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Yan Cui

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

ResearcherUnclaimed source record
math.APmath.OCComputer Visioncond-mat.mes-hallcond-mat.mtrl-sciMachine Learningmath.STNeurons and CognitionOperating SystemsQuantitative MethodsSocial and Information NetworksStatistics Theory

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Published work

10 published item(s)

preprint2026arXiv

Linking spatial biology and clinical histology via Haiku

Integrating molecular, morphological, and clinical data is essential for basic and translational biomedical research, yet systematic frameworks for jointly modeling these modalities remain limited. Here we present Haiku, a tri-modal contrastive learning model trained on multiplexed immunofluorescence (mIF). It comprises 26.7 million spatial proteomics patches from 3,218 tissue sections across 1,606 patients spanning 11 organ types, with matched hematoxylin and eosin (H&E) histology and clinical metadata aligned in a shared embedding space. Haiku enables three-way cross-modal retrieval, improves downstream classification and clinical prediction tasks over unimodal baselines, and supports zero-shot biomarker inference through fusion retrieval conditioned on clinical metadata-only text descriptions. Across tasks, Haiku outperforms competing approaches, achieving cross-modal retrieval (Recall@50 up to 0.611 versus near-zero baseline), survival prediction (C-index 0.737, +7.91% relative improvement), and zero-shot biomarker inference (mean Pearson correlation 0.718 across 52 biomarkers). Furthermore, we introduce a counterfactual prediction framework in which modifying only clinical metadata while fixing tissue morphology surfaces niche-specific molecular shifts associated with breast cancer stage progression and lung cancer survival outcomes. In a lung adenocarcinoma case study, the counterfactual analysis recovers niche-specific shifts characterized by increased CD8 and granzyme B, reduced PD-L1, and decreased Ki67, broadly consistent with patterns reported for favorable outcomes. We present these counterfactual results as exploratory, hypothesis-generating signals rather than mechanistic claims. These capabilities demonstrate that tri-modal alignment via Haiku enables integrative analysis of spatial biology, bridging molecular measurements with clinical context for biological exploration.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A unified weighted inequality for fourth-order partial differential operators and applications

In this paper, we establish a fundamental inequality for fourth order partial differential operator $\cal P=α\partial_s+β\partial_{ss}+Δ^2$ ($α, β\in\mathbb{R}$) with an abstract exponential-type weight function. Such kind of weight functions including not only the regular weight functions but also the singular weight functions. Using this inequality we are able to prove some Carleman estimates for the operator $\cal P$ with some suitable boundary conditions in the case of $β<0$ or $α\neq 0, β=0$. As application, we obtain a resolvent estimate for $\cal P$, which can imply a log-type stabilization result for the plate equation with clamped boundary conditions or hinged boundary conditions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Criteria for finite time blow up for a system of Klein-Gordon equations

We give three conditions on initial data for the blowing up of the corresponding solutions to some system of Klein-Gordon equations on the three dimensional Euclidean space. We first use Levine's concavity argument to show that the negativeness of energy leads to the blowing up of local solutions in finite time. For the data of positive energy, we give a sufficient condition so that the corresponding solution blows up in finite time. This condition embodies datum with arbitrarily large energy. At last we use Payne-Sattinger's potential well argument to classify the datum with energy not so large (to be exact, below the ground states) into two parts: one part consists of datum leading to blowing-up solutions in finite time, while the other part consists of datum that leads to the global solutions.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Estimation and Inference of Time-Varying Auto-Covariance under Complex Trend: A Difference-based Approach

We propose a difference-based nonparametric methodology for the estimation and inference of the time-varying auto-covariance functions of a locally stationary time series when it is contaminated by a complex trend with both abrupt and smooth changes. Simultaneous confidence bands (SCB) with asymptotically correct coverage probabilities are constructed for the auto-covariance functions under complex trend. A simulation-assisted bootstrapping method is proposed for the practical construction of the SCB. Detailed simulation and a real data example round out our presentation.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

On the Observability Inequality of Coupled Wave Equations: the Case without Boundary

