dimensionality reduction

Shared Representation Discovery for Multi-Subject Neural Data Analysis

This paper introduces ShaReD, a method for analyzing multi-subject neural data without requiring temporal or anatomical alignment, and demonstrates its effectiveness on synthetic and animal data.

ResiRuler: A Toolkit for Visualizing Residue-Residue Distances and Structural Changes in Biomolecular Models

ResiRuler quantifies and visualizes residue-residue distances and structural changes across protein ensembles to identify conformational differences.

Bridging Biomedical Atlas Ecosystem: Cross-Atlas Alignment And Scalable Tissue Specimen Registration

The paper introduces methods to scale up the Human Reference Atlas by aligning tissue datasets across reference systems and using millitomes for bulk registration.

Spectral projectors of temporally integrated functional brain networks

The paper develops a spectral-geometric framework to analyze functional brain networks, showing that temporal integration and projection order affect network structure representation.

An AI-assisted platform for quantitative histopathological analysis in interstitial lung disease

FibroSight is a deep learning platform that quantifies lung remodeling in ILD histology, showing strong correlation with expert scoring and distinguishing fibrotic from inflammatory changes.

Beyond the Default: Optimizing Molecular Networking with arteMIS

The paper introduces arteMIS, a framework for optimizing molecular network parameters in metabolomics, showing improved network quality over default settings.

Inverse-scattering in biological samples via beam-propagation

This paper demonstrates that using an amplitude-only cost function with angular and defocus diversity in multi-slice beam propagation improves inverse-scattering reconstruction quality in biological samples.

Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data

Celldega provides an open-source toolkit for scalable, interactive visualization and analysis of spatial-omics data, supporting the entire analysis lifecycle from quality control to public sharing.

MOFTy: Multimodal Gaussian Process Factor Analysis with Numerical Information Field Theory

MOFTy disentangles spatial structures and recovers cross-modal patterns in multi-omics data by separating smooth gradients from fine-scale heterogeneity.

From Consensus to Individual Differences: Typicality Links Brain and Behavior Across Naturalistic Contexts

This paper introduces typicality as a framework to link individual differences in behavior to neural systems by analyzing naturalistic movie viewing and behavioral tasks.

Mapping Whole-Brain Factors of Microstructural Similarity with Diffusion MRI

The paper identifies shared dimensions of variation in diffusion MRI statistics and maps spatial patterns of microstructural similarity across the brain.

Biomarker Fidelity Score - A Quantitative Framework for Individual-Level Validation of Explainability Methods in 3D Alzheimer's Disease MRI Classification

The paper introduces a quantitative framework to validate explainability methods in Alzheimer's disease MRI classification at the individual level using biomarker-aligned spatial overlap scores.

Pharmacobehavioral space of MoSeq syllables significantly overlaps with scalar locomotion features

The paper reanalyzes MoSeq data and finds that the performance advantage of MoSeq syllables over scalar features depends on analytical methods and dataset structure, not inherent superiority.

SketchDNA: A GUI-Enabled Toolkit for Multiscale Modeling of Topological DNA Structures

SketchDNA provides a GUI tool for creating multiscale DNA models, enabling simulations of topological DNA structures and their dynamics.

Brain morphological pattern is associated with the presence, severity, and transition of transdiagnostic psychiatric disorders in preadolescents

In 8,672 ABCD preadolescents, one canonical-correlation-derived brain morphology variate links higher cognition with lower psychopathology and tracks cumulative psychiatric diagnoses and 2-year diagnostic transitions.

Sparse Autoencoders Reveal Structural and Family-level Features in BiRNA-BERT

The paper uses sparse autoencoders to analyze BiRNA-BERT, revealing biologically meaningful features and improving RNA-type classification.

bulk2scDiff: A Pseudobulk-Conditioned Diffusion Model for Bulk-to-Single-Cell RNASeq Generation

bulk2scDiff generates single-cell RNA-seq data from bulk profiles using a diffusion model, showing good reconstruction of cell populations in cancer datasets.

Maturation of Sleep EEG Complexity in Preterm Newborns: Insights from Lempel-Ziv and Joint Lempel-Ziv Analyses

This study uses Lempel-Ziv Complexity metrics to analyze EEG data from preterm infants, showing how sleep state complexity and maturation change with postmenstrual age.

Dynamic Quantum Clustering of Glioma RNA-seq Reveals Interpretable Tumor States Linked to Diagnosis and Survival

The paper applies Dynamic Quantum Clustering to glioma RNA-seq data to identify tumor states linked to diagnosis and survival without using clinical labels.

Dynamic fusion of structural and functional connectivity via joint connectivity matrix ICA

This paper introduces a dynamic fusion framework to integrate structural and functional connectivity data, revealing differences between schizophrenia patients and controls.

FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean

This study evaluates FP8 quantization in GenomeOcean, finding it preserves biological fidelity while improving efficiency, but throughput gains fall short of theoretical limits.

Proteoform Barcode: An Intuitive Visualization Framework for Top-Down Proteomics

The paper introduces a visualization framework for top-down proteomics data, called proteoform barcode, which displays proteoform abundance and functional information, enabling disease diagnosis.

dbverse scales spatial omics analysis with embedded analytical databases

dbverse enables efficient analysis of large spatial omics datasets by using embedded databases, outperforming traditional methods in runtime.

Streamlining large-scale high-resolution electron tomography with VolWeaver

The paper optimizes a transmission electron tomography workflow for malaria parasites and introduces VolWeaver to integrate high-resolution tomographic data into serial section volume reconstructions.

SpatialMOC: Accurate reconstruction of spatial multi-omics landscapes through cross-modality prediction

SpatialMOC reconstructs missing spatial multi-omics data by integrating spatial context and cross-modality learning, outperforming existing methods across multiple tissues and modalities.

Zone Equalisation Normalisation For Improved Alignment of Epigenetic Signal

This paper introduces ZEN, a normalization method for genomic data that reduces technical noise while preserving biological signals, improving alignment across different experimental platforms.

IsoMobil: Resolving Molecular Ambiguity in Mass Spectrometry-based Spatial Omics Through Ion Mobility

IsoMobil reduces high-dimensional ion mobility mass spectrometry data by grouping isotopologues, improving interpretation at the molecular-species level.

Principal Genes: A PCA-based approach to highly variable genes selection for scRNA-Seq analysis

This paper introduces a PCA-based method for selecting highly variable genes in scRNA-Seq data, showing it is comparable or better than dispersion-based methods and faster.

Learning Discrete Cell and Niche Codes from Spatial Transcriptomics Using Dual Residual Vector Quantization

SQUINT learns discrete cell and niche codes from spatial transcriptomics data using residual vector quantization, outperforming baselines in identification and cross-section integration.

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.