arXiv subjects

Hongjie Yu

Publications and source records attributed to Hongjie Yu.

8 recordsLinked to original sources

arXiv2026

ReMAP-PET: Beyond Visual Understanding -- Learning Region-Guided Metabolic Alignment Semantics from Brain PET

Positron Emission Tomography (PET) reveals brain metabolism and is clinically central to neurodegenerative disease assessment, yet existing 3D brain foundation models treat PET as generic volumetric data, missing the structured regional metabolic information that distinguishes it from structural neuroimaging. To address these limitations, we propose ReMAP-PET, a framework that moves beyond visual encoding by supervising a partially-tuned MedicalNet 3D ResNet-50 with brain regional standardized uptake value ratio (SUVR) profiles through joint regression and contrastive objectives, enabling the encoder to learn the metabolic semantics underlying PET modality. On 1015 paired PET--SUVR samples, ReMAP-PET achieves 0.070 SUVR MAE and 77.8% PET SUVR Recall@1, substantially outperforming five frozen pretrained baselines. We further connect the metabolic embedding to clinical language via contrastive alignment with frozen BioClinicalBERT and demonstrate end-to-end PET-to-report generation through SUVR-constrained verbalization. Linear probing on diagnostic classification and cognitive regression tasks confirms that the embeddings retain clinically relevant information without task-specific fine-tuning. Our results show that grounding PET encoders in regional metabolic semantics -- rather than treating PET as generic volumetric data -- yields representations that are structured, interpretable, and language-compatible, pointing to a new direction for metabolic-aware PET understanding.

cs.CV↗

arXiv2025

VIBES: A Multi-Scale Modeling Approach Integrating Within-Host and Between-Hosts Dynamics in Epidemics

Infectious disease spread is a multi-scale process composed of within-host (biological) and between-host (social) drivers and disentangling them from each other is a central challenge in epidemiology. Here, we introduce VIBES, a multi-scale modeling framework that explicitly integrates viral dynamics based on patient-level data with population-level transmission on a data-driven network of social contacts. Using SARS-CoV-2 as a case study, we analyze three emergent epidemic properties, namely the generation time, serial interval, and pre-symptomatic transmission. First, we established a purely biological baseline, thus independent of the reproduction number (R), from the within-host model, estimating a generation time of 6.3 days for symptomatic individuals and 43.1% presymptomatic transmission. Then, using the full model incorporating social contacts, we found a shorter generation time (5.4 days at R=3.0) and an increase in pre-symptomatic transmission (52.8% at R=3.0), disentangling the impact of social drivers from a purely biological baseline. We further show that as pathogen transmissibility increases (R from 1.3 to 6), competition among infectious individuals shortens the generation time and serial interval by up to 21% and 13%, respectively. Conversely, a social intervention, like isolation, increases the proportion of pre-symptomatic transmission by about 30%. Our framework also estimates metrics that are challenging to obtain empirically, such as the generation time for asymptomatic individuals (5.6 days; 95%CI: 5.1-6.0 at R=1.3). Our findings establish multi-scale modeling as a powerful tool for mechanistically quantifying how pathogen biology and human social behavior shape epidemic dynamics as well as for assessing public health interventions.

q-bio.PE↗

arXiv2025

Human Mobility in Epidemic Modeling

Human mobility forms the backbone of contact patterns through which infectious diseases propagate, fundamentally shaping the spatio-temporal dynamics of epidemics and pandemics. While traditional models are often based on the assumption that all individuals have the same probability of infecting every other individual in the population, a so-called random homogeneous mixing, they struggle to capture the complex and heterogeneous nature of real-world human interactions. Recent advancements in data-driven methodologies and computational capabilities have unlocked the potential of integrating high-resolution human mobility data into epidemic modeling, significantly improving the accuracy, timeliness, and applicability of epidemic risk assessment, contact tracing, and intervention strategies. This review provides a comprehensive synthesis of the current landscape in human mobility-informed epidemic modeling. We explore diverse sources and representations of human mobility data, and then examine the behavioral and structural roles of mobility and contact in shaping disease transmission dynamics. Furthermore, the review spans a wide range of epidemic modeling approaches, ranging from classical compartmental models to network-based, agent-based, and machine learning models. And we also discuss how mobility integration enhances risk management and response strategies during epidemics. By synthesizing these insights, the review can serve as a foundational resource for researchers and practitioners, bridging the gap between epidemiological theory and the dynamic complexities of human interaction while charting clear directions for future research.

