arXiv subjects

Yuan Fang

Publications and source records attributed to Yuan Fang.

197 records · Page 11Linked to original sources

arXiv2020

Recent Advances in Network-based Methods for Disease Gene Prediction

Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations. Considering the huge number of possible mutations, in addition to its high cost, another important drawback of GWAS analysis is the large number of false-positives. Thus, researchers search for more evidence to cross-check their results through different sources. To provide the researchers with alternative low-cost disease-gene association evidence, computational approaches come into play. Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease-gene association prediction. In this survey, we aim to provide a comprehensive and an up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods. To summarize, we first elucidate the task definition for disease gene prediction. Secondly, we categorize existing network-based efforts into network diffusion methods, traditional machine learning methods with handcrafted graph features and graph representation learning methods. Thirdly, an empirical analysis is conducted to evaluate the performance of the selected methods across seven diseases. We also provide distinguishing findings about the discussed methods based on our empirical analysis. Finally, we highlight potential research directions for future studies on disease gene prediction.

q-bio.QM↗

arXiv2020

Multi-View Collaborative Network Embedding

Real-world networks often exist with multiple views, where each view describes one type of interaction among a common set of nodes. For example, on a video-sharing network, while two user nodes are linked if they have common favorite videos in one view, they can also be linked in another view if they share common subscribers. Unlike traditional single-view networks, multiple views maintain different semantics to complement each other. In this paper, we propose MANE, a multi-view network embedding approach to learn low-dimensional representations. Similar to existing studies, MANE hinges on diversity and collaboration - while diversity enables views to maintain their individual semantics, collaboration enables views to work together. However, we also discover a novel form of second-order collaboration that has not been explored previously, and further unify it into our framework to attain superior node representations. Furthermore, as each view often has varying importance w.r.t. different nodes, we propose MANE+, an attention-based extension of MANE to model node-wise view importance. Finally, we conduct comprehensive experiments on three public, real-world multi-view networks, and the results demonstrate that our models consistently outperform state-of-the-art approaches.

cs.LG↗

arXiv2020

Charge density wave and weak Kondo effect in a Dirac semimetal CeSbTe

Using angle-resolved photoemission spectroscopy (ARPES) and low-energy electron diffraction (LEED), together with density-functional theory (DFT) calculation, we report the formation of charge density wave (CDW) and its interplay with the Kondo effect and topological states in CeSbTe. The observed Fermi surface (FS) exhibits parallel segments that can be well connected by the observed CDW ordering vector, indicating that the CDW order is driven by the electron-phonon coupling (EPC) as a result of the nested FS. The CDW gap is large (~0.3 eV) and momentum-dependent, which naturally explains the robust CDW order up to high temperatures. The gap opening leads to a reduced density of states (DOS) near the Fermi level (EF), which correspondingly suppresses the many-body Kondo effect, leading to very localized 4f electrons at 20 K and above. The topological Dirac cone at the X point is found to remain gapless inside the CDW phase. Our results provide evidence for the competition between CDW and the Kondo effect in a Kondo lattice system. The robust CDW order in CeSbTe and related compounds provide an opportunity to search for the long-sought-after axionic insulator.

cond-mat.str-el↗

arXiv2020

Spatial Transformer Point Convolution

Point clouds are unstructured and unordered in the embedded 3D space. In order to produce consistent responses under different permutation layouts, most existing methods aggregate local spatial points through maximum or summation operation. But such an aggregation essentially belongs to the isotropic filtering on all operated points therein, which tends to lose the information of geometric structures. In this paper, we propose a spatial transformer point convolution (STPC) method to achieve anisotropic convolution filtering on point clouds. To capture and represent implicit geometric structures, we specifically introduce spatial direction dictionary to learn those latent geometric components. To better encode unordered neighbor points, we design sparse deformer to transform them into the canonical ordered dictionary space by using direction dictionary learning. In the transformed space, the standard image-like convolution can be leveraged to generate anisotropic filtering, which is more robust to express those finer variances of local regions. Dictionary learning and encoding processes are encapsulated into a network module and jointly learnt in an end-to-end manner. Extensive experiments on several public datasets (including S3DIS, Semantic3D, SemanticKITTI) demonstrate the effectiveness of our proposed method in point clouds semantic segmentation task.

