Predicting effective drug combinations using gradient tree boosting based on features extracted from drug-protein heterogeneous network.

BACKGROUND: Although targeted drugs have contributed to impressive advances in the treatment of cancer patients, their clinical benefits on tumor therapies are greatly limited due to intrinsic and acquired resistance of cancer cells against such drugs. Drug combinations synergistically interfere with protein networks to inhibit the activity level of carcinogenic genes more effectively, and therefore play an increasingly important role in the treatment of complex disease. RESULTS: In this paper, we combined the drug similarity network, protein similarity network and known drug-protein associations into a drug-protein heterogenous network. Next, we ran random walk with restart (RWR) on the heterogenous network using the combinatorial drug targets as the initial probability, and obtained the converged probability distribution as the feature vector of each drug combination. Taking these feature vectors as input, we trained a gradient tree boosting (GTB) classifier to predict new drug combinations. We conducted performance evaluation on the widely used drug combination data set derived from the DCDB database. The experimental results show that our method outperforms seven typical classifiers and traditional boosting algorithms. CONCLUSIONS: The heterogeneous network-derived features introduced in our method are more informative and enriching compared to the primary ontology features, which results in better performance. In addition, from the perspective of network pharmacology, our method effectively exploits the topological attributes and interactions of drug targets in the overall biological network, which proves to be a systematic and reliable approach for drug discovery.

Effect of oxygen stoichiometry on the structure, optical and epsilon-near-zero properties of indium tin oxide films.

Transparent conductive oxide (TCO) films showing epsilon near zero (ENZ) properties have attracted great research interest due to their unique property of electrically tunable permittivity. In this work, we report the effect of oxygen stoichiometry on the structure, optical and ENZ properties of indium tin oxide (ITO) films fabricated under different oxygen partial pressures. By using spectroscopic ellipsometry (SE) with fast data acquisition capabilities, we observed modulation of the material index and ENZ wavelength under electrostatic gating. Using a two-layer model based on Thomas-Fermi screening model and the Drude model, the optical constants and Drude parameters of the ITO thin films are determined during the gating process. The maximum carrier modulation amplitude ΔN of the accumulation layer is found to vary significantly depending on the oxygen stoichiometry. Under an electric field gate bias of 2.5 MV/cm, the largest ENZ wavelength modulation up to 27.9 nm at around 1550 nm is observed in ITO thin films deposited with oxygen partial pressure of P O 2 =10 Pa. Our work provides insights to the optical properties of ITO during electrostatic gating process for electro-optic modulators (EOMs) applications.

Design of a compact waveguide optical isolator based on multimode interferometers using magneto-optical oxide thin films grown on silicon-on-insulator substrates.

We report the design of a waveguide optical isolator based on multimode interferometer (MMI) structure using silicon on insulator (SOI) and deposited magneto-optical (MO) thin films. The optical isolator is based on a vertical 1 × 2 SOI MMI utilizing the nonreciprocal phase shift (NRPS) difference of different TM modes of the MO garnet thin film/SOI waveguide. By constructing a silicon/MO thin film/silicon structure, we demonstrate that the NRPS of the fundamental and first order TM modes can show opposite signs for certain device dimensions, therefore significantly reduce the device length. For a 310.42 µm long device, 20 dB isolation bandwidth larger than 1.6 nm with total insertion loss of 0.817 dB is achieved at 1550 nm wavelength. The fabrication tolerances and materials losses are also discussed to satisfy the state-of-the-art fabrication technology and material properties.

Switching the Optical Chirality in Magnetoplasmonic Metasurfaces Using Applied Magnetic Fields.

Chiral nanophotonic devices are promising candidates for chiral molecule sensing, polarization of diverse nanophotonics, and display technologies. Active chiral nanophotonic devices, where the optical chirality can be controlled by an external stimulus has triggered great research interest. However, efficient modulation of the optical chirality has been challenging. Here, we demonstrate switching of the extrinsic chirality by applied magnetic fields in a magnetoplasmonic metasurface device based on a magneto-optical oxide material, Ce1Y2Fe5O12 (Ce:YIG). Due to the low optical loss and strong magneto-optical effect of Ce:YIG, we experimentally demonstrated giant and continuous far-field circular dichroism (CD) modulation by applied magnetic fields from -0.6 ± 0.2° to +1.9 ± 0.1° at 950 nm wavelength under glancing incident conditions. The far-field CD modulation is due to both magneto-optical circular dichroism and near-field modulation of the superchiral fields by applied magnetic fields. Finally, we demonstrate magnetic-field-tunable chiral imaging in millimeter-scale magnetoplasmonic metasurfaces fabricated using self-assembly.