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Guang Shi

Guang Shi appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

ResearcherUnclaimed source record
math.FABiological Physicscond-mat.softMachine LearningArtificial Intelligenceastro-ph.SRBiomoleculeseess.SPGenomicsmath.RAphysics.optics

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Published work

10 published item(s)

preprint2026arXiv

Loop Extrusion Reversal by Condensin Motor is Mediated by Catch Bonds

Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that condensin, a member of the SMC family involved in mitosis, takes occasional backward steps, thus coughing up the gains in the length of the extruded loop. To reveal the mechanism of the forward and backward steps simultaneously, we developed a theory using the stochastic kinetic model and the scrunching mechanism for LE. The calculations quantitatively account for the measured force-dependent step size and dwell time distributions in both the directions. By postulating the existence of an intermediate state in the ATP-driven cycle that is poised to take a forward or a backward step, we predict that its lifetime increases as the external mechanical force increases till a critical value and subsequently decreases at higher forces. The surprising finding of lifetime increase in an active motor, at sub-piconewton forces, is the characteristic of catch bonds, known in force-induced rupture of several passive protein complexes. The identification of catch bond-like states in condensin not only expands our understanding of LE but also highlights the significance of mechanical forces in regulating genome organization.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Adaptive Spike-Like Representation of EEG Signals for Sleep Stages Scoring

Recently there has seen promising results on automatic stage scoring by extracting spatio-temporal features from electroencephalogram (EEG). Such methods entail laborious manual feature engineering and domain knowledge. In this study, we propose an adaptive scheme to probabilistically encode, filter and accumulate the input signals and weight the resultant features by the half-Gaussian probabilities of signal intensities. The adaptive representations are subsequently fed into a transformer model to automatically mine the relevance between features and corresponding stages. Extensive experiments on the largest public dataset against state-of-the-art methods validate the effectiveness of our proposed method and reveal promising future directions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Cancer Subtyping by Improved Transcriptomic Features Using Vector Quantized Variational Autoencoder

Defining and separating cancer subtypes is essential for facilitating personalized therapy modality and prognosis of patients. The definition of subtypes has been constantly recalibrated as a result of our deepened understanding. During this recalibration, researchers often rely on clustering of cancer data to provide an intuitive visual reference that could reveal the intrinsic characteristics of subtypes. The data being clustered are often omics data such as transcriptomics that have strong correlations to the underlying biological mechanism. However, while existing studies have shown promising results, they suffer from issues associated with omics data: sample scarcity and high dimensionality. As such, existing methods often impose unrealistic assumptions to extract useful features from the data while avoiding overfitting to spurious correlations. In this paper, we propose to leverage a recent strong generative model, Vector Quantized Variational AutoEncoder (VQ-VAE), to tackle the data issues and extract informative latent features that are crucial to the quality of subsequent clustering by retaining only information relevant to reconstructing the input. VQ-VAE does not impose strict assumptions and hence its latent features are better representations of the input, capable of yielding superior clustering performance with any mainstream clustering method. Extensive experiments and medical analysis on multiple datasets comprising 10 distinct cancers demonstrate the VQ-VAE clustering results can significantly and robustly improve prognosis over prevalent subtyping systems.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox

Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Normal incidence narrowband transmission filtering in zero-contrast gratings

We report narrowband transmission filtering based on zero-contrast grating (ZCG) reflectors at normal incidence. Computational results show that the filtering is realized through symmetry-protected modes coupling. The guided modes introduced by the slab layer make the filter frequencies flexible to modify. The rectangular structure of the filter allows simple fabrication and integration into optical systems. The quality factor of the filters could exceed 106. Owing to the low refraction index dispersion of the semiconductor and their scale-invariant operations, these filters can be applied in a broad infrared range from near infrared to terahertz wavelengths.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

The confirmation and revision on the orbital period change of the possible type Ia supernova progenitor V617 Sagittarii

