystals and thus an increase in the critical interfacial interaction. © 2018 Society of Chemical Industry