SearcharxivSearch

arXiv subjects

Shanjun Mao

Publications and source records attributed to Shanjun Mao.

10 recordsLinked to original sources

High-Dimensional Noise to Low-Dimensional Manifolds: A Manifold-Space Diffusion Framework for Degraded Hyperspectral Image Classification

Recently, Hyperspectral Image (HSI) classification has attracted increasing attention in remote sensing. However, HSI data are inherently high-dimensional but low-rank, with discriminative information concentrated on a low-dimensional latent manifold. In real-world remote sensing scenarios, the superposition of multiple degradation factors disrupts this intrinsic manifold structure, driving samples away from their original low-dimensional distribution and introducing substantial redundant and non-discriminative variations. To better handle this challenge, this paper proposes a manifold-space diffusion framework (MSDiff) for robust hyperspectral classification under complex degradation conditions. Specifically, the proposed method first maps high-dimensional, degradation-affected HSI data into a compact low-dimensional manifold through a discriminative spectral-spatial reconstruction task, preserving class semantics and reducing redundant variations. A diffusion-based generative model is then applied to regularize the spectral-spatial distribution within the manifold, enabling progressive refinement and stabilization of latent features against residual degradations. The key advantage of the proposed framework lies in performing diffusion-based distribution modeling directly on the low-dimensional manifold, effectively decoupling degradation-induced disturbances from intrinsic discriminative structures and enhancing representation stability under complex degradations. Experimental results on multiple hyperspectral benchmarks demonstrate consistent performance improvements over state-of-the-art methods under diverse composite degradation settings. The code will be available at https://github.com/yangboxiang1207/MSDiff

cs.CV

Time-Varying Network Driver Estimation (TNDE) Quantifies Stage-Specific Regulatory Effects From Single-Cell Snapshots

Identifying key driver genes governing biological processes such as development and disease progression remains a challenge. While existing methods can reconstruct cellular trajectories or infer static gene regulatory networks (GRNs), they often fail to quantify time-resolved regulatory effects within specific temporal windows. Here, we present Time-varying Network Driver Estimation (TNDE), a computational framework quantifying dynamic gene driver effects from single-cell snapshot data under a linear Markov assumption. TNDE leverages a shared graph attention encoder to preserve the local topological structure of the data. Furthermore, by incorporating partial optimal transport, TNDE accounts for unmatched cells arising from proliferation or apoptosis, thereby enabling trajectory alignment in non-equilibrium processes. Benchmarking on simulated datasets demonstrates that TNDE outperforms existing baseline methods across diverse complex regulatory scenarios. Applied to mouse erythropoiesis data, TNDE identifies stage-specific driver genes, the functional relevance of which is corroborated by biological validation. TNDE offers an effective quantitative tool for dissecting dynamic regulatory mechanisms underlying complex biological processes.

q-bio.MN

Variable Selection for Multi-Source Count Data with Controlled False Discovery Rate

The rapid generation of complex, highly skewed, and zero-inflated multi-source count data poses significant challenges for variable selection, particularly in biomedical domains like tumor development and metabolic dysregulation. To address this, we propose a new variable selection method, Zero-Inflated Poisson-Gamma Simultaneous Knockoff (ZIPG-SK), specifically designed for multi-source count data. Our method leverages a gaussian copula based on the Zero-Inflated Poisson-Gamma (ZIPG) distribution to construct knockoffs that properly account for the properties of count data, including high skewness and zero inflation, while effectively incorporating covariate information. This framework enables the detection of common features across multi-source datasets with guaranteed false discovery rate (FDR) control. Furthermore, we enhance the power of the method by incorporating e-value aggregation, which effectively mitigates the inherent randomness in knockoff generation. Through extensive simulations, we demonstrate that ZIPG-SK significantly outperforms existing methods, achieving superior power across various scenarios. We validate the utility of our method on real-world colorectal cancer (CRC) and type 2 diabetes (T2D) datasets, identifying key variables whose characteristics align with established findings and simultaneously provide new mechanistic insights.

stat.AP

STW-MD: A Novel Spatio-Temporal Weighting and Multi-Step Decision Tree Method for Considering Spatial Heterogeneity in Brain Gene Expression Data

Motivation: Gene expression during brain development or abnormal development is a biological process that is highly dynamic in spatio and temporal. Due to the lack of comprehensive integration of spatial and temporal dimensions of brain gene expression data, previous studies have mainly focused on individual brain regions or a certain developmental stage. Our motivation is to address this gap by incorporating spatio-temporal information to gain a more complete understanding of the mechanisms underlying brain development or disorders associated with abnormal brain development, such as Alzheimer's disease (AD), and to identify potential determinants of response. Results: In this study, we propose a novel two-step framework based on spatial-temporal information weighting and multi-step decision trees. This framework can effectively exploit the spatial similarity and temporal dependence between different stages and different brain regions, and facilitate differential gene analysis in brain regions with high heterogeneity. We focus on two datasets: the AD dataset, which includes gene expression data from early, middle, and late stages, and the brain development dataset, spanning fetal development to adulthood. Our findings highlight the advantages of the proposed framework in discovering gene classes and elucidating their impact on brain development and AD progression across diverse brain regions and stages. These findings align with existing studies and provide insights into the processes of normal and abnormal brain development. Availability: The code of STW-MD is available at https://github.com/tsnm1/STW-MD.

q-bio.QM

LRBmat: A Novel Gut Microbial Interaction and Individual Heterogeneity Inference Method for Colorectal Cancer