This work reports new photometric results of eclipsing cataclysmic variable V617 Sagittarii (V617 Sgr). We analyzed the orbital period change of V617 Sgr, by employing three new CCD eclipse timings since 2010 along with all the available data from the literature. It was found that the orbital period of V617 Sgr undergoes an obvious long-term increase, which confirms the result revealed by Steiner et al. (2006). The rate of orbital period increase was calculated to be ${\dot{P}}$ = +2.14(0.05) $\times$ 10$^{-7}$ day/year. This suggests the lifetime of the secondary star will attain to the end in a timescale of 0.97 $\times$ 10$^6$ years faster than that predicted previously. In particular, a cyclic variation with a period of 4.5 year and an amplitude of 2.3 minutes may present in the O-C diagram. Dominated by the wind-accretion mechanism, high mass transfer from the low mass secondary to the white dwarf is expected to sustain in the V Sge-type star V617 Sgr during its long-term evolution. The mass transfer rate $|\dot{M}_{tr}|$ was estimated to be in the range of about 2.2 $\times$ 10$^{-7}$ to 5.2 $\times$ 10$^{-7}$ M$_{\odot}$ yr$^{-1}$. Accordingly, the already massive ($\geq$ 1.2 M$_{\odot}$) white dwarf primary will process stable nuclear burning, accrete a fraction of mass from its companion to reach the standard Chandrasekhar mass limit ($\simeq$ 1.38 M$_{\odot}$), and ultimately produce a type Ia supernova (SN Ia) within about 4 $\sim$ 8 $\times$ 10$^{5}$ years or earlier.

0 citations0 reviewsNo code linkedOpen access
preprint2012arXiv

Quasi--bases for Modules over a Commutative Ring

In this paper we present the definition of quasi-bases for modules over a ring that is commutative but not necessarily division and discuss properties that guarantee the existence of quasi-bases. Based on this result we further prove that every finitely generated module over $L^{0}(\mathcal{F},K)$ has a quasi-basis, where $K$ is the scalar field of real numbers or complex numbers and $L^{0}(\mathcal{F},K)$ is the algebra of equivalence classes of $K$--valued random variables defined on a probability space $(Ω,\mathcal{F},P)$.

0 citations0 reviewsNo code linkedOpen access
preprint2011arXiv

A geometric form of the Hahn-Banach extension theorem for L0 linear functions and the Goldstine-Weston theorem in random normed modules

In this paper, we present a geometric form of the Hahn-Banach extension theorem for $L^{0}-$linear functions and prove that the geometric form is equivalent to the analytic form of the Hahn-Banach extension theorem. Further, we use the geometric form to give a new proof of a known basic strict separation theorem in random locally convex modules. Finally, using the basic strict separation theorem we establish the Goldstine-Weston theorem in random normed modules under the two kinds of topologies----the $(ε,λ)-$topology and the locally $L^{0}-$convex topology, and also provide a counterexample showing that the Goldstine-Weston theorem under the locally $L^{0}-$convex topology can only hold for random normed modules with the countable concatenation property.

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preprint2011arXiv

The Algebraic Structure of Finitely Generated $L^{0}(\mathcal{F},K)$-Modules and the Helly Theorem in Random Normed Modules

Let $K$ be the scalar field of real numbers or complex numbers and $L^{0}(\mathcal{F},K)$ the algebra of equivalence classes of $K-$valued random variables defined on a probability space $(Ω,\mathcal{F},P)$. In this paper, we first characterize the algebraic structure of finitely generated $L^{0}(\mathcal{F},K)$-modules and then combining the recently developed separation theorem in random locally convex modules we prove the Helly theorem in random normed modules with the countable concatenation property under the framework of random conjugate spaces at the same time a simple counterexample shows that it is necessary to require the countable concatenation property. By the way,we also give an application to the existence problem of the random solution of a system of random linear functional equations.

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preprint2010arXiv

The Goldstine-Weston theorem in random normed modules

This article generalize the classical Goldstine-Weston theorem on normed spaces to one on random normed modules: the image of a random normed module $(E,\|\cdot\|)$ under the random natural embedding $J$ is dense in its double random conjugate space $E^{**}$ with respect to the $(ε,λ)$ weak star topology; and $J(E)$ is also dense in $E^{**}$ with respect to the locally $L^{0}$-convex weak star topology if $E$ has the countable concatenation property.

0 citations0 reviewsNo code linkedOpen access