arXiv subjects

Ziqi Yan

Publications and source records attributed to Ziqi Yan.

At least 19 recordsLinked to original sources

arXiv2026

DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects

Birth defects are a major cause of fetal loss, neonatal morbidity and long-term disability. In the subset with suspected genetic etiologies, exome and genome sequencing have moved many cases from variant detection to post-sequencing interpretation: clinicians must rank patient-specific candidate variants under incomplete fetal or infant phenotypes and heterogeneous evidence from population genetics, variant-effect prediction, gene-disease validity, phenotype ontologies, cellular and pathway context, protein structure and clinical literature. We present DeepBD, a grounded agentic workflow for variant prioritization and diagnostic interpretation of genetic birth defects. DeepBD organizes the workflow into LLM-assisted case structuring, a pretrained evidence engine, specialist evidence modules and a grounded diagnostic review layer. The evidence engine learns patient-specific variant scores from structured rule evidence, sequence and variant-effect representations and phenotype-conditioned biological context, whereas specialist modules and the agentic layer provide tool-based refinement, candidate-pool review and diagnosis-oriented synthesis from ranked candidates. Developed using an in-house fetal and infant cohort comprising 18,622 cases, DeepBD achieved Recall@1/3/5/10 of 0.658/0.882/0.912/0.929 on an internal held-out solved-case benchmark, outperforming standalone Exomiser, DeepRare and prompted LLM reranking baselines evaluated on Exomiser-derived top-20 candidate variants. Ablation and overlap analyses show that rule evidence, mechanistic context, and specialist refinement provide complementary signals. These findings support a grounded agentic workflow that separates evidence integration, tool-based refinement, and LLM-assisted diagnostic review for retrospective variant prioritization in genetic birth defects.

q-bio.GN↗

arXiv2026

Non-Lorentzian Supergravity from Matrix Theory

It was recently shown that the decoupling limits leading to matrix (gauge) theories on D-branes give rise to non-Lorentzian target space geometries. Perturbatively, matrix theory describes a quantum gravity theory whose low-energy supergravity description exhibits non-Lorentzian behavior. Focusing on the D-particle case associated with the Banks-Fischler-Shenker-Susskind matrix theory, and using techniques from ambitwistor string theory, we show evidence that the dynamics of this non-Lorentzian gravity should be related to anomalies in the current algebra of the associated fundamental string worldsheet theory. At large N, the D-particle backreaction deforms the non-Lorentzian supergravity to the Lorentzian IIA theory, providing a holographic description of the BFSS matrix theory. At a moderately large N such that the D-particles decouple at the leading order, this non-Lorentzian supergravity maps holographically to the leading-order contribution of weakly coupled bulk gravity. This approximately non-Lorentzian regime is related to the null reduction of eleven-dimensional supergravity. Within the non-Lorentzian supergravity, non-trivial dynamics arises from the backreaction of extended brane objects that form BPS states with the D-particles. Finally, we generalize these results to other D-brane and string soliton holographic constructions.

hep-th↗

arXiv2026

FGFRFT: Fast Graph Fractional Fourier Transform via Exact Spectral Splitting and Fourier-Series Approximation

The graph fractional Fourier transform (GFRFT) for unitary graph Fourier transform (GFT) matrices can be interpreted through the scalar function $e^{j\alpha\theta}$ on the unit circle. Under the principal branch, its Fourier-series representation encounters an intrinsic obstruction at the spectral point $\lambda=-1$ for non-integer orders. To address this issue, we propose a fast graph fractional Fourier transform (FGFRFT) based on exact spectral splitting: the $\lambda=-1$ component is treated exactly, and the complementary component is approximated by a truncated Fourier series in integer powers of the GFT matrix. This construction yields an offline--online implementation that reduces the online complexity of repeated operator updates from $O(N^3)$ to $O(2LN^2)$ for truncation order $L$, while preserving differentiability with respect to the transform order. We further derive truncation-error bounds, approximate unitarity and additivity, and reconstruction-error bounds. Experiments on approximation accuracy, transform-order learning, image denoising, and point-cloud denoising show that FGFRFT provides substantial online acceleration while remaining close to the exact GFRFT under the tested settings.

eess.SP↗

arXiv2025

Dynamic Multiple-Parameter Joint Time-Vertex Fractional Fourier Transform and its Intelligent Filtering Methods

