benchmarking

EEG Pathology Detection via Clinical Concept Bottleneck Models

This paper introduces concept bottleneck models for EEG pathology detection, showing comparable performance to black-box models but with interpretability trade-offs.

Asymmetric inter-kingdom gene transfer and a horizontal transposon invasion in a powdery mildew fungus

The paper identifies recent horizontal DNA transfer events between plants and fungi, revealing asymmetric transfer patterns and dynamic evolutionary fates of transferred sequences.

Localization accuracy in single-molecule fluorescence microscopy

This study compares the accuracy of two single-molecule localization methods in microscopy, finding that MINFLUX significantly outperforms camera-based methods.

Metabolically encoded cell-surface glycoRNA remodeling enhances antitumor immunity

This study shows that tumor cells remodel cell-surface glycoRNA through metabolic reprogramming, impairing immune responses and linking glycoRNA to antitumor immunity and tumor progression.

Direct and indirect effects: estimating the contributions along individual pathways during transient dynamics

The paper introduces two computational methods to estimate pathway-specific effects during transient dynamics and applies them to ecological models to understand population-level dynamics.

Antigen-aware TCR embeddings reveal conserved immune patterns for personalized immune monitoring

TCRmeta integrates antigen specificity with TCR repertoires to enable cross-individual and longitudinal immune monitoring by revealing conserved patterns and technical variation robustness.

The choice of structural template can create apparent links between predicted protein stability and longevity in tetrapods

The paper investigates how structural templates affect apparent links between protein stability predictions and longevity in tetrapods, finding that template choice can create spurious associations.

A spatial transmission model for evaluating interventions during highly pathogenic avian influenza outbreaks

The paper evaluates control measures for avian influenza outbreaks using a spatial transmission model, showing that intervention effectiveness varies with outbreak stage and policy objectives.

CortexDecoder: fMRI-to-image Reconstruction from Cortical Flatmaps

CortexDecoder reconstructs images from fMRI flatmaps using Vision Transformers and SDXL, achieving performance comparable to state-of-the-art methods.

Denoising broadband CARS hyperspectral images on variance-stabilized data: a unified benchmark

This paper benchmarks six hyperspectral denoising methods for BCARS images using variance-stabilized data, finding that CCV offers a balance of speed and accuracy.

Context Shapes Alpha-Band Electrophysiological Signatures Under Psilocybin

The paper examines how naturalistic context affects psilocybin's frequency-specific electrophysiological effects using EEG data from 56 participants.

De novo design of metalloenzymes using Metal Mer

This paper introduces a computational pipeline for de novo metalloenzyme design using Metal Mer, achieving high selectivity and activity in catalytic reactions without directed evolution.

Understanding Performance Plateaus and Representation Collapse in 3D MRI Transformers Trained to Classify Brain Disease

This paper investigates why performance plateaus in 3D MRI transformers for brain disease classification and finds that representation collapse, not task difficulty, causes the plateau.

Cross-species multi-omics integration reveals lung alterations in acute kidney injury across mouse, pig, and human airway organoid models

This paper integrates multi-omics data across species to show AKI-induced lung alterations, identifying conserved pathways and human-validated targets for distant organ failure.

Agreement between Garmin and Ultrahuman wearables and their association with continuous glucose monitoring: an n-of-1 study

This study compares agreement between Garmin and Ultrahuman wearables and their association with continuous glucose monitoring in one adult, finding close agreement on sleep duration but variable heart rate and glucose correlations.

Shared and genus-specific impact of domestication on mammal oral microbiomes revealed through museomics

This study uses dental calculus metagenomics to show that domestication affects oral microbiomes across three mammalian genera, with genus-specific variations observed.

Available time-series of terrestrial animals provide low reliability in population trend estimates

The paper assesses the reliability of population trend estimates from time-series data of terrestrial animals, finding most are too short or noisy to detect meaningful trends.

DecoDiPhy: Deconvolving Phylogenetic Distance Mixtures

DecoDiPhy deconvolves phylogenetic distance mixtures to improve interpretability and downstream analysis in metagenomics.

Grazing versus mowing: productivity and forage quality of mixtures and cultivars of perennial ryegrass

This study compares the productivity and forage quality of perennial ryegrass cultivars and mixtures under different defoliation treatments, finding that grazing affects rankings differently than mechanical cutting.

A high-throughput UAV millimetric imaging pipeline for plant density phenotyping reveals high heritability in wheat-pea sole crops and intercrops.

The paper develops a UAV-based imaging pipeline to predict plant density in wheat and pea crops, showing high heritability across diverse intercropping scenarios.

Psychopharmacological Effects of Cannabidiol in Rodent Models of Autism Spectrum Disorder: A Systematic Review of Behavioral Outcomes, Neurobiological Mechanisms, and Methodological Quality

This review evaluates CBD's effects on rodent ASD models, finding beneficial behavioral and neurobiological outcomes but highlighting methodological limitations.

Constructed Negatives Shape the Evaluation of Sequence-Based Protein--Protein Interaction Models

The paper evaluates how different constructed negative examples affect sequence-based protein-protein interaction models, showing significant variability in performance metrics based on negative construction methods.

Directional coordination along the cortical hierarchy is selectively reorganized in schizophrenia

This study identifies a dynamic directional coordination axis in the cortical hierarchy that is selectively reorganized in schizophrenia, linked to symptoms and cognition.

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

Hidden introns and repeated gains shape the heavily interrupted tRNA genes of Asgard archaea

The paper identifies and corrects missed introns in tRNA genes of Asgard archaea, revealing repeated intron gains and their splicing motif preferences.

Counterfactual effect of Colombian protected areas on multispecies functional connectivity

The paper evaluates the counterfactual effect of Colombian protected areas on multispecies functional connectivity from 2000 to 2022, finding that PAs generally improved connectivity but with varying effectiveness based on pressure and size.

Molecular anatomy of the entorhinal cortex

This study creates a molecular atlas of the mouse entorhinal cortex using snRNAseq and compares it to macaque data, revealing conserved molecular patterns and gradients in neuron subtypes.

A Benchmark of Unsupervised Circadian Phase Inference Methods for Bulk Transcriptomic Data

This study benchmarks unsupervised circadian phase inference methods on bulk transcriptomic data, finding CHIRAL performs best with lower error than other methods.

Non-exonic read content reorganises lncRNA co-expression networks in renal and other cancers

The paper shows that non-exonic read fractions reorganize lncRNA co-expression networks in renal and other cancers, with varying impacts across cancer types.

Photoplethysmography-based glucose estimation with feature selection

This paper estimates glucose levels from PPG signals using feature selection and machine learning, finding modest predictive power but below clinical standards.