arXiv subjects

Yucheng Guo

Publications and source records attributed to Yucheng Guo.

At least 37 records · Page 2Linked to original sources

arXiv2026

TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling

The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we propose TrinityDNA, a novel DNA foundational model designed to address these challenges. The model integrates biologically informed components, including Groove Fusion for capturing DNA's structural features and Gated Reverse Complement (GRC) to handle the inherent symmetry of DNA sequences. Additionally, we introduce a multi-scale attention mechanism that allows the model to attend to varying levels of sequence dependencies, and an evolutionary training strategy that progressively adapts the model to both prokaryotic and eukaryotic genomes. TrinityDNA provides a more accurate and efficient approach to genomic sequence modeling, offering significant improvements in gene function prediction, regulatory mechanism discovery, and other genomics applications. Our model bridges the gap between machine learning techniques and biological insights, paving the way for more effective analysis of genomic data. Additionally, we introduced a new DNA long-sequence CDS annotation benchmark to make evaluations more comprehensive and oriented toward practical applications.

cs.CE↗

arXiv2026

First statistical constraints on galactic scale outflows properties traced by their extended Mg II emission with MUSE

Galaxies evolve within vast gaseous halos that fuel star formation and carry signatures of feedback-driven outflows. Deep integral field data have enabled the study of MgII halos, which trace galaxy-scale outflows in emission, but their faintness has limited studies to single-object analyses. Here, we present the first statistical study of MgII-emitting halos using deep MUSE observations of 47 star-forming galaxies at $0.7<z<2.0$. Building on our previous work, where we developed and applied an outflow modeling framework for a single MgII halo, we now extend this approach to a larger sample, enabling robust population-level insights on the properties of circumgalactic outflows traced by their extended MgII emission. We detect extended emission out to tens of kiloparsecs and model the outflows as an ensemble of radially accelerating shells. Galaxies with MgII outflows tend to have higher SFRs, sSFRs, and younger stellar populations, consistent with star-formation-driven winds. The observations are consistent with winds that accelerate linearly with radius, from launching velocities of ~60 km/s up to maximum velocities that correlate with stellar mass and reach ~490 km/s. Their inner regions are highly opaque, and we find a tentative trend between stellar mass and central optical depth. The opening angle of the outflow shows some dependency on the host-galaxy stellar mass, with less massive galaxies showing primarily wide opening angles, and more massive galaxies showing a broader range of values, with both wide and narrow opening angles. The distribution of the spatial extent of MgII halos exhibits a clear peak at half-light radius (HLR) of ~5 kpc, with an extended tail of larger HLR values, up to ~20 kpc. Compact halo sizes (HLR $< 8$ kpc) correlate with stellar mass, but extended halos do not, which could suggest a difference in the powering mechanism between compact and extended halos.

astro-ph.GA↗

arXiv2026

RPO: Fine-Tuning Visual Generative Models via Rich Vision-Language Preferences

Traditional preference tuning methods for LLMs/Visual Generative Models often rely solely on reward model labeling, which can be opaque, offer limited insights into the rationale behind preferences, and are prone to issues such as reward hacking or overfitting. We introduce Rich Preference Optimization (RPO), a novel pipeline that leverages rich feedback signals from Vision Language Models (VLMs) to improve the curation of preference pairs for fine-tuning visual generative models like text-to-image diffusion models. Our approach begins with prompting VLMs to generate detailed critiques of synthesized images, from which we further prompt VLMs to extract reliable and actionable image editing instructions. By implementing these instructions, we create refined images, resulting in synthetic, informative preference pairs that serve as enhanced tuning datasets. We demonstrate the effectiveness of our pipeline and the resulting datasets in fine-tuning state-of-the-art diffusion models.

cs.LG↗

arXiv2025

Time-series Forecast for Indoor Zone Air Temperature with Long Horizons: A Case Study with Sensor-based Data from a Smart Building

