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...     

应变纤锌矿ZnO/MgxZn1-xO量子点中离子施主束缚激子的光学性质

Within the framework of the effective-mass approximation and the dipole approximation, considering the three-dimensional confinement of the electron and hole and the strong built-in electric field(BEF) in strained wurtzite Zn O/Mg0:25Zn0:75O quantum dots(QDs), the optical properties of ionized donor-bound excitons(D+, X)are investigated theoretically using a variational method. The computations are performed in the case of finite band offset. Numerical results indicate that the optical properties of(D+, X) complexes sensitively depend on the donor position, the QD size and the BEF. The binding energy of(D+, X) complexes is larger when the donor is located in the vicinity of the left interface of the QDs, and it decreases with increasing QD size. The oscillator strength reduces with an increase in the dot height and increases with an increase in the dot radius. Furthermore, when the QD size decreases, the absorption peak intensity shows a marked increment, and the absorption coefficient peak has a blueshift. The strong BEF causes a redshift of the absorption coefficient peak and causes the absorption peak intensity to decrease remarkably. The physical reasons for these relationships have been analyzed in depth.     

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     

Cathode plasma electrolytic deposition of Al2O3 coatings doped with SiC particles

Semiconductor particles doped Al₂O₃ coatings were prepared by cathode plasma electrolytic deposition in Al(NO₃)₃ electrolyte dispersed with SiC micro- and nano-particles (average particle sizes of 0.5–1.7?µm and 40?nm respectively). The effects of the concentrations and particle sizes of the SiC on the microstructures and tribological performances of the composite coatings were studied. In comparison with the case of dispersing with SiC microparticles, the dispersion of SiC nanoparticles in the coatings was more uniform. When the concentration of SiC nanoparticles was 5?g/L, the surface roughness of the composite coating was reduced by 63%, compared with that of the unmodified coating. Friction results demonstrated that the addition of 5?g/L SiC nanoparticles reduced the friction coefficient from 0.60 to 0.38 and decreased the wear volume under dry friction. The current density and bath voltage were measured to analyze the effects of SiC particles on the deposition process. The results showed that the SiC particles could alter the electrical behavior of the coatings during the deposition process, weaken the bombardment of the plasma, and improve the structures of the coatings.     

Scanning tunneling spectroscopic study of monolayer 1T-TaS2 and 1T-TaSe2

Nano Research - The isostructural and isoelectronic transition-metal-dichalcogenides 1T-TaS2 and 1T-TaSe2 are layered materials with intricate electronic structures. Combining the molecular beam...