Dynamic graph signal processing provides a principled framework for analyzing time-varying data defined on irregular graph domains. However, existing joint time-vertex transforms such as the joint time-vertex fractional Fourier transform assign only one fractional order to the spatial domain and another one to the temporal domain, thereby restricting their capacity to model the complex and continuously varying dynamics of graph signals. To address this limitation, we propose a novel dynamic multiple-parameter joint time-vertex fractional Fourier transform (DMPJFRFT) framework, which introduces time-varying fractional parameters to achieve adaptive spectral modeling of dynamic graph structures. By assigning distinct fractional orders to each time step, the proposed transform enables dynamic and flexible representation of spatio-temporal signal evolution in the joint time-vertex spectral domain. Theoretical properties of the DMPJFRFT are systematically analyzed, and two filtering approaches: a gradient descent-based method and a neural network-based method, are developed for dynamic signal restoration. Experimental results on dynamic graph and video datasets demonstrate that the proposed framework effectively captures temporal topology variations and achieves superior performance in denoising and deblurring tasks compared with some state-of-the-art graph-based transforms and neural networks.

eess.SP↗

arXiv2025

JFRFFNet: A Data-Model Co-Driven Graph Signal Denoising Model with Partial Prior Information

Wiener filtering in the joint time-vertex fractional Fourier transform (JFRFT) domain has shown high effectiveness in denoising time-varying graph signals. Traditional filtering models use grid search to determine the transform-order pair and compute filter coefficients, while learnable ones employ gradient-descent strategies to optimize them; both require complete prior information of graph signals. To overcome this shortcoming, this letter proposes a data-model co-driven denoising approach, termed neural-network-aided joint time-vertex fractional Fourier filtering (JFRFFNet), which embeds the JFRFT-domain Wiener filter model into a neural network and updates the transform-order pair and filter coefficients through a data-driven approach. This design enables effective denoising using only partial prior information. Experiments demonstrate that JFRFFNet achieves significant improvements in output signal-to-noise ratio compared with some state-of-the-art methods.

eess.SP↗

arXiv2025

Axions, Three-Forms, and M-Theory

Scalar fields with masses protected by global shift symmetries, commonly referred to as axions, are abundantly used in effective field theories in cosmology and particle physics. However, global symmetries cannot be expected to be protected at the fundamental level. Finding consistent ultra-violet completions for axions is therefore a necessity. In this work, we identify the axion with the position mode of a charged 3-brane in (4+1)-dimensions. The shift symmetry of the axion is then a residual diffeomorphism in the fifth dimension orthogonal to the brane. Meanwhile, the brane is coupled to a flux in the fifth dimension. From the (3+1)-dimensional perspective, this construction generates (perturbatively) a mass for the axion and matches previously known proposals in the literature based on the coupling between the axion and a three-form gauge field. In a second step, we uplift this (4+1)-dimensional model to M-theory, where the same three-form is found to couple to the membrane with a (2+1)-dimensional worldvolume. In particular, our proposal also elucidates the duality between the axion and a two-form gauge field in the literature. We show that this dual two-form couples to the boundary of an open membrane in M-theory. Finally, we comment on the relations to and differences from other closed and open string axion monodromy models.

hep-th↗

arXiv2025

Trainable Joint Time-Vertex Fractional Fourier Transform

To address limitations of the graph fractional Fourier transform (GFRFT) Wiener filtering and the traditional joint time-vertex fractional Fourier transform (JFRFT) Wiener filtering, this study proposes a filtering method based on the hyper-differential form of the JFRFT. The gradient backpropagation mechanism is employed to enable the adaptive selection of transform order pair and filter coefficients. First, leveraging the hyper-differential form of the GFRFT and the fractional Fourier transform, the hyper-differential form of the JFRFT is constructed and its properties are analyzed. Second, time-varying graph signals are divided into dynamic graph sequences of equal span along the temporal dimension. A spatiotemporal joint representation is then established through vectorized reorganization, followed by the joint time-vertex Wiener filtering. Furthermore, by rigorously proving the differentiability of the transform orders, both the transform orders and filter coefficients are embedded as learnable parameters within a neural network architecture. Through gradient backpropagation, their synchronized iterative optimization is achieved, constructing a parameters-adaptive learning filtering framework. This method leverages a model-driven approach to learn the optimal transform order pair and filter coefficients. Experimental results indicate that the proposed framework improves the time-varying graph signals denoising performance, while reducing the computational burden of the traditional grid search strategy.

eess.SP↗

arXiv2025

Carroll Geometry Meets De Sitter Space via Holography

We explain how to relate the ideas of Carroll geometry, matrix theory on instantonic objects, and infinite boost limits of M-theory. Based on these new insights, we explore the implications for possible holographic constructions involving a de Sitter or flat space bulk. We show that Carroll-like (including particle Carroll) geometry in a hypothetical de Sitter holography mirrors the recently realized important role played by Galilei-like geometry in matrix theory and the AdS/CFT correspondence. This also allows us to generate examples of holography with a Carroll-like bulk.

hep-th↗

arXiv2025

Heterotic String Sigma Models: Discrete Light Cone Quantization and Its Current-Current Deformation