With the press of global climate change, extreme weather and sudden weather changes are becoming increasingly common. To maintain a comfortable indoor environment and minimize the contribution of the building to climate change as much as possible, higher requirements are placed on the operation and control of HVAC systems, e.g., more energy-efficient and flexible to response to the rapid change of weather. This places demands on the rapid modeling and prediction of zone air temperatures of buildings. Compared to the traditional simulation-based approach such as EnergyPlus and DOE2, a hybrid approach combined physics and data-driven is more suitable. Recently, the availability of high-quality datasets and algorithmic breakthroughs have driven a considerable amount of work in this field. However, in the niche of short- and long-term predictions, there are still some gaps in existing research. This paper aims to develop a time series forecast model to predict the zone air temperature in a building located in America on a 2-week horizon. The findings could be further improved to support intelligent control and operation of HVAC systems (i.e. demand flexibility) and could also be used as hybrid building energy modeling.

cs.LG↗

arXiv2025

Revealing the Electronic Structure of van der Waals Antiferromagnetic NiPS$_3$ through Synchrotron-Based $μ$-ARPES and Alkali Metal Dosing

This study presents a comprehensive analysis of the band structure in NiPS$_3$, a van der Waals layered antiferromagnet, utilizing high-resolution synchrotron-based angle-resolved photoemission spectroscopy (ARPES) and corroborative density functional theory (DFT) calculations. By tuning the parameters of the light source, we obtained a very clear and wide energy range band structure of NiPS$_3$. Comparison with DFT calculations allows for the identification of the orbital character of the observed bands. Our DFT calculations perfectly match the experimental results, and no adaptations were made to the calculations based on the experimental outcomes. The appearance of novel electronic structure upon alkali metal dosing (AMD) were also obtained in this ARPES study. Above valence band maximum, structure of conduction bands and bands from defect states were firstly observed in NiPS$_3$. We provide the direct determination of the band gap of NiPS$_3$ as 1.3 eV from the band structure by AMD. In addition, detailed temperature dependent ARPES spectra were obtained across a range that spans both below and above the Néel transition temperature of NiPS$_3$. We found that the paramagnetic and antiferromagnetic states have almost identical spectra, indicating the highly localized nature of Ni $d$ states.

cond-mat.mtrl-sci↗

arXiv2025

Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains underexplored. This paper follows the guidance of the central dogma to redesign both the data and model pipeline and offers a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions between coding and non-coding regions through masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive experiments show that Life-Code achieves state-of-the-art results on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

cs.LG↗

arXiv2025

Spin Excitations and Flat Electronic Bands in a Cr-based Kagome Superconductor

In the quest for topology- and correlation-driven quantum states, kagome lattice materials have garnered significant interest for their band structures, featuring flat bands (FBs) from the quantum destructive interference of the electronic wavefunction. Tuning an FB to the chemical potential could induce electronic instabilities and emergent orders. Despite extensive studies, direct evidence of FBs tuned to the chemical potential and their role in emergent orders in bulk materials remains lacking. Using angle-resolved photoemission spectroscopy, resonant inelastic X-ray scattering, and density functional theory, we show that the low-energy structure of the Cr-based kagome metal superconductor {\Cr} is dominated by FBs at the Fermi level. We also observe low-energy magnetic excitations evolving across the low-temperature transition, largely consistent with the FB shift. Our results suggest that the low-temperature order contains a magnetic origin and that the kagome FBs may play a role in the emergence of this order.

cond-mat.str-el↗

arXiv2025

MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

q-bio.GN↗

arXiv2025

Strain-tunability of the multipolar Berry curvature in altermagnet MnTe

The anomalous Hall effect describes the generation of a transverse voltage by a longitudinal current even in the absence of an external magnetic field. While typically observed in ferromagnets, it has also been predicted to arise in altermagnets, materials characterized by rotational symmetries that enable broken time reversal symmetry despite compensated collinear magnetic ordering. These symmetries enforce band (anti)crossings that can generate significant contributions to the Berry curvature that drives the anomalous Hall effect. This Berry curvature is predicted to exhibit a characteristic multipolar order, resulting in a symmetry-enforced distribution at or near net compensation which is highly sensitive to perturbations that distort this balance. However, exploring the predicted multipolar Berry curvature of altermagnets and its reversible manipulation remains challenging. Here, we demonstrate evidence for the multipolar nature of the altermagnetic Berry curvature in MnTe by tuning the anomalous Hall effect via uniaxial stress. Upon straining, the magnitude of the anomalous Hall conductivity changes and, at a critical strain of 0.14%, the sign is reversed. Symmetry analysis and density functional theory calculations reveal that this tunability is a direct consequence of the altermagnetic multipolar Berry curvature. Our results provide insight into the role of crystal and magnetic symmetries in the realization of higher-order Berry curvature distributions and their unique tunability.

