benchmarking

msengine: Adaptive Open-Source Signal Extraction for HDX MS

msengine improves HDX-MS signal extraction by adaptively adjusting mass and retention-time boundaries, increasing accepted targets and reducing processing time.

Stage-specific proteomic signatures of synaptopathy in Alzheimers disease

The paper identifies stage-specific synaptic proteomic signatures in Alzheimer's disease and links them to plasma proteins associated with disease progression and cognitive decline.

The effects of temporal smoothing and interpolation on EEG microstate parameters, syntax, and our view of resting-state brain dynamics

This paper examines how temporal smoothing and interpolation affect EEG microstate parameters, showing that strong smoothing alters brain dynamics and recommends avoiding intense smoothing to preserve accurate representations.

LLM-powered automatic scoring tools for memory recall

This paper introduces an LLM-powered pipeline for automatically scoring free recall of naturalistic stimuli, achieving high agreement with human raters and low cost.

CADENCE: Open-source software for signal conditioning, feature extraction, visualization and analysis of cardiac optical mapping data

CADENCE is an open-source MATLAB-based tool for processing cardiac optical mapping data, offering end-to-end analysis with features for denoising, conduction velocity, alternans, and rotor detection across multiple species and tissue types.

Mechanisms Matter: Transportability of Cellular Perturbation Effects

The paper shows deep learning models struggle to generalize cellular perturbation responses across contexts, highlighting the importance of causal mechanisms over distributional similarity.

Quantifying performance inflation from hidden sample dependence in biomedical image classification benchmarks

The paper quantifies how increasing train-test sample relatedness inflates classification performance in biomedical image benchmarks using a microscopy dataset.

Impaired astrocytic Cx43 syncytial network in lateral habenula affects synaptic connectivity and drives adolescent stress-induced depression

This study identifies impaired astrocytic Cx43 syncytial networks in the lateral habenula as a driver of adolescent stress-induced depression through disrupted synaptic connectivity and neuronal function.

Reduction of complex dynamic touch information to a single stable perceptual feature

The paper investigates how hardness perception from brief taps is influenced by spectral energy and frequency cues, finding that spectral energy is a robust but not complete cue for material identification.

SpatialOmicsLab: an integrated research environment for AI co-scientists in spatial transcriptomics

SpatialOmicsLab provides an integrated environment with AI tools for spatial transcriptomics analysis, outperforming expert workflows in multiple tasks.

RASTRO: Branching Point Decision-Making in Unitig Graphs

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

Exploring noise in TCR specificity data through supervised learning

This paper introduces a supervised learning denoising method to identify low-quality labels in TCR specificity data, improving model reliability by filtering noisy examples.

Reliable extraction of clinical-trial evidence with provenance, verification, and targeted review

The paper evaluates EviSearch, a clinical evidence-curation system, showing high accuracy and improved results with targeted review.

Charting Cervical Spinal Cord Morphometry Across the Lifespan

The paper generates lifespan normative charts for cervical spinal cord morphometry using MRI data, revealing non-linear changes and sex differences across ages 0-100.

Genotype-dependent behavioral signatures of opioid withdrawal revealed by automated behavioral quantification

This study uses automated behavioral quantification to show that opioid withdrawal behaviors vary with genetic background, but severity can still be assessed within strains.

Automated Segmentation and Tractography of Brainstem and Subcortical White Matter

The paper develops an automated pipeline for segmenting and parcellating brainstem and subcortical white matter pathways using diffusion MRI data.

A sunflower FLS2 guides reconstruction of recognition of a Xanthomonas flg22 escape variant across divergent FLS2 receptors

The paper identifies a sunflower FLS2 receptor that recognizes a flg22 escape variant and uses structural and engineering approaches to reconstruct recognition in divergent FLS2 homologues.

Mechanical fidelity of brain tissue phantoms: A comparative experimental characterization of equilibrium and dissipative behavior

This study compares the mechanical behavior of synthetic brain phantoms and porcine brain tissue at different strain rates, identifying limitations in current materials and suggesting improvements.

AXIS: Agentic Extraction and Integration of Simulation Scenarios for Quantitative Systems Pharmacology

AXIS converts published QSP models and their companion publications into executable simulation configurations by integrating entity grounding, scenario extraction, and parameter assignment.

Mapping social relevance in affective scenes: A large-scale multidimensional rating study

The paper presents a multidimensional rating dataset of 296 affective scenes, capturing social and emotional features with high reliability and validity.

Machine-assisted systematic review and meta-analysis of citrus flavonoids in streptozotocin-induced painful diabetic neuropathy

This study uses a machine-assisted approach to conduct a systematic review and meta-analysis of citrus flavonoids' effects on diabetic neuropathic pain in animal models.

PaleoRigor: a bounded research agent with a reproducible evidence trail for paleomicrobiome data processing

PaleoRigor uses a language model with constraints to process paleomicrobiome data, ensuring reproducibility and preventing invalid operations.

Benchmarking longitudinal local centiles for radiographic knee osteoarthritis prognosis

This paper benchmarks longitudinal local centile maps for predicting radiographic knee osteoarthritis progression using MRI data.

Additive-input encoding fails operator-level target-held-out prediction on current Perturb-seq screens

The paper shows that additive-input models fail to generalize in Perturb-seq screens when predicting new perturbation targets.

Continuous Integration and Software Quality in Scientific Software: A Large-Scale Empirical Analysis of GitHub Repositories

This study analyzes GitHub repositories to show that continuous integration and testing improve software quality and academic impact in scientific software.

fuzzyfold: a high-performance framework for stochastic RNA folding kinetics

The paper introduces fuzzyfold, a Rust-based software framework for stochastic RNA folding kinetics, enabling efficient simulation of long RNA molecules and flexible model integration.

When Does a Pathway Score Preserve a Mediated Effect? Aggregation Geometry, Minimax Adequacy, and Gap Inference for High-Dimensional Mediation

The paper analyzes when pathway scores preserve mediated effects in high-dimensional mediation, introducing a minimax adequacy loss and evaluating performance on TCGA lung adenocarcinoma data.

KENT: Fast Pathogen Screening with NVIDIA Jetson Cluster in Resource-Constrained Areas

KENT enables fast metagenomic pathogen screening on low-memory hardware using NVIDIA Jetson Nano clusters, achieving speedups while maintaining accuracy comparable to desktop-based methods.

Application of deep learning and explainable AI-supported medical decision-making for facial phenotyping in genetic syndromes

This study evaluates if explainable AI (XAI) improves diagnostic accuracy and confidence in genetic syndrome recognition using facial images, finding mixed results with AI predictions having greater impact than XAI explanations.

Validated Semantic Scoring Improves Filtering of Generic Concepts from Knowledge-Graphs for Drug Repurposing Queries

This paper introduces a semantic precision score to filter generic concepts from biomedical knowledge graphs, outperforming existing methods in drug repurposing queries.