We propose a two-dimensional superstring sigma model that defines a self-contained corner of heterotic string theory, whose second quantization is heterotic matrix string theory. This worldsheet theory arises from a BPS decoupling limit that zooms in on the heterotic string, under which the target space geometry becomes non-Lorentzian. This construction generalizes the Gomis-Ooguri formulation of non-relativistic string theory to the heterotic case. We show how such a worldsheet theory provides a first-principles definition of the heterotic string in the discrete light cone quantization via T-duality. By turning on a current-current deformation akin to a $T\bar{T}$ deformation, the conventional heterotic string theory with a Lorentzian target space is recovered. We analyze the gauge and gravitational anomalies with respect to the lowest-order quantum corrections in the sigma model and show how the worldsheet theory is consistent with non-Lorentzian supergravity in the target space.

hep-th↗

arXiv2025

Dual Non-Lorentzian Backgrounds for Matrix Theories

We study properties of non-Lorentzian geometries arising from BPS decoupling limits of string theory that are central to matrix theory and the AdS/CFT correspondence. We focus on duality transformations between ten-dimensional non-Lorentzian geometries coupled to matrix theory on D-branes. We demonstrate that T- and S-duality transformations exhibit novel asymmetric properties: depending not only on the choice of transformation but also on the value of the background fields, the codimension of the foliation structure of the dual non-Lorentzian background may be different or the same. This duality asymmetry underlies features observed in the study of non-commutativity and Morita equivalence in matrix and gauge theory. Finally, we show how the holographic correspondence involving non-commutative Yang-Mills fits into our framework, from which we further obtain novel holographic examples with non-Lorentzian bulk geometries.

hep-th↗

arXiv2024

Conformal Mapping of Non-Lorentzian Geometries in SU(1,2) Conformal Field Theory

We realize an explicit conformal mapping between the state and operator pictures in a class of (2+1)-dimensional non-Lorentzian field theories with SU(1,2)$\times$U(1) conformal symmetry. The state picture arises from null reducing four-dimensional relativistic conformal field theories on a three-sphere, yielding a non-Lorentzian geometry with the conformal Killing symmetry group SU(1,2). This is complementary to the operator picture recently studied by Lambert et al., where the geometry acquires an $\Omega$-deformation. We then use the geometric mapping between the two pictures to derive a correspondence between the generators. This provides a concrete realization of the state-operator correspondence in non-Lorentzian conformal field theories.

hep-th↗

arXiv2024

Matrix Theory Reloaded: A BPS Road to Holography

We revisit the decoupling limits that lead to matrix theories on D-branes. We highlight the BPS nature of these limits, in which the target space geometry becomes non-Lorentzian and wrapped D-branes experience instantaneous gravitational forces. Applied to curved D-brane geometries, we show that a single BPS decoupling limit induces the bulk near-horizon limit leading to AdS/CFT. By consecutively applying two such limits, we systematically generate further examples of holography, including novel versions with non-Lorentzian bulk geometry. Uplifted to M-theory, we are led to a unified framework where each BPS decoupling limit corresponds to a Discrete Light Cone Quantisation (DLCQ). We conjecture that a DLCQ${}^n$/DLCQ${}^{m}$ correspondence, with $m>n$, captures the notion of holography in string theory. In particular, AdS${}_5$/CFT${}_4$ can be viewed as an example of DLCQ${}^0$/DLCQ${}^{1}$, with the extra DLCQ on the field theory side corresponding to the near-horizon limit in the bulk geometry. We further show that undoing these BPS decoupling limits can be viewed as deformations of matrix theories. We explain how these deformations are related to the $T\bar{T}$ deformation in two dimensions. In the context of holography, this allows us to view the ten-dimensional near-horizon brane geometry as an intrinsic deformation of the flat non-Lorentzian geometry that arises asymptotically. In field theoretic terms, these generalisations lead to $T\bar{T}$-like flow equations for the D$p$-brane DBI action.

hep-th↗

arXiv2024

Exact approaches on the string worldsheet

We review different exact approaches to string theory. In the context of the Green-Schwarz superstring, we discuss the action in curved backgrounds and its supercoset formulation, with particular attention to superstring backgrounds of the $AdS_3$ type supported by both Ramond-Ramond and Neveu-Schwarz-Neveu-Schwarz fluxes. This is the basis for the discussion of classical integrability, of worldsheet-scattering factorisation in the uniform lightcone gauge, and eventually of the string spectrum through the mirror thermodynamic Bethe ansatz, which for $AdS_3$ backgrounds was only derived and analysed very recently. We then illustrate some aspects of the Ramond-Neveu-Schwarz string, and introduce the formalism of Berkovits-Vafa-Witten, which has seen very recent applications to $AdS_3$ physics, which we also briefly review. Finally, we present the relation between M-theory in the discrete lightcone quantisation and decoupling limits of string theory that exhibit non-relativistic behaviours, highlighting the connection with integrable $T\bar{T}$ deformations, as well as the relation between spin-matrix theory and Landau-Lifshitz models. This review is based on lectures given at the Young Researchers Integrability School and Workshop 2022 "Taming the string worldsheet" at NORDITA, Stockholm.