cond-mat.mtrl-sci↗

arXiv2025

Dichotomy of flat bands in the van der Waals ferromagnet Fe$_5$GeTe$_2$

Quantum materials with bands of narrow bandwidth near the Fermi level represent a promising platform for exploring a diverse range of fascinating physical phenomena, as the high density of states within the small energy window often enables the emergence of many-body physics. On one hand, flat bands can arise from strong Coulomb interactions that localize atomic orbitals. On the other hand, quantum destructive interference can quench the electronic kinetic energy. Although both have a narrow bandwidth, the two types of flat bands should exhibit very distinct spectral properties arising from their distinctive origins. So far, the two types of flat bands have only been realized in very different material settings and chemical environments, preventing a direct comparison. Here, we report the observation of the two types of flat bands within the same material system--an above-room-temperature van der Waals ferromagnet, Fe$_{5-x}$GeTe$_2$, distinguishable by a switchable iron site order. The contrasting nature of the flat bands is also identified by the remarkably distinctive temperature-evolution of the spectral features, indicating that one arises from electron correlations in the Fe(1) site-disordered phase, while the other geometrical frustration in the Fe(1) site-ordered phase. Our results therefore provide a direct juxtaposition of the distinct formation mechanism of flat bands in quantum materials, and an avenue for understanding the distinctive roles flat bands play in the presence of magnetism, topology, and lattice geometrical frustration, utilizing sublattice ordering as a key control parameter.

cond-mat.str-el↗

arXiv2025

EnTao-GPM: DNA Foundation Model for Predicting the Germline Pathogenic Mutations

Distinguishing pathogenic mutations from benign polymorphisms remains a critical challenge in precision medicine. EnTao-GPM, developed by Fudan University and BioMap, addresses this through three innovations: (1) Cross-species targeted pre-training on disease-relevant mammalian genomes (human, pig, mouse), leveraging evolutionary conservation to enhance interpretation of pathogenic motifs, particularly in non-coding regions; (2) Germline mutation specialization via fine-tuning on ClinVar and HGMD, improving accuracy for both SNVs and non-SNVs; (3) Interpretable clinical framework integrating DNA sequence embeddings with LLM-based statistical explanations to provide actionable insights. Validated against ClinVar, EnTao-GPM demonstrates superior accuracy in mutation classification. It revolutionizes genetic testing by enabling faster, more accurate, and accessible interpretation for clinical diagnostics (e.g., variant assessment, risk identification, personalized treatment) and research, advancing personalized medicine.

q-bio.GN↗

arXiv2025

Kramers nodal lines in intercalated TaS$_2$ superconductors

Kramers degeneracy is one fundamental embodiment of the quantum mechanical nature of particles with half-integer spin under time reversal symmetry. Under the chiral and noncentrosymmetric achiral crystalline symmetries, Kramers degeneracy emerges respectively as topological quasiparticles of Weyl fermions and Kramers nodal lines (KNLs), anchoring the Berry phase-related physics of electrons. However, an experimental demonstration for ideal KNLs well isolated at the Fermi level is lacking. Here, we establish a class of noncentrosymmetric achiral intercalated transition metal dichalcogenide superconductors with large Ising-type spin-orbit coupling, represented by In$_x$TaS$_2$, to host an ideal KNL phase. We provide evidence from angle-resolved photoemission spectroscopy with spin resolution, angle-dependent quantum oscillation measurements, and ab-initio calculations. Our work not only provides a realistic platform for realizing and tuning KNLs in layered materials, but also paves the way for exploring the interplay between KNLs and superconductivity, as well as applications pertaining to spintronics, valleytronics, and nonlinear transport.

cond-mat.supr-con↗

arXiv2024

MusE GAs FLOw and Wind (MEGAFLOW) XIII. Cool gas traced by MgII around isolated galaxies

