AIMC Topic: Computational Biology

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Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach.

Scientific reports
The increasing interest in bioactive peptides with therapeutic potentials has been reflected in a large variety of biological databases published over the last years. However, the knowledge discovery process from these heterogeneous data sources is a...

TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings.

BMC medical genomics
BACKGROUND: Cytokines are a class of small proteins that act as chemical messengers and play a significant role in essential cellular processes including immunity regulation, hematopoiesis, and inflammation. As one important family of cytokines, tumo...

A Comprehensive Analysis of MicroRNAs in Human Osteoporosis.

Frontiers in endocrinology
MicroRNAs (miRNAs) are single-stranded RNA molecules that control gene expression in various processes, such as cancers, Alzheimer's disease, and bone metabolic diseases. However, the regulatory roles of miRNAs in osteoporosis have not been systemati...

LMI-DForest: A deep forest model towards the prediction of lncRNA-miRNA interactions.

Computational biology and chemistry
The interactions between miRNAs and long non-coding RNAs (lncRNAs) are subject to intensive recent studies due to its critical role in gene regulations. Computational prediction of lncRNA-miRNA interactions has become a popular alternative strategy t...

Machine learning analysis of DNA methylation in a hypoxia-immune model of oral squamous cell carcinoma.

International immunopharmacology
BACKGROUND: Hypoxia status and immunity are related with the development and prognosis of oral squamous cell carcinoma (OSCC). Here, we constructed a hypoxia-immune model to explore its upstream mechanism and identify potential CpG sites.

PyHIST: A Histological Image Segmentation Tool.

PLoS computational biology
The development of increasingly sophisticated methods to acquire high-resolution images has led to the generation of large collections of biomedical imaging data, including images of tissues and organs. Many of the current machine learning methods th...

A Method for Identifying Vesicle Transport Proteins Based on LibSVM and MRMD.

Computational and mathematical methods in medicine
With the development of computer technology, many machine learning algorithms have been applied to the field of biology, forming the discipline of bioinformatics. Protein function prediction is a classic research topic in this subject area. Though ma...

Identification and Classification of Enhancers Using Dimension Reduction Technique and Recurrent Neural Network.

Computational and mathematical methods in medicine
Enhancers are noncoding fragments in DNA sequences, which play an important role in gene transcription and translation. However, due to their high free scattering and positional variability, the identification and classification of enhancers have a h...

Overparameterized neural networks implement associative memory.

Proceedings of the National Academy of Sciences of the United States of America
Identifying computational mechanisms for memorization and retrieval of data is a long-standing problem at the intersection of machine learning and neuroscience. Our main finding is that standard overparameterized deep neural networks trained using st...