In this paper, we study the observability and controllability of wave equations coupled by first or zero order terms on a compact manifold. We adopt the approach in Dehman-Lebeau's paper \cite{DehmanLebeau09} to prove that: the weak observability inequality holds for wave equations coupled by first order terms on compact manifold without boundary if and only if a class of ordinary differential equations related to the symbol of the first order terms along the Hamiltonian flow are exactly controllable. We also compute the higher order part of the observability constant and the observation time. By duality, we obtain the controllability of the dual control system in a finite co-dimensional space. This gives the full controllability under the assumption of unique continuation of eigenfunctions. Moreover, these results can be applied to the systems of wave equations coupled by zero order terms of cascade structure after an appropriate change of unknowns and spaces. Finally, we provide some concrete examples as applications where the unique continuation property indeed holds.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Regulation of Irregular Neuronal Firing by Autaptic Transmission

The importance of self-feedback autaptic transmission in modulating spike-time irregularity is still poorly understood. By using a biophysical model that incorporates autaptic coupling, we here show that self-innervation of neurons participates in the modulation of irregular neuronal firing, primarily by regulating the occurrence frequency of burst firing. In particular, we find that both excitatory and electrical autapses increase the occurrence of burst firing, thus reducing neuronal firing regularity. In contrast, inhibitory autapses suppress burst firing and therefore tend to improve the regularity of neuronal firing. Importantly, we show that these findings are independent of the firing properties of individual neurons, and as such can be observed for neurons operating in different modes. Our results provide an insightful mechanistic understanding of how different types of autapses shape irregular firing at the single-neuron level, and they highlight the functional importance of autaptic self-innervation in taming and modulating neurodynamics.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

An Evaluation of Yelp Dataset

Yelp is one of the largest online searching and reviewing systems for kinds of businesses, including restaurants, shopping, home services et al. Analyzing the real world data from Yelp is valuable in acquiring the interests of users, which helps to improve the design of the next generation system. This paper targets the evaluation of Yelp dataset, which is provided in the Yelp data challenge. A bunch of interesting results are found. For instance, to reach any one in the Yelp social network, one only needs 4.5 hops on average, which verifies the classical six degree separation theory; Elite user mechanism is especially effective in maintaining the healthy of the whole network; Users who write less than 100 business reviews dominate. Those insights are expected to be considered by Yelp to make intelligent business decisions in the future.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Asymptotic stability of wave equations coupled by velocities

This paper is devoted to study the asymptotic stability of wave equations with constant coefficients coupled by velocities. By using Riesz basis approach, multiplier method and frequency domain approach respectively, we find the sufficient and necessary condition, that the coefficients satisfy, leading to the exponential stability of the system. In addition, we give the optimal decay rate in one dimensional case.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Coexistence and interconvertibility of ferromagnetic and antiferromagnetic phases in the single crystal of Mn$_3$ single-molecule magnet

We report the coexistence of ferromagnetic and antiferromagnetic phases in the single crystal of Mn$_3$ single-molecule magnet. The coexistent state appears within a certain period of time in the progress of either oxidation or reduction during a reversible oxidation-reduction process, when the sample is exposed in the air (oxygen) or the methyl vapor. We noticed an apparent change in the molecular structure, which is also reversible in terms of that the methyl group is dropped or added to the molecules during the oxidation or reduction. The absence or presence of the methyl group in the molecules exert an essential impact upon the intermolecular exchange interaction, and the ferromagnetic phase comes from the heterogenous intermolecular bonds between pairs of molecules of which one molecule has a methyl group whereas the other has lost the methyl group. The reversible change in molecular structure suggests the magnetic structure of Mn$_3$ might be designed and modulated at molecular scale, which implies Mn$_3$ has a great application potential.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

EOS: Automatic In-vivo Evolution of Kernel Policies for Better Performance

Today's monolithic kernels often implement a small, fixed set of policies such as disk I/O scheduling policies, while exposing many parameters to let users select a policy or adjust the specific setting of the policy. Ideally, the parameters exposed should be flexible enough for users to tune for good performance, but in practice, users lack domain knowledge of the parameters and are often stuck with bad, default parameter settings. We present EOS, a system that bridges the knowledge gap between kernel developers and users by automatically evolving the policies and parameters in vivo on users' real, production workloads. It provides a simple policy specification API for kernel developers to programmatically describe how the policies and parameters should be tuned, a policy cache to make in-vivo tuning easy and fast by memorizing good parameter settings for past workloads, and a hierarchical search engine to effectively search the parameter space. Evaluation of EOS on four main Linux subsystems shows that it is easy to use and effectively improves each subsystem's performance.

0 citations0 reviewsNo code linkedOpen access