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ReorientExpress: reference-free orientation of nanopore cDNA reads with deep learning.
Genome biology
Nov 29, 2019
We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of reads, and in particular when trained on a...
SGL-SVM: A novel method for tumor classification via support vector machine with sparse group Lasso.
Journal of theoretical biology
Nov 28, 2019
At present, with the in-depth study of gene expression data, the significant role of tumor classification in clinical medicine has become more apparent. In particular, the sparse characteristics of gene expression data within and between groups. Ther...
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning.
Nature communications
Nov 27, 2019
The majority of our human genome transcribes into noncoding RNAs with unknown structures and functions. Obtaining functional clues for noncoding RNAs requires accurate base-pairing or secondary-structure prediction. However, the performance of such p...
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.
Nature methods
Nov 25, 2019
We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves t...
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology.
BMC bioinformatics
Nov 25, 2019
BACKGROUND: The Gene Ontology (GO) knowledgebase is the world's largest source of information on the functions of genes. Since the beginning of GO project, various tools have been developed to perform GO enrichment analysis experiments. GO enrichment...
A scalable multi-signal approach for the parallelization of self-organizing neural networks.
Neural networks : the official journal of the International Neural Network Society
Nov 23, 2019
Self-Organizing Neural Networks (SONNs) have a wide range of applications with massive computational requirements that often need to be satisfied with optimized parallel algorithms and implementations. In literature, SONN have been generally parallel...
ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network.
EBioMedicine
Nov 22, 2019
BACKGROUND: The spatial distributions of different types of cells could reveal a cancer cell's growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key "hallmarks of cancer". Ho...
ImaGene: a convolutional neural network to quantify natural selection from genomic data.
BMC bioinformatics
Nov 22, 2019
BACKGROUND: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determini...
Using the Chou's 5-steps rule to predict splice junctions with interpretable bidirectional long short-term memory networks.
Computers in biology and medicine
Nov 21, 2019
Neural models have been able to obtain state-of-the-art performances on several genome sequence-based prediction tasks. Such models take only nucleotide sequences as input and learn relevant features on their own. However, extracting the interpretabl...
Brain tumor segmentation approach based on the extreme learning machine and significantly fast and robust fuzzy C-means clustering algorithms running on Raspberry Pi hardware.
Medical hypotheses
Nov 18, 2019
Automatic decision support systems have gained importance in health sector in recent years. In parallel with recent developments in the fields of artificial intelligence and image processing, embedded systems are also used in decision support systems...
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