hSNMF: Hybrid Spatially Regularized NMF for Image-Derived Spatial Transcriptomics

High-resolution spatial transcriptomics platforms, such as Xenium, generate single-cell images that capture both molecular and spatial context, but their extremely high dimensionality poses major challenges for representation learning and clustering. In this study, we analyze data from the Xenium platform, which captures high-resolution images of tumor microarray (TMA) tissues and converts them into cell-by-gene matrices suitable for computational analysis. We benchmark and extend nonnegative matrix factorization (NMF) for spatial transcriptomics by introducing two spatially regularized variants. First, we propose Spatial NMF (SNMF), a lightweight baseline that enforces local spatial smoothness by diffusing each cell's NMF factor vector over its spatial neighborhood. Second, we introduce Hybrid Spatial NMF (hSNMF), which performs spatially regularized NMF followed by Leiden clustering on a hybrid adjacency that integrates spatial proximity (via a contact-radius graph) and transcriptomic similarity through a tunable mixing parameter alpha. Evaluated on a cholangiocarcinoma dataset, SNMF and hSNMF achieve markedly improved spatial compactness (CHAOS < 0.004, Moran's I > 0.96), greater cluster separability (Silhouette > 0.12, DBI < 1.8), and higher biological coherence (CMC and enrichment) compared to other spatial baselines. Availability and implementation: https://github.com/ishtyaqmahmud/hSNMF

Scalable Transit Delay Prediction at City Scale: A Systematic Approach with Multi-Resolution Feature Engineering and Deep Learning

Urban bus transit agencies need reliable, network-wide delay predictions to provide accurate arrival information to passengers and support real-time operational control. Accurate predictions help passengers plan their trips, reduce waiting time, and allow operations staff to adjust headways, dispatch extra vehicles, and manage disruptions. Although real-time feeds such as GTFS-Realtime (GTFS-RT) are now widely available, most existing delay prediction systems handle only a few routes, depend on hand-crafted features, and offer little guidance on how to design a scalable, reusable architecture. We present a city-scale prediction pipeline that combines multi-resolution feature engineering, dimensionality reduction, and deep learning. The framework generates 1,683 spatiotemporal features by exploring 23 aggregation combinations over H3 cells, routes, segments, and temporal patterns, and compresses them into 83 components using Adaptive PCA while preserving 95% of the variance. To avoid the "giant cluster" problem that occurs when dense urban areas fall into a single H3 region, we introduce a hybrid H3+topology clustering method that yields 12 balanced route clusters (coefficient of variation 0.608) and enables efficient distributed training. We compare five model architectures on six months of bus operations from the Société de transport de Montréal (STM) network in Montréal. A global LSTM with cluster-aware features achieves the best trade-off between accuracy and efficiency, outperforming transformer models by 18 to 52% while using 275 times fewer parameters. We also report multi-level evaluation at the elementary segment, segment, and trip level with walk-forward validation and latency analysis, showing that the proposed pipeline is suitable for real-time, city-scale deployment and can be reused for other networks with limited adaptation.

Efficient Imputation for Patch-based Missing Single-cell Data via Cluster-regularized Optimal Transport

Missing data in single-cell sequencing datasets poses significant challenges for extracting meaningful biological insights. However, existing imputation approaches, which often assume uniformity and data completeness, struggle to address cases with large patches of missing data. In this paper, we present CROT, an optimal transport-based imputation algorithm designed to handle patch-based missing data in tabular formats. Our approach effectively captures the underlying data structure in the presence of significant missingness. Notably, it achieves superior imputation accuracy while significantly reducing runtime, demonstrating its scalability and efficiency for large-scale datasets. This work introduces a robust solution for imputation in heterogeneous, high-dimensional datasets with structured data absence, addressing critical challenges in both biological and clinical data analysis. Our code is available at Anomalous Github.

