AIMC Topic: Software

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MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature.

Bioinformatics (Oxford, England)
SUMMARY: The field of literature-based discovery is growing in step with the volume of literature being produced. From modern natural language processing algorithms to high quality entity tagging, the methods and their impact are developing rapidly. ...

Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition.

Database : the journal of biological databases and curation
High-quality metadata annotations for data hosted in large public repositories are essential for research reproducibility and for conducting fast, powerful and scalable meta-analyses. Currently, a majority of sequencing samples in the National Center...

Modeling multi-species RNA modification through multi-task curriculum learning.

Nucleic acids research
N6-methyladenosine (m6A) is the most pervasive modification in eukaryotic mRNAs. Numerous biological processes are regulated by this critical post-transcriptional mark, such as gene expression, RNA stability, RNA structure and translation. Recently, ...

Large-scale entity representation learning for biomedical relationship extraction.

Bioinformatics (Oxford, England)
MOTIVATION: The automatic extraction of published relationships between molecular entities has important applications in many biomedical fields, ranging from Systems Biology to Personalized Medicine. Existing works focused on extracting relationships...

treeheatr: an R package for interpretable decision tree visualizations.

Bioinformatics (Oxford, England)
SUMMARY: treeheatr is an R package for creating interpretable decision tree visualizations with the data represented as a heatmap at the tree's leaf nodes. The integrated presentation of the tree structure along with an overview of the data efficient...

[Research on Current Situation of Quality Management of Artificial Intelligence Medical Device Enterprises].

Zhongguo yi liao qi xie za zhi = Chinese journal of medical instrumentation
OBJECTIVE: To understand the current situation of artificial intelligence production enterprise quality management system, so as to provide reference basis for the research and standardization of Artificial Intelligence Medical Device (AIMD) product ...

Tractography Processing with the Sparse Closest Point Transform.

Neuroinformatics
We propose a novel approach for processing diffusion MRI tractography datasets using the sparse closest point transform (SCPT). Tractography enables the 3D geometry of white matter pathways to be reconstructed; however, algorithms for processing them...

GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins.

Briefings in bioinformatics
As an important reversible lipid modification, S-palmitoylation mainly occurs at specific cysteine residues in proteins, participates in regulating various biological processes and is associated with human diseases. Besides experimental assays, compu...

Integration and transfer learning of single-cell transcriptomes via cFIT.

Proceedings of the National Academy of Sciences of the United States of America
Large, comprehensive collections of single-cell RNA sequencing (scRNA-seq) datasets have been generated that allow for the full transcriptional characterization of cell types across a wide variety of biological and clinical conditions. As new methods...

Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data.

Molecular biology and evolution
Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. A previous method for achieving this goal, CDROM, employs gene expression distances as proxies for function...