arXiv subjects

Yunyi Shen

Publications and source records attributed to Yunyi Shen.

28 records · Page 2Linked to original sources

arXiv2024

Detecting stellar flares in photometric data using hidden Markov models

We present a hidden Markov model (HMM) for discovering stellar flares in light curve data of stars. HMMs provide a framework to model time series data that are not stationary; they allow for systems to be in different states at different times and consider the probabilities that describe the switching dynamics between states. In the context of stellar flares discovery, we exploit the HMM framework by allowing the light curve of a star to be in one of three states at any given time step: Quiet, Firing, or Decaying. This three state HMM formulation is designed to enable straightforward identification of stellar flares, their duration, and associated uncertainty. This is crucial for estimating the flare's energy, and is useful for studies of stellar flare energy distributions. We combine our HMM with a celerite model that accounts for quasi periodic stellar oscillations. Through an injection recovery experiment, we demonstrate and evaluate the ability of our method to detect and characterize flares in stellar time series. We also show that the proposed HMM flags fainter and lower energy flares more easily than traditional sigma clipping methods. Lastly, we visually demonstrate that simultaneously conducting detrending and flare detection can mitigate biased estimations arising in multistage modelling approaches. Thus, this method paves a new way to calculating stellar flare energy. We conclude with an example application to one star observed by TESS, showing how the HMM compares with sigma clipping when using real data.

astro-ph.SR↗

arXiv2024

Estimating sparse direct effects in multivariate regression with the spike-and-slab LASSO

The multivariate regression interpretation of the Gaussian chain graph model simultaneously parametrizes (i) the direct effects of $p$ predictors on $q$ outcomes and (ii) the residual partial covariances between pairs of outcomes. We introduce a new method for fitting sparse Gaussian chain graph models with spike-and-slab LASSO (SSL) priors. We develop an Expectation Conditional Maximization algorithm to obtain sparse estimates of the $p \times q$ matrix of direct effects and the $q \times q$ residual precision matrix. Our algorithm iteratively solves a sequence of penalized maximum likelihood problems with self-adaptive penalties that gradually filter out negligible regression coefficients and partial covariances. Because it adaptively penalizes individual model parameters, our method is seen to outperform fixed-penalty competitors on simulated data. We establish the posterior contraction rate for our model, buttressing our method's excellent empirical performance with strong theoretical guarantees. Using our method, we estimated the direct effects of diet and residence type on the composition of the gut microbiome of elderly adults.

stat.ME↗

arXiv2024

Double trouble: Predicting new variant counts across two heterogeneous populations

Collecting genomics data across multiple heterogeneous populations (e.g., across different cancer types) has the potential to improve our understanding of disease. Despite sequencing advances, though, resources often remain a constraint when gathering data. So it would be useful for experimental design if experimenters with access to a pilot study could predict the number of new variants they might expect to find in a follow-up study: both the number of new variants shared between the populations and the total across the populations. While many authors have developed prediction methods for the single-population case, we show that these predictions can fare poorly across multiple populations that are heterogeneous. We prove that, surprisingly, a natural extension of a state-of-the-art single-population predictor to multiple populations fails for fundamental reasons. We provide the first predictor for the number of new shared variants and new total variants that can handle heterogeneity in multiple populations. We show that our proposed method works well empirically using real cancer and population genetics data.

stat.ME↗

arXiv2023

The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models

Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the design, the effect of the experiment and prior knowledge about the effect. Estimation of the precision matrix is a fundamental task to infer biological graphical structures like microbial networks. We compare the marginal posterior precision of the precision matrix under four priors: flat, conjugate Normal-Wishart, Normal-MGIG and a general independent. Under the flat and conjugate priors, the Laplace-approximated posterior precision is not a function of the design matrix rendering useless any efforts to find an optimal experimental design to infer the precision matrix. In contrast, the Normal-MGIG and general independent priors do allow for the search of optimal experimental designs, yet there is a sharp upper bound on the information that can be extracted from a given experiment. We confirm our theoretical findings via a simulation study comparing i) the KL divergence between prior and posterior and ii) the Stein's loss difference of MAPs between random and no experiment. Our findings provide practical advice for domain scientists conducting experiments to better infer the precision matrix as a representation of a biological network.

stat.ME↗

arXiv2023

Geometric theory on large-scale and local determination of density dependence of a recovering large carnivore population

