dimensionality reduction

Agentic AI enables cell segmentation-free cell-type inference and cell-type-guided cell segmentation in spatial transcriptomics

This paper introduces SSAF-T, a segmentation-free framework for cell-type inference in spatial transcriptomics that avoids cell segmentation and enables accurate cell-type-guided segmentation.

Maximum Likelihood Localization Maps

This paper introduces a non-iterative method to create molecular probability maps from single-molecule localization data, preserving positional likelihood without coordinate-based rendering.

Towards a foundation model for raw nanopore signal through discrete tokenization

This paper introduces Brieno, a self-supervised model for raw nanopore signals that improves read classification and methylation detection without reference genomes.

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

RoDPAA integrates multi-view microbiome data using dissimilarity-based principal angle analysis, recovering shared structure in IBD cohorts where log-ratio methods failed.

The C. elegans Connectome Toolbox: an open, extensible framework for multimodal connectomic data integration and analysis

The paper introduces the C. elegans Connectome Toolbox, a framework for integrating and analyzing multimodal connectomic data, enabling comparison across datasets and modalities.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Deep Recovery of Effective Migration Surfaces

This paper introduces dreems, a graph neural network that efficiently estimates effective migration surfaces from genetic data, achieving lower error and faster computation than existing methods.

Light-sheet fluorescence microscopy of optically cleared human head-and-neck organs: three-dimensional tissue assessment and histological correlation

This study uses optical clearing and light-sheet fluorescence microscopy to visualize 3D microanatomy of human head-and-neck tissues and correlate it with conventional histology.

PHATE-Derived Ancestry Coordinates Capture Continuous Population Structure in Human Genomic Data

This paper shows PHATE can better capture continuous population structure in genomic data than PCA or UMAP by tuning scale and balancing populations.

PhenoMe: An interactive AI framework for interpretable, microscopy-driven phenotyping

PhenoMe provides an open-source framework for analyzing microscopy images using foundation model-derived embeddings and experimental metadata to enable phenotyping and data exploration.

NeuralFieldManifold: Uncovering the Manifold Geometry of Local Field Potentials

This paper introduces a geometric framework for analyzing local field potentials (LFPs) by modeling their dynamics as low-dimensional K-tori and validates it across neural datasets.

A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin

MUTUAL enables cross-modality analysis between transcriptome and chromatin by learning a shared RNA-ATAC space from multiome data without refitting.

Low-pass filtering revisited: ramped phase randomization for cryo-EM map comparison and data augmentation

This paper introduces ramped phase randomization to improve cryo-EM map comparison and data augmentation by reducing fine-scale detail while preserving low-frequency content and enhancing machine learning performance.

RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease

The paper evaluates segmentation methods for reconstructing cell-like profiles from spatial transcriptomics data but finds no reliable method under the given constraints.

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

MiniMAP: An automatic pipeline for paediatric lower limb musculoskeletal model generation

MiniMAP generates custom paediatric musculoskeletal models using CT data and demographic factors, achieving accurate bone geometry predictions with minimal error.

NeuroPack: Advanced Learnable Packaging Toolkit Towards Ultra-High Compression Ratio for Volumetric Neuroimaging

NeuroPack compresses 3D neuroimaging data with high fidelity and ultra-high compression ratios using a hyperprior-driven deep learning toolkit.

Eigenmode decomposition of asymmetries in whole-brain effective connectivity reveals multiscale hierarchical dynamics

This paper decomposes whole-brain effective connectivity to reveal multiscale hierarchical dynamics and their relation to temporal irreversibility and individual-specific signatures.

Algorithmic Geometry Shapes the Biological Meaning of Thalamocortical Structural Covariance

The paper compares five algorithms for deriving structural covariance networks in the thalamocortical system and finds they emphasize different neurobiological aspects based on their mathematical properties.

A comprehensive identification protocol for postcranial bones of Southeast Asian Ruminantia. Part 2: Morphological criteria for small and medium-sized species

This paper develops a morphological identification framework for small and medium-sized ruminant postcranial bones using statistical classifiers to improve taxonomic accuracy in Southeast Asia.

Coordinated Drift of Image Representations in Human EEG

The paper investigates drift in human EEG responses to images across sessions, finding coordinated drift along image identity dimensions and preserved global structure.

Multimodal epi-mode 3D quantitative phase and fluorescence microscopy enables supervised volumetric virtual fluorescence in bulk tissue

This paper introduces a multimodal microscope that uses a cGAN to generate virtual fluorescence images from phase contrast data, enabling virtual histological staining of bulk tissues.

Ground-truth evaluation of sparse autoencoder features on spatial, single-cell and language-model embeddings

The paper evaluates sparse autoencoder features on various embeddings, finding that reproducibility does not guarantee meaningfulness, and proposes reporting features with concept coverage and purity.

Auditory tracking magnitude, temporal alignment, and anatomical distribution during wakefulness and propofol-based anesthesia

The paper examines how auditory tracking changes during wakefulness and propofol anesthesia by analyzing response magnitude, temporal alignment, and anatomical distribution using sEEG data.

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

This paper introduces STRIDE, a sequencing depth-insensitive metric for comparing sparse single-cell Hi-C data, enabling robust analysis of 3D genome organization.

Bayesian in situ point spread function modeling enables high-fidelity three-dimensional nanoscopy in deep tissue

This paper introduces Bayesian in situ PSF modeling to improve 3D nanoscopy in deep tissue by accounting for optical distortions and uncertainties in PSF estimation.

The sex determination gene fruitless is essential for male Aedes aegypti mosquito swarming and attraction to female flight sounds

This study shows that the fruitless gene in male Aedes aegypti mosquitoes is essential for swarming and attraction to female flight sounds, with its disruption causing loss of these behaviors.

ProtCell: a foundation model for single-cell proteomics

ProtCell connects fragmented proteomic profiles, extends information beyond measured panels, and guides more informative measurements.

Rapid changes in wing size and shape during the transition to laboratory conditions in a Neotropical drosophilid

This study tracks rapid wing size and shape changes in Drosophila sturtevanti across generations in lab conditions, showing genetic and environmental influences on morphology.

Universal principles of protein resource allocation among cellular organelles revealed by yeast large-scale absolute quantitative proteomics

This study uses yeast large-scale absolute quantitative proteomics to reveal universal principles of protein resource allocation among cellular organelles and its relationship to physiological parameters and species divergence.