> For the complete documentation index, see [llms.txt](https://irosyadi.gitbook.io/irosyadi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://irosyadi.gitbook.io/irosyadi/research/ncbi-paper-with-code.md).

# NCBI Papers with Code

List of awesome NCBI Papers with Code Supplement.

## CNN

1. Dual CNN for Relation Extraction with Knowledge-Based Attention and Word Embeddings\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664687/>\
   Code: <https://github.com/mrlijun2017/Dual-CNN-RE>
2. CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751796/>\
   Code: <https://github.com/whiteclarence/CNN-BLPred>
3. Design of deep convolutional networks for prediction of image rapid serial visual presentation events\
   Paper: <https://www.ncbi.nlm.nih.gov/pubmed/29060296>\
   Code: <https://github.com/ZijingMao/ROICNN>
4. A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data\
   Paper: <https://www.ncbi.nlm.nih.gov/pubmed/30649185>\
   Code: <https://github.com/zzUMN/Combine-CNN-Enhancer-and-Promoters>
5. A novel attention-based hybrid CNN-RNN architecture for sEMG-based gesture recognition\
   Paper:<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207326/>\
   Code: <https://github.com/biopatrec/biopatrec>
6. GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text\
   Paper: <https://www.ncbi.nlm.nih.gov/pubmed/29272325>\
   Code: <https://github.com/valdersoul/GRAM-CNN>
7. Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction\
   Paper: <https://www.ncbi.nlm.nih.gov/pubmed/30351403>\
   Code: <https://github.com/zhanglabtools/DNADataAugmentation>
8. EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937476/>\
   Code: <https://github.com/shervinea/enzynet>
9. Multi-timescale drowsiness characterization based on a video of a driver's face\
   Paper: <https://www.telecom.ulg.ac.be/mts-drowsiness/>\
   <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165048/>\
   Code: <https://github.com/QMassoz/mts-drowsiness>
10. CLoDSA: a tool for augmentation in classification, localization, detection, semantic segmentation and instance segmentation tasks\
    Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567576/>\
    Code: <https://github.com/joheras/CLoDSA>
11. Deep learning with convolutional neural networks for EEG decoding and visualization\
    Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5655781/>\
    Code: <https://github.com/robintibor/braindecode/>\
    Code: <https://github.com/TNTLFreiburg/braindecode>

## Rice/Paddy Classification

1. Classifying Oryza sativa accessions into Indica and Japonica using logistic regression model with phenotypic data\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842562/>\
   Code: <https://github.com/bongsongkim/logit.regression.rice>
2. SNNRice6mA: A Deep Learning Method for Predicting DNA N6-Methyladenine Sites in Rice Genome\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797597/>\
   Code: <https://github.com/yuht4/SNNRice6mA>
3. Automatic estimation of heading date of paddy rice using deep learning\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6626381/>\
   Code: <https://github.com/svdesai/heading-date-estimation>
4. Distillation of crop models to learn plant physiology theories using machine learning\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6541271/>\
   Code: <https://github.com/ky0on/simriw>
5. Evaluating remote sensing datasets and machine learning algorithms for mapping plantations and successional forests in Phnom Kulen National Park of Cambodia\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814064/>\
   Code: <https://github.com/Jojo666/PKNP-Data>
6. PlantCV v2: Image analysis software for high-throughput plant phenotyping\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5713628/>\
   Code: <https://github.com/danforthcenter/plantcv-v2-paper>
7. Crop Yield Prediction Using Deep Neural Networks\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540942/>\
   Code: <https://github.com/saeedkhaki92/Yield-Prediction-DNN>
8. Using Deep Learning for Image-Based Plant Disease Detection\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032846/>\
   Code: <https://github.com/salathegroup/plantvillage_deeplearning_paper_analysis>
9. Deep Plant Phenomics: A Deep Learning Platform for Complex Plant Phenotyping Tasks\
   Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500639/>\
   Code: <https://github.com/p2irc/deepplantphenomics>
10. DeepWeeds: A Multiclass Weed Species Image Dataset for Deep Learning\
    Paper: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375952/>\
    Code: <https://github.com/AlexOlsen/DeepWeeds>

## Papers with Code

* [CVPR 2020 Papers with Code/Data](https://www.paperdigest.org/2020/06/cvpr-2020-papers-with-code-data/)
* [ECCV 2020: Some Highlights](https://yassouali.github.io/ml-blog/eccv2020/)
