AIMC Topic: Benchmarking

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NPI-GNN: Predicting ncRNA-protein interactions with deep graph neural networks.

Briefings in bioinformatics Sep 2, 2021
Noncoding RNAs (ncRNAs) play crucial roles in many biological processes. Experimental methods for identifying ncRNA-protein interactions (NPIs) are always costly and time-consuming. Many computational approaches have been developed as alternative way...
Internet Benchmarking Datasets as Topic RNA, Untranslated Deep Learning Protein Binding Proteins Humans Software Sensitivity and Specificity
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Evaluation of machine learning approaches for cell-type identification from single-cell transcriptomics data.

Briefings in bioinformatics Sep 2, 2021
Single-cell transcriptomics technologies have vast potential in advancing our understanding of cellular heterogeneity in complex tissues. While methods to interpret single-cell transcriptomics data are developing rapidly, challenges in most analysis ...
Support Vector Machine Lymphocytes, Tumor-Infiltrating Benchmarking Datasets as Topic Single-Cell Analysis Mice Logistic Models Pancreas Humans Cells, Cultured Phenotype Brain Animals Leukocytes, Mononuclear Transcriptome
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Anticancer peptides prediction with deep representation learning features.

Briefings in bioinformatics Sep 2, 2021
Anticancer peptides constitute one of the most promising therapeutic agents for combating common human cancers. Using wet experiments to verify whether a peptide displays anticancer characteristics is time-consuming and costly. Hence, in this study, ...
Neoplasms Peptides Drug Discovery Antineoplastic Agents Humans Neural Networks, Computer Computer Simulation Amino Acid Sequence Deep Learning Computational Biology Benchmarking
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Identification of haploinsufficient genes from epigenomic data using deep forest.

Briefings in bioinformatics Sep 2, 2021
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...
Neurodevelopmental Disorders Haploinsufficiency Deep Learning Promoter Regions, Genetic Epigenesis, Genetic Histones Humans Decision Trees Enhancer Elements, Genetic Discriminant Analysis Software Internet Neoplasms Benchmarking Alleles Genome, Human
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DeepCNV: a deep learning approach for authenticating copy number variations.

Briefings in bioinformatics Sep 2, 2021
Copy number variations (CNVs) are an important class of variations contributing to the pathogenesis of many disease phenotypes. Detecting CNVs from genomic data remains difficult, and the most currently applied methods suffer from an unacceptably hig...
Humans Deep Learning Datasets as Topic Genome, Human False Positive Reactions Disease ROC Curve DNA Copy Number Variations Area Under Curve Benchmarking
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PharmKG: a dedicated knowledge graph benchmark for bomedical data mining.

Briefings in bioinformatics Jul 20, 2021
Biomedical knowledge graphs (KGs), which can help with the understanding of complex biological systems and pathologies, have begun to play a critical role in medical practice and research. However, challenges remain in their embedding and use due to ...
Software Biomedical Research Benchmarking Data Mining Semantics Humans Neural Networks, Computer
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Merged Affinity Network Association Clustering: Joint multi-omic/clinical clustering to identify disease endotypes.

Cell reports Apr 13, 2021
Although clinical and laboratory data have long been used to guide medical practice, this information is rarely integrated with multi-omic data to identify endotypes. We present Merged Affinity Network Association Clustering (MANAclust), a coding-fre...
Feces Proteomics Cluster Analysis Atlases as Topic Unsupervised Machine Learning Female Epigenome Nasal Cavity Case-Control Studies Benchmarking Adult Datasets as Topic Humans Adolescent Asthma Microbiota Middle Aged Precision Medicine Gene Expression Regulation Child, Preschool Male Allergens Gene Expression Profiling Child Transcriptome
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The Machines Are Coming: Implications for Image Reading Centers of the Future.

Ophthalmology Jun 1, 2020
Humans Deep Learning Tomography, Optical Coherence Benchmarking Retina
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ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data.

GigaScience Apr 1, 2020
BACKGROUND: Classification algorithms assign observations to groups based on patterns in data. The machine-learning community have developed myriad classification algorithms, which are used in diverse life science research domains. Algorithm choice c...
Humans Machine Learning Benchmarking Software Algorithms
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Quantitative Assessment of the Effects of Compression on Deep Learning in Digital Pathology Image Analysis.

JCO clinical cancer informatics Mar 1, 2020
PURPOSE: Deep learning (DL), a class of approaches involving self-learned discriminative features, is increasingly being applied to digital pathology (DP) images for tasks such as disease identification and segmentation of tissue primitives (eg, nucl...
Quality Control Deep Learning Data Compression Humans Image Interpretation, Computer-Assisted Pathology, Clinical ROC Curve Observer Variation Algorithms Telepathology Signal Processing, Computer-Assisted Neoplasms Benchmarking
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