AIMC Topic: Software

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MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. ...

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

Bioinformatics (Oxford, England)
MOTIVATION: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondar...

When Machines Think: Radiology's Next Frontier.

Radiology
Artificial intelligence (AI), machine learning, and deep learning are terms now seen frequently, all of which refer to computer algorithms that change as they are exposed to more data. Many of these algorithms are surprisingly good at recognizing obj...

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

Nucleic acids research
The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large n...

[A Software Platform of Treatment Planning System for Radiotherapy Snake Robot].

Zhongguo yi liao qi xie za zhi = Chinese journal of medical instrumentation
A software platform integrated of radiation treatment planning system and navigation system has been developed for a newly-developed snake robot. This platform is developed in a module-plugin form based on 3D Slicer medical image visualization and an...

Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment.

Bioinformatics (Oxford, England)
MOTIVATION: The concept of a 'mechanism-based taxonomy of human disease' is currently replacing the outdated paradigm of diseases classified by clinical appearance. We have tackled the paradigm of mechanism-based patient subgroup identification in th...

CAPi: Computational Model for Apicoplast Inhibitors Prediction Against Plasmodium Parasite.

Current computer-aided drug design
BACKGROUND: Discovery of apicoplast as a drug target offers a new direction in the development of novel anti-malarial compounds, especially against the drug-resistant strains. Drugs such as azithromycin were reported to block the apicoplast developme...

A transfer learning approach to goodness of pronunciation based automatic mispronunciation detection.

The Journal of the Acoustical Society of America
Goodness of pronunciation (GOP) is the most widely used method for automatic mispronunciation detection. In this paper, a transfer learning approach to GOP based mispronunciation detection when applying maximum F1-score criterion (MFC) training to de...

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.

Bioinformatics (Oxford, England)
SUMMARY: As one of the most important tasks in protein sequence analysis, protein remote homology detection is critical for both basic research and practical applications. Here, we present an effective web server for protein remote homology detection...

DeepLoc: prediction of protein subcellular localization using deep learning.

Bioinformatics (Oxford, England)
MOTIVATION: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of...