Density-dependent population growth is a feature of large carnivores like wolves ($\textit{Canis lupus}$), with mechanisms typically attributed to resource (e.g. prey) limitation. Such mechanisms are local phenomena and rely on individuals having access to information, such as prey availability at their location. Using over four decades of wolf population and range expansion data from Wisconsin (USA) wolves, we found that the population not only exhibited density dependence locally but also at landscape scale. Superficially, one may consider space as yet another limiting resource to explain landscape-scale density dependence. However, this view poses an information puzzle: most individuals do not have access to global information such as range-wide habitat availability as they would for local prey availability. How would the population "know" when to slow their range expansion? To understand observed large-scale spatial density dependence, we propose a reaction-diffusion model, first introduced by Fisher and Kolmogorov, with a "travelling wave" solution, wherein the population expands from a core range that quickly achieves local carrying capacity. Early-stage acceleration and later-stage deceleration of population growth can be explained by early elongation of an expanding frontier and a later collision of the expanding frontier with a habitat boundary. Such a process does not require individuals to have global density information. We illustrate our proposal with simulations and spatial visualizations of wolf recolonization in the western Great Lakes region over time relative to habitat suitability. We further synthesize previous studies on wolf habitat selection in the western Great Lakes region and argue that the habitat boundary appeared to be driven by spatial variation in mortality, likely associated with human use of the landscape.

q-bio.PE↗

arXiv2023

Identify local limiting factors of species distribution using min-linear logistic regression

Logistic regression is a commonly used building block in ecological modeling, but its additive structure among environmental predictors often assumes compensatory relationships between predictors, which can lead to problematic results. In reality, the distribution of species is often determined by the least-favored factor, according to von Liebig's Law of the Minimum, which is not addressed in modeling. To address this issue, we introduced the min-linear logistic regression model, which has a built-in minimum structure of competing factors. In our empirical analysis of the distribution of Asiatic black bears ($\textit{Ursus thibetanus}$), we found that the min-linear model performs well compared to other methods and has several advantages. By using the model, we were able to identify ecologically meaningful limiting factors on bear distribution across the survey area. The model's inherent simplicity and interpretability make it a promising tool for extending into other widely used ecological models.

q-bio.QM↗

arXiv2022

Bayesian Chain Graph LASSO Models to Learn Sparse Microbial Networks with Predictors

Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is flawed given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes as it does not represent the adjacency matrix. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence and thus, agrees with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via Bayesian LASSO. In addition, we propose an adaptive extension so that different shrinkage can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting and compositional responses via appropriate hierarchical structure. We apply our model to a human gut and a soil microbial compositional datasets and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data. The CG-LASSO software is available as an R package at https://github.com/YunyiShen/CAR-LASSO.

stat.AP↗

arXiv2021

CARlasso: An R package for the estimation of sparse microbial networks with predictors

Microbiome data analyses require statistical tools that can simultaneously decode microbes' reactions to the environment and interactions among microbes. We introduce CARlasso, the first user-friendly open-source and publicly available R package to fit a chain graph model for the inference of sparse microbial networks that represent both interactions among nodes and effects of a set of predictors. Unlike in standard regression approaches, the edges represent the correct conditional structure among responses and predictors that allows the incorporation of prior knowledge from controlled experiments. In addition, CARlasso 1) enforces sparsity in the network via LASSO; 2) allows for an adaptive extension to include different shrinkage to different edges; 3) is computationally inexpensive through an efficient Gibbs sampling algorithm so it can equally handle small and big data; 4) allows for continuous, binary, counting and compositional responses via proper hierarchical structure, and 5) has a similar syntax to lm for ease of use. The package also supports Bayesian graphical LASSO and several of its hierarchical models as well as lower level one-step sampling functions of the CAR-LASSO model for users to extend.

stat.AP↗

arXiv2016

The $\mathrm{GL}_n$-Connes-Marcolli Systems

In this paper, we generalize the results of Laca, Larsen, and Neshveyev on the $\mathrm{GL}_2$-Connes-Marcolli system to the $\mathrm{GL}_n$ systems. We introduce the $\mathrm{GL}_n$-Connes-Marcolli systems and discuss the question of the existence and the classification of KMS equilibrium states at different inverse temperatures $β$. In particular, using an ergodicity argument, we prove that in the range $n-1 <β\leq n$, there is only one KMS state. We show that there are no KMS states for $β n$.

math.OA↗

arXiv2014

Motives of Noncommutative Tori

In this article, we propose a way of seeing the noncommutative tori in the category of noncommutative motives. As an algebra, the noncommutative torus is lack the smoothness property required to define a noncomutative motive. Thus, instead of working with the algebra, we work with the category of holomorphic bundles. It is known that these are related to the coherent sheaves of an elliptic curve. We describe the cyclic homology of the category of holomorphic bundle on a noncommutative torus. We then introduce a notion of (weak) t-structure in dg categories. By applying the t-structure to a noncommutative torus, we show that it induces a decomposition of the motivic Galois group of the Tannakian subcategory generated by the auxiliary elliptic curve.

math.AG↗