hep-th↗

arXiv2023

Non-Lorentzian IIB Supergravity from a Polynomial Realization of SL(2,R)

We derive the action and symmetries of the bosonic sector of non-Lorentzian IIB supergravity by taking the non-relativistic string limit. We find that the bosonic field content is extended by a Lagrange multiplier that implements a restriction on the Ramond-Ramond fluxes. We show that the SL(2,R) transformation rules of non-Lorentzian IIB supergravity form a novel, nonlinear polynomial realization. Using classical invariant theory of polynomial equations and binary forms, we will develop a general formalism describing the polynomial realization of SL(2,R) and apply it to the special case of non-Lorentzian IIB supergravity. Using the same formalism, we classify all the relevant SL(2,R) invariants. Invoking other bosonic symmetries, such as the local boost and dilatation symmetry, we show how the bosonic part of the non-Lorentzian IIB supergravity action is formed uniquely from these SL(2,R) invariants. This work also points towards the concept of a non-Lorentzian bootstrap, where bosonic symmetries in non-Lorentzian supergravity are used to bootstrap the bosonic dynamics in Lorentzian supergravity, without considering the fermions.

hep-th↗

arXiv2023

Anisotropic Compactification of Nonrelativistic M-Theory

We study a decoupling limit of M-theory where the three-form gauge potential becomes critical. This limit leads to nonrelativistic M-theory coupled to a non-Lorentzian spacetime geometry. Nonrelativistic M-theory is U-dual to M-theory in the discrete light cone quantization, a non-perturbative approach related to the Matrix theory description of M-theory. We focus on the compactification of nonrelativistic M-theory over a two-torus that exhibits anisotropic behaviors due to the foliation structure of the spacetime geometry. We develop a frame covariant formalism of the toroidal geometry, which provides a geometrical interpretation of the recently discovered polynomial realization of SL(2,Z) duality in nonrelativistic type IIB superstring theory. We will show that the nonrelativistic IIB string background fields transform as polynomials of an effective Galilean "boost velocity" on the two-torus. As an application, we construct an action principle describing a single M5-brane in nonrelativistic M-theory and study its compactification over the anisotropic two-torus. This procedure leads to a D3-brane action in nonrelativistic IIB string theory that makes the SL(2,Z) invariance manifest in the polynomial realization.

hep-th↗

arXiv2023

Worldsheet Formalism for Decoupling Limits in String Theory

We study the bosonic sector of a decoupling limit of type IIA superstring theory, where a background Ramond-Ramond one-form is fined tuned to its critical value, such that it cancels the associated background D0-brane tension. The light excitations in this critical limit are D0-branes, whose dynamics is described by the Banks-Fischler-Shenker-Susskind (BFSS) Matrix theory that corresponds to M-theory in the Discrete Light-Cone Quantization (DLCQ). We develop the worldsheet formalism for the fundamental string in the same critical limit of type IIA superstring theory. We show that the fundamental string develops singularities on its worldsheet, whose topology is described by nodal Riemann spheres as in ambitwistor string theory. We study the T-duality transformations of this string sigma model and provide a worldsheet derivation for the recently revived and expanded duality web that unifies a zoo of decoupling limits in type II superstring theories. By matching the string worldsheet actions, we demonstrate how some of these decoupling limits are related to tensionless (and ambitwistor) string theory, Carrollian string theory, the Spin Matrix limits of the AdS/CFT correspondence, and more.

hep-th↗

arXiv2023

Unification of Decoupling Limits in String and M-theory

We study and extend the duality web unifying different decoupling limits of type II superstring theories and M-theory. We systematically build connections to different corners, such as Matrix theories, nonrelativistic string and M-theory, tensionless (and ambitwistor) string theory, Carrollian string theory, and Spin Matrix limits of AdS/CFT. We discuss target space, worldsheet, and worldvolume aspects of these limits in arbitrary curved backgrounds.

hep-th↗

arXiv2023

A New Extrapolation Economy Cascadic Multigrid Method for Image Restoration Problems

In this paper, a new extrapolation economy cascadic multigrid method is proposed to solve the image restoration model. The new method combines the new extrapolation formula and quadratic interpolation to design a nonlinear prolongation operator, which provides more accurate initial values for the fine grid level. An edge preserving denoising operator is constructed to remove noise and preserve image edges. The local smoothing operator reduces the influence of staircase effect. The experiment results show that the new method not only improves the computational efficiency but also ensures good recovery quality.

math.NA↗