Latent Causal Diffusions for Single-Cell Perturbation Modeling

Perturbation screens hold the potential to systematically map regulatory processes at single-cell resolution, yet modeling and predicting transcriptome-wide responses to perturbations remains a major computational challenge. Existing methods often underperform simple baselines, fail to disentangle measurement noise from biological signal, and provide limited insight into the causal structure governing cellular responses. Here, we present the latent causal diffusion (LCD), a generative model that frames single-cell gene expression as a stationary diffusion process observed under measurement noise. LCD outperforms established approaches in predicting the distributional shifts of unseen perturbation combinations in single-cell RNA-sequencing screens while simultaneously learning a mechanistic dynamical system of gene regulation. To interpret these learned dynamics, we develop an approach we call causal linearization via perturbation responses (CLIPR), which yields an approximation of the direct causal effects between all genes modeled by the diffusion. CLIPR provably identifies causal effects under a linear drift assumption and recovers causal structure in both simulated systems and a genome-wide perturbation screen, where it clusters genes into coherent functional modules and resolves causal relationships that standard differential expression analysis cannot. The LCD-CLIPR framework bridges generative modeling with causal inference to predict unseen perturbation effects and map the underlying regulatory mechanisms of the transcriptome.

Open World Knowledge Aided Single-Cell Foundation Model with Robust Cross-Modal Cell-Language Pre-training

Recent advancements in single-cell multi-omics, particularly RNA-seq, have provided profound insights into cellular heterogeneity and gene regulation. While pre-trained language model (PLM) paradigm based single-cell foundation models have shown promise, they remain constrained by insufficient integration of in-depth individual profiles and neglecting the influence of noise within multi-modal data. To address both issues, we propose an Open-world Language Knowledge-Aided Robust Single-Cell Foundation Model (OKR-CELL). It is built based on a cross-modal Cell-Language pre-training framework, which comprises two key innovations: (1) leveraging Large Language Models (LLMs) based workflow with retrieval-augmented generation (RAG) enriches cell textual descriptions using open-world knowledge; (2) devising a Cross-modal Robust Alignment (CRA) objective that incorporates sample reliability assessment, curriculum learning, and coupled momentum contrastive learning to strengthen the model's resistance to noisy data. After pretraining on 32M cell-text pairs, OKR-CELL obtains cutting-edge results across 6 evaluation tasks. Beyond standard benchmarks such as cell clustering, cell-type annotation, batch-effect correction, and few-shot annotation, the model also demonstrates superior performance in broader multi-modal applications, including zero-shot cell-type annotation and bidirectional cell-text retrieval.

Statistical Inference for Fuzzy Clustering

Clustering is a central tool in biomedical research for discovering heterogeneous patient subpopulations, where group boundaries are often diffuse rather than sharply separated. Traditional methods produce hard partitions, whereas soft clustering methods such as fuzzy $c$-means (FCM) allow mixed memberships and better capture uncertainty and gradual transitions. Despite the widespread use of FCM, principled statistical inference for fuzzy clustering remains limited. We develop a new framework for weighted fuzzy $c$-means (WFCM) for settings with potential cluster size imbalance. Cluster-specific weights rebalance the classical FCM criterion so that smaller clusters are not overwhelmed by dominant groups, and the weighted objective induces a normalized density model with scale parameter $σ$ and fuzziness parameter $m$. Estimation is performed via a blockwise majorize--minimize (MM) procedure that alternates closed-form membership and centroid updates with likelihood-based updates of $(σ,\bw)$. The intractable normalizing constant is approximated by importance sampling using a data-adaptive Gaussian mixture proposal. We further provide likelihood ratio tests for comparing cluster centers and bootstrap-based confidence intervals. We establish consistency and asymptotic normality of the maximum likelihood estimator, validate the method through simulations, and illustrate it using single-cell RNA-seq and Alzheimer disease Neuroimaging Initiative (ADNI) data. These applications demonstrate stable uncertainty quantification and biologically meaningful soft memberships, ranging from well-separated cell populations under imbalance to a graded AD versus non-AD continuum consistent with disease progression.

Refinement Contrastive Learning of Cell-Gene Associations for Unsupervised Cell Type Identification

Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic cellular structure and ignore the pivotal role of cell-gene associations, which limits their ability to distinguish closely related cell types. To this end, we propose a Refinement Contrastive Learning framework (scRCL) that explicitly incorporates cell-gene interactions to derive more informative representations. Specifically, we introduce two contrastive distribution alignment components that reveal reliable intrinsic cellular structures by effectively exploiting cell-cell structural relationships. Additionally, we develop a refinement module that integrates gene-correlation structure learning to enhance cell embeddings by capturing underlying cell-gene associations. This module strengthens connections between cells and their associated genes, refining the representation learning to exploiting biologically meaningful relationships. Extensive experiments on several single-cell RNA-seq and spatial transcriptomics benchmark datasets demonstrate that our method consistently outperforms state-of-the-art baselines in cell-type identification accuracy. Moreover, downstream biological analyses confirm that the recovered cell populations exhibit coherent gene-expression signatures, further validating the biological relevance of our approach. The code is available at https://github.com/THPengL/scRCL.