cs.CV↗

arXiv2020

Adaptive Task Sampling for Meta-Learning

Meta-learning methods have been extensively studied and applied in computer vision, especially for few-shot classification tasks. The key idea of meta-learning for few-shot classification is to mimic the few-shot situations faced at test time by randomly sampling classes in meta-training data to construct few-shot tasks for episodic training. While a rich line of work focuses solely on how to extract meta-knowledge across tasks, we exploit the complementary problem on how to generate informative tasks. We argue that the randomly sampled tasks could be sub-optimal and uninformative (e.g., the task of classifying "dog" from "laptop" is often trivial) to the meta-learner. In this paper, we propose an adaptive task sampling method to improve the generalization performance. Unlike instance based sampling, task based sampling is much more challenging due to the implicit definition of the task in each episode. Therefore, we accordingly propose a greedy class-pair based sampling method, which selects difficult tasks according to class-pair potentials. We evaluate our adaptive task sampling method on two few-shot classification benchmarks, and it achieves consistent improvements across different feature backbones, meta-learning algorithms and datasets.

cs.CV↗

arXiv2020

Emotion Recognition in Audio and Video Using Deep Neural Networks

Humans are able to comprehend information from multiple domains for e.g. speech, text and visual. With advancement of deep learning technology there has been significant improvement of speech recognition. Recognizing emotion from speech is important aspect and with deep learning technology emotion recognition has improved in accuracy and latency. There are still many challenges to improve accuracy. In this work, we attempt to explore different neural networks to improve accuracy of emotion recognition. With different architectures explored, we find (CNN+RNN) + 3DCNN multi-model architecture which processes audio spectrograms and corresponding video frames giving emotion prediction accuracy of 54.0% among 4 emotions and 71.75% among 3 emotions using IEMOCAP[2] dataset.

eess.AS↗

arXiv2020

Higher-order topological insulators in antiperovskites

We predict that a family of antiperovskite materials realize a higher order topological insulator phase, characterized by a previously introduced $\mathbb{Z}_4$ index. A tight binding model and a $k\cdot p$ model are used to capture the physics of the bulk, surface and hinge states of these materials. A phase diagram of the higher order and weak topological invariants is obtained for the tight binding model. The mirror Chern number is also discussed. In order to reveal the gapless hinge states in the presence of mirror Chern surface states, several ways of opening the surface gap are proposed and confirmed by calculation, including cleaving the crystal to reveal a low-symmetry surface, building a heterostructure, and applying strain. Upon opening the surface gap, we are able to study the hinge states by computing the momentum space band structure and real space distribution of mid-gap states.

cond-mat.str-el↗

arXiv2020

How does the presence of stevia glycosides impact surface bubbles stability?

The addition of sweeteners in fizzy beverages not only affects the sugar content but also the bubbles stability. In this article, we propose a model experiment, in which the lifetime of hundreds of single bubbles is measured, to assess the stability of bubbles in solutions containing either sucrose or sweeteners. We show that the bubbles are indeed more stable in presence of sweeteners, which are surface active molecules and adsorb at the interface. Additionally, we test an antifoam at different concentrations and show that our experiment allows to identify the best concentration to reproduce the stability obtained in sucrose when we replace this latter by a sweetener.