cs.SI↗

arXiv2023

$\ell$-adic local systems and Higgs bundles: the generic case

Let $X$ be a projective smooth geometrically connected curve defined over a finite field $\mathbb{F}_q$ of cardinality $q$. Let $S$ be a finite set of closed points of $X$. Let $\bar{X}$ and $\bar{S}$ be the base change of $X$, $S$ to an algebraic closure. We consider the set of $\ell$-adic ($\ell\nmid q$) local systems of rank $n$ over $\bar{X}-\bar{S}$ with prescribed tame regular semisimple and generic ramifications in $\bar{S}$. The genericity ensures that such an $\ell$-adic local system is automatically irreducible. We show that the number of these $\ell$-adic local systems fixed by Frobenius endomorphism equals the number of stable logarithmic Higgs bundles of rank $n$ and degree $e$ coprime to $n$, with a fixed residue, up to a power of $q$. In the split case, this number is equal to the number of stable parabolic Higgs bundles (with full flag structures) fixed by $\mathbb{G}_m$-action with generic parabolic weights.

math.AG↗

arXiv2023

Rank 2 $\ell$-adic local systems and Higgs bundles over a curve

Let $X$ be a smooth, projective, and geometrically connected curve defined over a finite field $\mathbb{F}_q$ of characteristic $p$ different from $2$ and $S\subseteq X$ a subset of closed points. Let $\overline{X}$ and $\overline{S}$ be their base changes to an algebraic closure of $\mathbb{F}_q$. We study the number of $\ell$-adic local systems $(\ell\neq p)$ in rank $2$ over $\overline{X}-\overline{S}$ with all possible prescribed tame local monodromies fixed by $k$-fold iterated action of Frobenius endomorphism for every $k\geq 1$. In all cases, we confirm conjectures of Deligne predicting that these numbers behave as if they were obtained from a Lefschetz fixed point formula. In fact, our counting results are expressed in terms of the numbers of some Higgs bundles.

math.AG↗

arXiv2021

Number of cuspidal automorphic representations and Hitchin's moduli spaces

Let $F$ be the function field of a projective smooth geometrically connected curve $X$ defined over a finite field $\mathbb{F}_q$. Let $G$ be a split semisimple algebraic group over $\mathbb{F}_q$. Let $S$ be a non-empty finite set of points of $X$. We are interested in the number of $G$ cuspidal automorphic representations whose local behaviors in $S$ are prescribed. In this article, we consider those cuspidal automorphic representations whose local component at each $v\in S$ contains a fixed irreducible Deligne-Lusztig induced representation of a hyperspecial group. We express that the count in terms of groupoid cardinality of $\mathbb{F}_q$-points of Hitchin moduli stacks of groups associated with $G$. In the course of the proof, we study the geometry of Hitchin moduli stacks and prove some vanishing results on the geometric side of a variant of the Arthur-Selberg trace formula for test functions with small support.

math.NT↗

arXiv2021

A coarse geometric expansion of a variant of Arthur's truncated traces and some applications

Let F be a global function field with constant field $\mathbb{F}_q$. Let G be a reductive group over $\mathbb{F}_q$. We establish a variant of Arthur's truncated kernel for G and for its Lie algebra which generalizes Arthur's original construction. We establish a coarse geometric expansion for our variant truncation. As applications, we consider some existence and uniqueness problems of some cuspidal automorphic representations for the functions field of the projective line $\mathbb{P}^1_{\mathbb{F}_q}$ with two points of ramifications.

math.NT↗

arXiv2018

Comptage des syst\`emes locaux $\ell$-adiques sur une courbe

Let $X_{1}$ be a projective, smooth and geometrically connected curve over $\mathbb{F}_{q}$ with $q=p^{n}$ elements where $p$ is a prime number, and let $X$ be its base change to an algebraic closure of $\mathbb{F}_{q}$. We give a formula for the number of irreducible $\ell$-adic local systems ($\ell\neq p$) with a fixed rank over $X$ fixed by the Frobenius endomorphism. We prove that this number behaves like a Lefschetz fixed point formula for a variety over $\mathbb{F}_q$, which generalises a result of Drinfeld in rank $2$ and proves a conjecture of Deligne. To do this, we pass to the automorphic side by Langlands correspondence, then use Arthur's non-invariant trace formula and link this number to the number of $\mathbb{F}_q$-points of the moduli space of stable Higgs bundles.

math.AG↗