AIMC Topic: Software

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iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization.

Bioinformatics (Oxford, England)
MOTIVATION: DNA methylation plays an important role in epigenetic modification, the occurrence, and the development of diseases. Therefore, identification of DNA methylation sites is critical for better understanding and revealing their functional me...

BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions.

Bioinformatics (Oxford, England)
MOTIVATION: Predicting entity relationship can greatly benefit important biomedical problems. Recently, a large amount of biomedical heterogeneous networks (BioHNs) are generated and offer opportunities for developing network-based learning approache...

DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions.

Bioinformatics (Oxford, England)
MOTIVATION: In silico drug-target interaction (DTI) prediction is important for drug discovery and drug repurposing. Approaches to predict DTIs can proceed indirectly, top-down, using phenotypic effects of drugs to identify potential drug targets, or...

CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets-application to peptide-MHC class II binding prediction.

Bioinformatics (Oxford, England)
SUMMARY: The ability to unveil binding patterns in peptide sets has important applications in several biomedical areas, including the development of vaccines. We present an open-source tool, CNN-PepPred, that uses convolutional neural networks to dis...

When Medical Devices Have a Mind of Their Own: The Challenges of Regulating Artificial Intelligence.

American journal of law & medicine
How can an agency like the U.S. Food & Drug Administration ("FDA") effectively regulate software that is constantly learning and adapting to real-world data? Continuously learning algorithms pose significant public health risks if a medical device ca...

Applying and improving AlphaFold at CASP14.

Proteins
We describe the operation and improvement of AlphaFold, the system that was entered by the team AlphaFold2 to the "human" category in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The AlphaFold system entered in CASP14 is ent...

[Design and Implementation of Software Platform for AI-ECG Algorithm Research].

Zhongguo yi liao qi xie za zhi = Chinese journal of medical instrumentation
A software platform for AI-ECG algorithm research is designed and implemented to better serve the research of ECG artificial intelligence classification algorithm and to solve the problem of subjects data information management. Matlab R2019b and MyS...

Glycowork: A Python package for glycan data science and machine learning.

Glycobiology
While glycans are crucial for biological processes, existing analysis modalities make it difficult for researchers with limited computational background to include these diverse carbohydrates into workflows. Here, we present glycowork, an open-source...

Peel learning for pathway-related outcome prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Traditional regression models are limited in outcome prediction due to their parametric nature. Current deep learning methods allow for various effects and interactions and have shown improved performance, but they typically need to be tr...

HEAL: an automated deep learning framework for cancer histopathology image analysis.

Bioinformatics (Oxford, England)
MOTIVATION: Digital pathology supports analysis of histopathological images using deep learning methods at a large-scale. However, applications of deep learning in this area have been limited by the complexities of configuration of the computational ...