cond-mat.soft↗

arXiv2020

Stability of Big Surface Bubbles: Impact of Evaporation and Bubbles Size

Surface bubbles have attracted much interest in the past decades. In this article, we propose to explore the lifetime and thinning dynamics of centimetric surface bubbles. We study the impact of the bubbles size as well as that of the atmospheric humidity through a careful control and systematic variation of the relative humidity in the measuring chamber. We first adress the question of the drainage under saturated water vapor conditions and show that a model including both capillary and gravity driven drainage provides the best prediction for this process. Additionally, unprecedented statistics on the bubbles lifetimes confirm experimentally that this parameter is set by evaporation to leading order. We make use of a model based on the overall thinning dynamics of the thin film and assume a rupture thickness of the order 10-100 nm to obtain a good representation of these data. For experiments conducted far from saturation, the convective evaporation of the bath is shown to dominate the overall mass loss in the cap film due to evaporation.

cond-mat.soft↗

arXiv2020

Infinite mixtures of multivariate normal-inverse Gaussian distributions for clustering of skewed data

Mixtures of multivariate normal inverse Gaussian (MNIG) distributions can be used to cluster data that exhibit features such as skewness and heavy tails. However, for cluster analysis, using a traditional finite mixture model framework, either the number of components needs to be known $a$-$priori$ or needs to be estimated $a$-$posteriori$ using some model selection criterion after deriving results for a range of possible number of components. However, different model selection criteria can sometimes result in different number of components yielding uncertainty. Here, an infinite mixture model framework, also known as Dirichlet process mixture model, is proposed for the mixtures of MNIG distributions. This Dirichlet process mixture model approach allows the number of components to grow or decay freely from 1 to $\infty$ (in practice from 1 to $N$) and the number of components is inferred along with the parameter estimates in a Bayesian framework thus alleviating the need for model selection criteria. We provide real data applications with benchmark datasets as well as a small simulation experiment to compare with other existing models. The proposed method provides competitive clustering results to other clustering approaches for both simulation and real data and parameter recovery are illustrated using simulation studies.

stat.ME↗

arXiv2020

A Bayesian approach for clustering skewed data using mixtures of multivariate normal-inverse Gaussian distributions

Non-Gaussian mixture models are gaining increasing attention for mixture model-based clustering particularly when dealing with data that exhibit features such as skewness and heavy tails. Here, such a mixture distribution is presented, based on the multivariate normal inverse Gaussian (MNIG) distribution. For parameter estimation of the mixture, a Bayesian approach via Gibbs sampler is used; for this, a novel approach to simulate univariate generalized inverse Gaussian random variables and matrix generalized inverse Gaussian random matrices is provided. The proposed algorithm will be applied to both simulated and real data. Through simulation studies and real data analysis, we show parameter recovery and that our approach provides competitive clustering results compared to other clustering approaches.

stat.CO↗

arXiv2020

SN 2010kd: Photometric and Spectroscopic Analysis of a Slow-Decaying Superluminous Supernova

This paper presents data and analysis of SN 2010kd, a low-redshift ($z = 0.101$) H-deficient superluminous supernova (SLSN), based on ultraviolet/optical photometry and optical spectroscopy spanning between $-$28 and +194 days relative to $\mathit{B}$ band maximum light. The $\mathit{B}$ band light curve comparison of SN 2010kd with a subset of well-studied SLSNe I at comparable redshifts indicates that it is a slow-decaying PTF12dam like SLSN. Analytical light-curve modeling using the $\mathtt{Minim}$ code suggests that the bolometric light curve of SN 2010kd favors circumstellar matter interaction for the powering mechanism. $\mathtt{SYNAPPS}$ modeling of the early-phase spectra does not identify broad H or He lines, whereas the photospheric-phase spectra are dominated by O I, O II, C II, C IV and Si II, particularly, presence of both low and high-velocity components of O II and Si II lines. The nebular-phase spectra of SN 2010kd are dominated by O I and Ca II emission lines similar to those seen in other SLSNe I. The line velocities in SN 2010kd exhibit flatter evolution curves similar to SN 2015bn but with comparatively higher values. SN 2010kd shows a higher single-zone local thermodynamic equilibrium temperature in comparison to PTF12dam and SN 2015bn, and it has an upper O I ejected mass limit of $\sim 10~M_\odot$. The host of SN 2010kd is a dwarf galaxy with a high star-formation rate ($\sim 0.18 \pm 0.04~M_\odot$ yr$^{-1}$) and extreme emission lines.