The circumgalactic medium (CGM) is a key component needed to understand the physical processes governing the flows of gas around galaxies. Quantifying its evolution and its dependence on galaxy properties is particularly important for our understanding of accretion and feedback mechanisms. We select a volume-selected sample of 66 {\it isolated} star-forming galaxies (SFGs) at $0.4< z <1.5$ with $\log(M_\star/M_{\odot})> 9$ from the MusE GAs FLOw and Wind (MEGAFLOW) survey. Using MgII 2796,2803 absorptions in background quasars, we measure the covering fraction $f_c$ and quantify how the cool gas profile depends on galaxy properties (such as star-formation rate (SFR), stellar mass ($M_\star$) or azimuthal angle relative to the line of sight) and how these dependencies evolve with redshift. The MgII covering fraction of isolated galaxies is a strong function of impact parameter, and is steeper than previously reported. The impact parameter $b_{50}$ at which $f_c = $50\% is $b_{50}=50\pm7$kpc ($65\pm7$ kpc) for $W_r^{2796}>$0.5 Å($W_r^{2796}>0.1$ Å), respectively. It is weakly correlated with SFR ($\propto$ SFR$^{0.08\pm0.09}$) and decreases with cosmic time ($\propto (1+z)^{0.8 \pm 0.7}$), contrary to the expectation of increasingly larger halos with time. The covering fraction is also higher along the minor axis than along the major axis at the $\approx 2 σ$ level. The CGM traced by \MgII{} is similar across the isolated galaxy population. Indeed, among the isolated galaxies with an impact parameter below 55 kpc, all have associated MgII absorption with $W_r^{2796}>$0.3Å, resulting in a steep covering fraction $f_c(b)$.

astro-ph.GA↗

arXiv2024

Cascade equation for the discontinuities in the Stefan problem with surface tension

The Stefan problem with surface tension is well known to exhibit discontinuities in the associated moving aggregate (i.e., in the domain occupied by the solid), whose structure has only been understood under translational or radial symmetry so far. In this paper, we derive an auxiliary partial differential equation of second-order hyperbolic type, referred to as the cascade equation, that captures said discontinuities in the absence of any symmetry assumptions. Specializing to the one-phase setting, we introduce a novel (global) notion of weak solution to the cascade equation, which is defined as a limit of mean-field game equilibria. For the spatial dimension two, we show the existence of such a weak solution and prove a natural perimeter estimate on the associated moving aggregate.

math.AP↗

arXiv2024

The MUSE eXtremely Deep Field: Detections of circumgalactic SiII* emission at z>~2

The circumgalactic medium (CGM) serves as a baryon reservoir that connects galaxies to the intergalactic medium and fuels star formation. The spatial distribution of the metal-enriched cool CGM has not yet been directly revealed at cosmic noon (z~2-4), as bright emission lines at these redshifts are not covered by optical integral field units. To remedy this situation, we aim for the first-ever detections and exploration of extended SiII* emission (low-ionization state, LIS), referred to as ``SiII* halos'', at redshifts ranging from z=2 to 4 as a means to trace the metal-enriched cool CGM. We use a sample of 39 galaxies with systemic redshifts of z=2.1-3.9 measured with the [CIII] doublet in the MUSE Hubble Ultra Deep Field catalog, which contains integration times spanning from ~30 to 140 hours. We search for extended SiII*1265, 1309, 1533 emission (fluorescent lines) around individual galaxies. We also stack a subsample of 14 UV-bright galaxies. We report five individual detections of SiII*1533 halos. We also confirm the presence of SiII*1533 halos in stacks for the subsample containing UV-bright sources. The other lines do not show secure detections of extended emission in either individual or stacking analyses. These detections may imply that the presence of metal-enriched CGM is a common characteristic for UV-bright galaxies. To investigate whether the origin of SiII* is continuum pumping as suggested in previous studies, we check the consistency of the equivalent width (EW) of SiII* emission and the EW of SiII absorption for the individual halo object with the most reliable detection. We confirm the equivalence, suggesting that photon conservation works for this object and pointing toward continuum pumping as the source of SiII*. We also investigate SiII* lines in a RAMSES-RT zoom-in simulation including continuum pumping and find ubiquitous presence of extended halos.

