AIMC Topic: Benchmarking

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A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain.

Database : the journal of biological databases and curation Jan 1, 2020
The ability to compare entities within a knowledge graph is a cornerstone technique for several applications, ranging from the integration of heterogeneous data to machine learning. It is of particular importance in the biomedical domain, where seman...
Semantics Biological Ontologies Pattern Recognition, Automated Gene Ontology Humans Benchmarking Knowledge Bases
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Predicting emergency department orders with multilabel machine learning techniques and simulating effects on length of stay.

Journal of the American Medical Informatics Association : JAMIA Dec 1, 2019
OBJECTIVE: Emergency departments (EDs) continue to pursue optimal patient flow without sacrificing quality of care. The speed with which a healthcare provider receives pertinent information, such as results from clinical orders, can impact flow. We s...
Machine Learning Diagnostic Tests, Routine Humans Emergency Service, Hospital Length of Stay Practice Patterns, Physicians' Benchmarking Decision Support Systems, Clinical
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Traditional Chinese medicine clinical records classification with BERT and domain specific corpora.

Journal of the American Medical Informatics Association : JAMIA Dec 1, 2019
Traditional Chinese Medicine (TCM) has been developed for several thousand years and plays a significant role in health care for Chinese people. This paper studies the problem of classifying TCM clinical records into 5 main disease categories in TCM....
Benchmarking Datasets as Topic Medical Records Deep Learning Medicine, Chinese Traditional Natural Language Processing
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ML-Net: multi-label classification of biomedical texts with deep neural networks.

Journal of the American Medical Informatics Association : JAMIA Nov 1, 2019
OBJECTIVE: In multi-label text classification, each textual document is assigned 1 or more labels. As an important task that has broad applications in biomedicine, a number of different computational methods have been proposed. Many of these methods,...
Neural Networks, Computer Machine Learning Deep Learning Data Mining Classification Computational Biology Natural Language Processing Benchmarking
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research Jul 2, 2019
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...
Thermodynamics Mutation, Missense Protein Interaction Mapping Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Datasets as Topic Crystallography, X-Ray Binding Sites Proteins Internet Benchmarking Humans Machine Learning Software Protein Binding
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PrankWeb: a web server for ligand binding site prediction and visualization.

Nucleic acids research Jul 2, 2019
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability cent...
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Benchmarking Amino Acid Sequence Ligands Thermodynamics Protein Interaction Domains and Motifs Datasets as Topic Binding Sites Protein Binding Proteins Internet Humans Machine Learning Software
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NetGO: improving large-scale protein function prediction with massive network information.

Nucleic acids research Jul 2, 2019
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...
Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Benchmarking Plants Amino Acid Sequence Prokaryotic Cells Sequence Alignment Sequence Homology, Amino Acid Sequence Analysis, Protein Computational Biology Proteins Databases, Protein Structure-Activity Relationship Models, Molecular Internet Machine Learning Software Animals Humans
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Cross-type biomedical named entity recognition with deep multi-task learning.

Bioinformatics (Oxford, England) May 15, 2019
MOTIVATION: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for...
Neural Networks, Computer Software Deep Learning Benchmarking
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Regulation of predictive analytics in medicine.

Science (New York, N.Y.) Feb 22, 2019
United States Food and Drug Administration Evidence-Based Medicine Decision Support Techniques United States Benchmarking Humans Artificial Intelligence Algorithms
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Identification of microRNA precursors using reduced and hybrid features.

Molecular bioSystems Jul 25, 2017
MicroRNAs (also called miRNAs) are a group of short non-coding RNA molecules. They play a vital role in the gene expression of transcriptional and post-transcriptional processes. However, abnormality of their expression has been observed in cancer, h...
Datasets as Topic MicroRNAs Humans RNA Precursors Least-Squares Analysis Sequence Analysis, RNA Multifactor Dimensionality Reduction Benchmarking Support Vector Machine
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