astro-ph.HE↗

arXiv2019

Strong band kinks in magic-thickness Yb films arising from interfacial electron-phonon coupling

Interfacial electron-phonon coupling in ultrathin films has attracted much interest; it can give rise to novel effects and phenomena, including enhanced superconductivity. Here we report an observation of strong kinks in the energy dispersions of quantum well states in ultrathin Yb films grown on graphite. These kinks, arising from interfacial electron-phonon coupling, are most prominent for films with a preferred ("magic") thickness of 4 monolayers, which are strained and hole doped by the substrate. The energy position of the kinks agrees well with the optical phonon energy of graphite, and the extracted electron-phonon coupling strength λ shows a large subband dependence, with a maximum value up to 0.6. The kinks decay rapidly with increasing film thickness, consistent with its interfacial origin. The variation of λ is correlated with evolution of the electronic wave function amplitudes at the interface. A Lifshitz transition occurs just beyond the magic thickness where the heavy Yb 5d bands begin to populate right below the Fermi level.

cond-mat.mes-hall↗

arXiv2017

Quantum phase space with a basis of Wannier functions

A quantum phase space with Wannier basis is constructed: (i) classical phase space is divided into Planck cells; (ii) a complete set of Wannier functions are constructed with the combination of Kohn's method and Löwdin method such that each Wannier function is localized at a Planck cell. With these Wannier functions one can map a wave function unitarily onto phase space. Various examples are used to illustrate our method and compare it to Wigner function. The advantage of our method is that it can smooth out the oscillations in wave functions without losing any information and is potentially a better tool in studying quantum-classical correspondence. In addition, we point out that our method can be used for time-frequency analysis of signals.

quant-ph↗

arXiv2017

Demonstration of Laser-produced Neutron Diagnostic by Radiative Capture Gamma-rays

We report a new scenario of time-of-flight (TOF) technique in which fast neutrons and delayed gamma-ray signals were both recorded in a millisecond time window in harsh environments induced by high-intensity lasers. The delayed gamma signals, arriving far later than the original fast neutron and often being ignored previously, were identified to be the results of radiative captures of thermalized neutrons. The linear correlation between gamma photon number and the fast neutron yield shows that these delayed gamma events can be employed for neutron diagnosis. This method can reduce the detecting efficiency dropping problem caused by prompt high-flux gamma radiation, and provides a new way for neutron diagnosing in high-intensity laser-target interaction experiments.

physics.ins-det↗

arXiv2017

Truly Multi-modal YouTube-8M Video Classification with Video, Audio, and Text

The YouTube-8M video classification challenge requires teams to classify 0.7 million videos into one or more of 4,716 classes. In this Kaggle competition, we placed in the top 3% out of 650 participants using released video and audio features. Beyond that, we extend the original competition by including text information in the classification, making this a truly multi-modal approach with vision, audio and text. The newly introduced text data is termed as YouTube-8M-Text. We present a classification framework for the joint use of text, visual and audio features, and conduct an extensive set of experiments to quantify the benefit that this additional mode brings. The inclusion of text yields state-of-the-art results, e.g. 86.7% GAP on the YouTube-8M-Text validation dataset.

cs.CV↗

arXiv2013

Density Functionals that Recognize Covalent, Metallic, and Weak Bonds

Computationally-efficient semilocal approximations of density functional theory at the level of the local spin density approximation (LSDA) or generalized gradient approximation (GGA) poorly describe weak interactions. We show improved descriptions for weak bonds (without loss of accuracy for strong ones) from a newly-developed semilocal meta-GGA (MGGA), by applying it to molecules, surfaces, and solids. We argue that this improvement comes from using the right MGGA dimensionless ingredient to recognize all types of orbital overlap.

cond-mat.mtrl-sci↗