AIMC Topic: Software

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netDx: interpretable patient classification using integrated patient similarity networks.

Molecular systems biology
Patient classification has widespread biomedical and clinical applications, including diagnosis, prognosis, and treatment response prediction. A clinically useful prediction algorithm should be accurate, generalizable, be able to integrate diverse da...

DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.

Cell systems
Systems biology requires not only genome-scale data but also methods to integrate these data into interpretable models. Previously, we developed approaches that organize omics data into a structured hierarchy of cellular components and pathways, call...

Predicting protein-peptide interaction sites using distant protein complexes as structural templates.

Scientific reports
Protein-peptide interactions play an important role in major cellular processes, and are associated with several human diseases. To understand and potentially regulate these cellular function and diseases it is important to know the molecular details...

Interpretable genotype-to-phenotype classifiers with performance guarantees.

Scientific reports
Understanding the relationship between the genome of a cell and its phenotype is a central problem in precision medicine. Nonetheless, genotype-to-phenotype prediction comes with great challenges for machine learning algorithms that limit their use i...

Knowledge Domain and Emerging Trends on Echinococcosis Research: A Scientometric Analysis.

International journal of environmental research and public health
The echinococcosis of humans and animals is a chronic helminthic disease caused by the larva of genus tapeworms. It is a globally distributed disease which is an important socioeconomic and public health problem in many low and middle-income countri...

Deep learning-based super-resolution in coherent imaging systems.

Scientific reports
We present a deep learning framework based on a generative adversarial network (GAN) to perform super-resolution in coherent imaging systems. We demonstrate that this framework can enhance the resolution of both pixel size-limited and diffraction-lim...

ChemSuite: A package for chemoinformatics calculations and machine learning.

Chemical biology & drug design
Prediction of biological and toxicological properties of small molecules using in silico approaches has become a wide practice in pharmaceutical research to lessen the cost and enhance productivity. The development of a tool "ChemSuite," a stand-alon...

Automating the process of identifying the preferred representational system in Neuro Linguistic Programming using Natural Language Processing.

Cognitive processing
Neuro Linguistic Programming (NLP) is a methodology used for recognition of human behavioral patterns and modification of the behavior. A significant part of this process is influenced by the theory of representational systems which equates to the fi...

Breast Microcalcification Diagnosis Using Deep Convolutional Neural Network from Digital Mammograms.

Computational and mathematical methods in medicine
Mammography is successfully used as an effective screening tool for cancer diagnosis. A calcification cluster on mammography is a primary sign of cancer. Early researches have proved the diagnostic value of the calcification, yet their performance is...

RPITER: A Hierarchical Deep Learning Framework for ncRNA⁻Protein Interaction Prediction.

International journal of molecular sciences
Non-coding RNAs (ncRNAs) play crucial roles in multiple fundamental biological processes, such as post-transcriptional gene regulation, and are implicated in many complex human diseases. Mostly ncRNAs function by interacting with corresponding RNA-bi...