AIMC Topic: Software

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Predictive and interpretable models via the stacked elastic net.

Bioinformatics (Oxford, England)
MOTIVATION: Machine learning in the biomedical sciences should ideally provide predictive and interpretable models. When predicting outcomes from clinical or molecular features, applied researchers often want to know which features have effects, whet...

Interest in artificial intelligence for the diagnosis of non-melanoma skin cancer: a survey among French general practitioners.

European journal of dermatology : EJD
General practitioners (GPs) are playing a key role in skin cancer screening. Non-melanoma skin cancer is frequent and difficult to diagnose. We aimed to assess whether GPs are facing difficulties in diagnosing non-pigmented skin tumours (NPSTs) and w...

A neuro-symbolic method for understanding free-text medical evidence.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: We introduce Medical evidence Dependency (MD)-informed attention, a novel neuro-symbolic model for understanding free-text clinical trial publications with generalizability and interpretability.

deepBlink: threshold-independent detection and localization of diffraction-limited spots.

Nucleic acids research
Detection of diffraction-limited spots in single-molecule microscopy images is traditionally performed with mathematical operators designed for idealized spots. This process requires manual tuning of parameters that is time-consuming and not always r...

A graph auto-encoder model for miRNA-disease associations prediction.

Briefings in bioinformatics
Emerging evidence indicates that the abnormal expression of miRNAs involves in the evolution and progression of various human complex diseases. Identifying disease-related miRNAs as new biomarkers can promote the development of disease pathology and ...

ChemGenerator: a web server for generating potential ligands for specific targets.

Briefings in bioinformatics
In drug discovery, one of the most important tasks is to find novel and biologically active molecules. Given that only a tip of iceberg of drugs was founded in nearly one-century's experimental exploration, it shows great significance to use in silic...

A deep learning approach for filtering structural variants in short read sequencing data.

Briefings in bioinformatics
Short read whole genome sequencing has become widely used to detect structural variants in human genetic studies and clinical practices. However, accurate detection of structural variants is a challenging task. Especially existing structural variant ...

Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations.

Briefings in bioinformatics
Non-coding RNAs (ncRNAs) play crucial roles in multiple biological processes. However, only a few ncRNAs' functions have been well studied. Given the significance of ncRNAs classification for understanding ncRNAs' functions, more and more computation...

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining.

Briefings in bioinformatics
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 ...