AIMC Topic: Benchmarking

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SynEL: A synthetic benchmark for entity linking.

PloS one
Large language models (LLMs) offer significant potential for constructing commonsense knowledge graphs from text, demonstrating adaptability across diverse domains. However, their effectiveness varies significantly with domain-specific language, high...

A Standardized Benchmark for Machine-Learned Molecular Dynamics Using Weighted Ensemble Sampling.

The journal of physical chemistry. B
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by inconsistent...

Benchmarking retrieval-augmented large language models in biomedical NLP: Application, robustness, and self-awareness.

Science advances
To reduce hallucinations in large language models (LLMs), retrieval-augmented LLMs (RALs) retrieve supporting knowledge from external databases. However, their performance on biomedical natural language processing (NLP) tasks remains underexplored. W...

Benchmarking Sequence-Based Compound-Protein Interaction Prediction through Constructing a Debiased Data Set CDPN.

Journal of chemical information and modeling
Accurate prediction of compound-protein interactions (CPIs) is critical for drug discovery, but existing data sets often suffer from biases that hinder model generalization. Here, we first highlighted that over-represented molecular scaffolds and imb...

Benchmarking deep learning methods for biologically conserved single-cell integration.

Genome biology
BACKGROUND: Advancements in single-cell RNA sequencing have enabled the analysis of millions of cells, but integrating such data across samples and methods while mitigating batch effects remains challenging. Deep learning approaches address this by l...

Meta simulation approach for evaluating machine learning method selection in data limited settings.

Scientific reports
Selecting appropriate machine learning (ML) methods for domain-specific tasks remains a persistent challenge, particularly in medicine where datasets are often small, heterogeneous, and incomplete. Traditional benchmarking strategies rely on limited ...

DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks.

Nature communications
Modeling long-range DNA dependencies is crucial for understanding genome structure and function across diverse biological contexts. However, effectively capturing these dependencies, which may span millions of base pairs in tasks such as three-dimens...

Benchmarking YOLOv8 to YOLOv13 for robust hand gesture recognition in human-robot interaction.

Scientific reports
Real-time and accurate hand gesture detection is essential for safe and intuitive Human-Robot Interaction (HRI), enabling robots to interpret non-verbal cues and respond appropriately in dynamic environments. This research evaluates the effectiveness...

Benchmarking diffusion models against state-of-the-art architectures for OCT fluid biomarker segmentation.

PloS one
OBJECTIVES: Retinal diseases, major causes of vision impairment and blindness, are assessed using optical coherence tomography (OCT) scans. Automated report generation for retinal OCT scans, powered by deep learning, can help standardize interpretati...

EasyGeSe - a resource for benchmarking genomic prediction methods.

BMC genomics
BACKGROUND: Genomic prediction is a widely used method to predict phenotypes from genotypic data. Advances in both biological and computer science have enabled the generation of vast amounts of data and the development of new algorithms, specifically...