Configurable γ Photon Spectrometer to Enable Precision Radioguided Tumor Resection

Surgical tumor resection aims to remove all cancer cells in the tumor margin and at centimeter-scale depths below the tissue surface. During surgery, microscopic clusters of disease are intraoperatively difficult to visualize and are often left behind, significantly increasing the risk of cancer recurrence. Radioguided surgery (RGS) has shown the ability to selectively tag cancer cells with gamma (γ) photon emitting radioisotopes to identify them, but require a mm-scale γ photon spectrometer to localize the position of these cells in the tissue margin (i.e., a function of incident γ photon energy) with high specificity. Here we present a 9.9 mm2 integrated circuit (IC)-based γ spectrometer implemented in 180 nm CMOS, to enable the measurement of single γ photons and their incident energy with sub-keV energy resolution. We use small 2 2 um reverse-biased diodes that have low depletion region capacitance, and therefore produce millivolt-scale voltage signals in response to the small charge generated by incident γ photons. A low-power energy spectrometry method is implemented by measuring the decay time it takes for the generated voltage signal to settle back to DC after a γ detection event, instead of measuring the voltage drop directly. This spectrometry method is implemented in three different pixel architectures that allow for configurable pixel sensitivity, energy-resolution, and energy dynamic range based on the widely heterogenous surgical and patient presentation in RGS. The spectrometer was tested with three common γ-emitting radioisotopes (64Cu, 133Ba, 177Lu), and is able to resolve activities down to 1 uCi with sub-keV energy resolution and 1.315 MeV energy dynamic range, using 5-minute acquisitions.

Multiscale Grassmann Manifolds for Single-Cell Data Analysis

Single-cell data analysis seeks to characterize cellular heterogeneity based on high-dimensional gene expression profiles. Conventional approaches represent each cell as a vector in Euclidean space, which limits their ability to capture intrinsic correlations and multiscale geometric structures. We propose a multiscale framework based on Grassmann manifolds that integrates machine learning with subspace geometry for single-cell data analysis. By generating embeddings under multiple representation scales, the framework combines their features from different geometric views into a unified Grassmann manifold. A power-based scale sampling function is introduced to control the selection of scales and balance in- formation across resolutions. Experiments on nine benchmark single-cell RNA-seq datasets demonstrate that the proposed approach effectively preserves meaningful structures and provides stable clustering performance, particularly for small to medium-sized datasets. These results suggest that Grassmann manifolds offer a coherent and informative foundation for analyzing single cell data.

Clustering by Denoising: Latent plug-and-play diffusion for single-cell data

Single-cell RNA sequencing (scRNA-seq) enables the study of cellular heterogeneity. Yet, clustering accuracy, and with it downstream analyses based on cell labels, remain challenging due to measurement noise and biological variability. In standard latent spaces (e.g., obtained through PCA), data from different cell types can be projected close together, making accurate clustering difficult. We introduce a latent plug-and-play diffusion framework that separates the observation and denoising space. This separation is operationalized through a novel Gibbs sampling procedure: the learned diffusion prior is applied in a low-dimensional latent space to perform denoising, while to steer this process, noise is reintroduced into the original high-dimensional observation space. This unique "input-space steering" ensures the denoising trajectory remains faithful to the original data structure. Our approach offers three key advantages: (1) adaptive noise handling via a tunable balance between prior and observed data; (2) uncertainty quantification through principled uncertainty estimates for downstream analysis; and (3) generalizable denoising by leveraging clean reference data to denoise noisier datasets, and via averaging, improve quality beyond the training set. We evaluate robustness on both synthetic and real single-cell genomics data. Our method improves clustering accuracy on synthetic data across varied noise levels and dataset shifts. On real-world single-cell data, our method demonstrates improved biological coherence in the resulting cell clusters, with cluster boundaries that better align with known cell type markers and developmental trajectories.