Many diseases are considered to be closely related to the changes in the gut microbial community, including colorectal cancer (CRC), which is one of the most common cancers in the world. The diagnostic classification and etiological analysis of CRC are two critical issues worthy of attention. Many methods adopt gut microbiota to solve it, but few of them simultaneously take into account the complex interactions and individual heterogeneity of gut microbiota, which are two common and important issues in genetics and intestinal microbiology, especially in high-dimensional cases. In this paper, a novel method with a Binary matrix based on Logistic Regression (LRBmat) is proposed to deal with the above problem. The binary matrix can directly weakened or avoided the influence of heterogeneity, and also contain the information about gut microbial interactions with any order. Moreover, LRBmat has a powerful generalization, it can combine with any machine learning method and enhance them. The real data analysis on CRC validates the proposed method, which has the best classification performance compared with the state-of-the-art. Furthermore, the association rules extracted from the binary matrix of the real data align well with the biological properties and existing literatures, which are helpful for the etiological analysis of CRC. The source codes for LRBmat are available at https://github.com/tsnm1/LRBmat.

q-bio.QM

Bayesian Inference of Gene Expression Dynamics in Alzheimer Brains

Alzheimer's disease (AD) is a serious neurodegenerative disease consisting of four stages where the illness gets progressively worse. It is of great significance to detect the gene regulatory mechanism as AD progresses and, thus, to help us better understand the causes of AD and find ways to treat or control AD. There are numerous researches to conduct this kind of study. However, the majority of methods are processing region by region of brain, stage by stage of AD, and then compare the results to detect changes. It is unclear how to combine these three dimensions, i.e., gene, region and stage, simultaneously to study gene expression dynamics of AD. This is the motivation of our research. In our study, we propose a statistical model of increments to clarify the relationship between gene expression in adjacent stages, so that we could better estimate the missing data we want and obtain a complete reasonable dynamic regulatory network model. Simulations are conducted to validate the statistical power of our algorithm. Moreover, a real data analysis shows that our method can capture the dynamic gene regulatory relationships among this complex brain data.

stat.ME

A Geometric Statistic for Quantifying Correlation Between Tree-Shaped Datasets

The magnitude of Pearson correlation between two scalar random variables can be visually judged from the two-dimensional scatter plot of an independent and identically distributed sample drawn from the joint distribution of the two variables: the closer the points lie to a straight slanting line, the greater the correlation. To the best of our knowledge, similar graphical representation or geometric quantification of tree correlation does not exist in the literature although tree-shaped datasets are frequently encountered in various fields, such as academic genealogy tree and embryonic development tree. In this paper, we introduce a geometric statistic to both represent tree correlation intuitively and quantify its magnitude precisely. The theoretical properties of the geometric statistic are provided. Large-scale simulations based on various data distributions demonstrate that the geometric statistic is precise in measuring the tree correlation. Its real application on mathematical genealogy trees also demonstrated its usefulness.

stat.ME

A Boosting Method to Face Image Super-resolution

Recently sparse representation has gained great success in face image super-resolution. The conventional sparsity-based methods enforce sparse coding on face image patches and the representation fidelity is measured by $\ell_{2}$-norm. Such a sparse coding model regularizes all facial patches equally, which however ignores distinct natures of different facial patches for image reconstruction. In this paper, we propose a new weighted-patch super-resolution method based on AdaBoost. Specifically, in each iteration of the AdaBoost operation, each facial patch is weighted automatically according to the performance of the model on it, so as to highlight those patches that are more critical for improving the reconstruction power in next step. In this way, through the AdaBoost training procedure, we can focus more on the patches (face regions) with richer information. Various experimental results on standard face database show that our proposed method outperforms state-of-the-art methods in terms of both objective metrics and visual quality.

cs.CV

A Bayesian statistical analysis of stochastic phenotypic plasticity model of cancer cells

The phenotypic plasticity of cancer cells has received special attention in recent years. Even though related models have been widely studied in terms of mathematical properties, a thorough statistical analysis on parameter estimation and model selection is still very lacking. In this study, we present a Bayesian approach on the relative frequencies of cancer stem cells (CSCs). Both Gibbs sampling and Metropolis-Hastings (MH) algorithm are used to perform point and interval estimations of cell-state transition rates between CSCs and non-CSCs. Extensive simulations demonstrate the validity of our model and algorithm. By applying this method to a published data on SW620 colon cancer cell line, the model selection favors the phenotypic plasticity model, relative to conventional hierarchical model of cancer cells. Moreover, it is found that the initial state of CSCs after cell sorting significantly influences the occurrence of phenotypic plasticity.

q-bio.CB

Control of epidemics via social partnership adjustment

Epidemic control is of great importance for human society. Adjusting interacting partners is an effective individualized control strategy. Intuitively, it is done either by shortening the interaction time between susceptible and infected individuals or by increasing the opportunities for contact between susceptible individuals. Here, we provide a comparative study on these two control strategies by establishing an epidemic model with non-uniform stochastic interactions. It seems that the two strategies should be similar, since shortening the interaction time between susceptible and infected individuals somehow increases the chances for contact between susceptible individuals. However, analytical results indicate that the effectiveness of the former strategy sensitively depends on the infectious intensity and the combinations of different interaction rates, whereas the latter one is quite robust and efficient. Simulations are shown in comparison with our analytical predictions. Our work may shed light on the strategic choice of disease control.

q-bio.PE