astro-ph.GA↗

arXiv2024

Topological Surface State Evolution in Bi$_2$Se$_3$ via Surface Etching

Topological insulators are materials with an insulating bulk interior while maintaining gapless boundary states against back scattering. Bi$_2$Se$_3$ is a prototypical topological insulator with a Dirac-cone surface state around $Γ$. Here, we present a controlled methodology to gradually remove Se atoms from the surface Se-Bi-Se-Bi-Se quintuple layers, eventually forming bilayer-Bi on top of the quintuple bulk. Our method allows us to track the topological surface state and confirm its robustness throughout the surface modification. Importantly, we report a relocation of the topological Dirac cone in both real space and momentum space, as the top surface layer transitions from quintuple Se-Bi-Se-Bi-Se to bilayer-Bi. Additionally, charge transfer among different surface layers is identified. Our study provides a precise method to manipulate surface configurations, allowing for the fine-tuning of the topological surface states in Bi$_2$Se$_3$, which represents a significant advancement towards nano-engineering of topological states.

cond-mat.mtrl-sci↗

arXiv2024

A galactic outflow traced by its extended Mg II emission out to a $\sim30$ kpc radius in the Hubble Ultra Deep Field with MUSE

We report the discovery of a rare Mg II $λ$$λ$ 2796, 2803 doublet emission halo around a star forming galaxy with $\log (M_\star$/M$_\odot) = 10.3 \pm 0.3$ at $z=0.737$ in deep (9.94 h) VLT/MUSE data from the MUSE-HUDF mosaic. While the central region prominently displays an absorption-dominated Mg II doublet, characterized by discernible P-Cyg features, our examination reveals a remarkably extended Mg II emission, spanning approximately $\sim30$ kpc from the central galaxy. We introduce a simple outflow radiative transfer modeling scheme based on the Sobolev approximation, and we employ a Bayesian Monte Carlo Markov Chain (MCMC) fitting to find the best-fitting parameters that match our data. The model reproduces several key features of the observed Mg II halo and allows us to constrain the kinematics and geometry of the outflowing gas. Our data are consistent with a biconical wind whose velocity increases with radius, pointing nearly towards the observer, with an opening angle of $59\pm4^{\circ}$ In general, we find that our outflow model performs better in the inner regions of the galactic wind ($\lesssim 10$ kpc $\approx 6$ half-light radii), reaching a velocity of $\sim120$ km s$^{-1}$ at 10 kpc from the central galaxy. However, discrepancies between the data and the model in the outer regions suggest the possible influence of additional mechanisms, such as inflows, satellite interactions, or turbulence, which might significantly shape the circumgalactic medium (CGM) of galaxies at larger impact parameters. This analysis underscores the complexity of galactic outflows and encourages further exploration of the processes governing the dynamics of galactic winds through spatially resolved studies of the CGM.

astro-ph.GA↗

arXiv2024

Spatially-resolved Spectroscopic Analysis of Ly$α$ Haloes: Radial Evolution of the Ly$α$ Line Profile out to 60 kpc

The extended Ly$α$ haloes (LAHs) have been found to be prevalent around high-redshift star-forming galaxies. However, the origin of the LAHs is still a subject of debate. Spatially resolved analysis of Ly$α$ profiles provides an important diagnostic. We analyse the average spatial extent and spectral variation of the circumgalactic LAHs by stacking a sample of 155 Ly$α$ emitters (LAEs) at redshift $3<z<4$ in the MUSE Extremely Deep Field. Our analysis reveals that, with respect to the Ly$α$ line of the target LAE, the peak of the Ly$α$ line at large distances becomes increasingly more blueshifted up to a projected distance of 60 kpc ($\approx 3 \times$ virial radius), with a velocity offset of $\approx$ 250 km/s. This trend is evident in both the mean and median stacks, suggesting that it is a general property of our LAE sample, which typically has a Ly$α$ luminosity $\mathrm{\approx 10^{41.1} erg\,s^{-1}}$. However, due to the absence of systemic redshift data, it remains unclear whether the Ly$α$ line peak at large projected distances is less redshifted compared to the inner regions or truly blueshifted with respect to the systemic velocity. We explore various scenarios to explain the large-scale kinematics of the Ly$α$ line.

astro-ph.GA↗