MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog

Interface solitons in quadratically nonlinear photonic lattices

We study the properties of two-color nonlinear localized modes which may exist at the interfaces separating two different periodic photonic lattices in quadratic media, focussing on the impact of phase mismatch of the photonic lattices on the properties, stability, and threshold power requirements for the generation of interface localized modes. We employ both an effective discrete model and continuum model with periodic potential and find good qualitative agreement between both models. Dynamics excitation of interface modes shows that, a two-color interface twisted mode splits into two beams with different escaping angles and carrying different energies when entering a uniform medium from the quadratic photonic lattice. The output position and energy contents of each two-color interface solitons can be controlled by judicious tuning ofComment: 6 pages, 8 figure

From Common to Special: When Multi-Attribute Learning Meets Personalized Opinions

Visual attributes, which refer to human-labeled semantic annotations, have gained increasing popularity in a wide range of real world applications. Generally, the existing attribute learning methods fall into two categories: one focuses on learning user-specific labels separately for different attributes, while the other one focuses on learning crowd-sourced global labels jointly for multiple attributes. However, both categories ignore the joint effect of the two mentioned factors: the personal diversity with respect to the global consensus; and the intrinsic correlation among multiple attributes. To overcome this challenge, we propose a novel model to learn user-specific predictors across multiple attributes. In our proposed model, the diversity of personalized opinions and the intrinsic relationship among multiple attributes are unified in a common-to-special manner. To this end, we adopt a three-component decomposition. Specifically, our model integrates a common cognition factor, an attribute-specific bias factor and a user-specific bias factor. Meanwhile Lasso and group Lasso penalties are adopted to leverage efficient feature selection. Furthermore, theoretical analysis is conducted to show that our proposed method could reach reasonable performance. Eventually, the empirical study carried out in this paper demonstrates the effectiveness of our proposed method

Nonlinear suppression of time-reversals in PT-symmetric optical couplers

We reveal a generic connection between the effect of time-reversals and nonlinear wave dynamics in systems with parity-time (PT) symmetry, considering a symmetric optical coupler with balanced gain and loss where these effects can be readily observed experimentally. We show that for intensities below a threshold level, the amplitudes oscillate between the waveguides, and the effects of gain and loss are exactly compensated after each period due to {periodic time-reversals}. For intensities above a threshold level, nonlinearity suppresses periodic time-reversals leading to the symmetry breaking and a sharp beam switching to the waveguide with gain. Another nontrivial consequence of linear PT-symmetry is that the threshold intensity remains the same when the input intensities at waveguides with loss and gain are exchanged.Comment: 5 pages, 4 figure

Spatial-Spectral Vortex Solitons in Quadratic Lattices

We predict the existence of spatial-spectral vortex solitons in one-dimensional periodic waveguide arrays with quadratic nonlinear response. In such vortices the energy flow forms a closed loop through the simultaneous effects of phase gradients at the fundamental frequency and second-harmonic fields, and the parametric frequency conversion between the spectral components. The linear stability analysis shows that such modes are stable in a broad parameter region.Comment: 4 pages, 3 figures, to appear in Optics Letter

Two-dimensional multi-pole solitons in nonlocal nonlinear media

We present the experimental observation of scalar multi-pole solitons in highly nonlocal nonlinear media, including dipole-, tri-pole, quadru-pole, and necklace-type solitons, organized as arrays of out-of-phase bright spots. These complex solitons are meta-stable, but with a large parameters range where the instability is weak, enabling their experimental observation.Comment: 12 pages, 2 figure