scholarly journals DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicolas Renaud ◽  
Cunliang Geng ◽  
Sonja Georgievska ◽  
Francesco Ambrosetti ◽  
Lars Ridder ◽  
...  
Keyword(s):  
Data Mining ◽  
Deep Learning ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Data Sets ◽  
Biological Processes ◽  
Learning Framework ◽  
Fundamental Information ◽  
Protein Interfaces

AbstractThree-dimensional (3D) structures of protein complexes provide fundamental information to decipher biological processes at the molecular scale. The vast amount of experimentally and computationally resolved protein-protein interfaces (PPIs) offers the possibility of training deep learning models to aid the predictions of their biological relevance. We present here DeepRank, a general, configurable deep learning framework for data mining PPIs using 3D convolutional neural networks (CNNs). DeepRank maps features of PPIs onto 3D grids and trains a user-specified CNN on these 3D grids. DeepRank allows for efficient training of 3D CNNs with data sets containing millions of PPIs and supports both classification and regression. We demonstrate the performance of DeepRank on two distinct challenges: The classification of biological versus crystallographic PPIs, and the ranking of docking models. For both problems DeepRank is competitive with, or outperforms, state-of-the-art methods, demonstrating the versatility of the framework for research in structural biology.

scholarly journals DeepRank: A deep learning framework for data mining 3D protein-protein interfaces

2021 ◽  
Author(s):  
Nicolas Renaud ◽  
Cunliang Geng ◽  
Sonja Georgievska ◽  
Francesco Ambrosetti ◽  
Lars Ridder ◽  
...  
Keyword(s):  
Data Mining ◽  
Deep Learning ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Data Sets ◽  
Biological Processes ◽  
Learning Framework ◽  
Fundamental Information ◽  
Protein Interfaces

AbstractThree-dimensional (3D) structures of protein complexes provide fundamental information to decipher biological processes at the molecular scale. The vast amount of experimentally and computationally resolved protein-protein interfaces (PPIs) offers the possibility of training deep learning models to aid the predictions of their biological relevance.We present here DeepRank, a general, configurable deep learning framework for data mining PPIs using 3D convolutional neural networks (CNNs). DeepRank maps features of PPIs onto 3D grids and trains a user-specified CNN on these 3D grids. DeepRank allows for efficient training of 3D CNNs with data sets containing millions of PPIs and supports both classification and regression.We demonstrate the performance of DeepRank on two distinct challenges: The classification of biological versus crystallographic PPIs, and the ranking of docking models. For both problems DeepRank is competitive or outperforms state-of-the-art methods, demonstrating the versatility of the framework for research in structural biology.

scholarly journals Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

2021 ◽  
Vol 17 (2) ◽  
pp. e1008767
Author(s):  
Zutan Li ◽  
Hangjin Jiang ◽  
Lingpeng Kong ◽  
Yuanyuan Chen ◽  
Kun Lang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Biological Processes ◽  
Biological Functions ◽  
Learning Framework ◽  
Wide Range ◽  
Genomic Scale ◽  
Downstream Gene Expression ◽  
Fold Cross Validation

N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, the existing experimental techniques for detecting 6mA sites are cost-ineffective, which implies the great need of developing new computational methods for this problem. In this paper, we developed, without requiring any prior knowledge of 6mA and manually crafted sequence features, a deep learning framework named Deep6mA to identify DNA 6mA sites, and its performance is superior to other DNA 6mA prediction tools. Specifically, the 5-fold cross-validation on a benchmark dataset of rice gives the sensitivity and specificity of Deep6mA as 92.96% and 95.06%, respectively, and the overall prediction accuracy is 94%. Importantly, we find that the sequences with 6mA sites share similar patterns across different species. The model trained with rice data predicts well the 6mA sites of other three species: Arabidopsis thaliana, Fragaria vesca and Rosa chinensis with a prediction accuracy over 90%. In addition, we find that (1) 6mA tends to occur at GAGG motifs, which means the sequence near the 6mA site may be conservative; (2) 6mA is enriched in the TATA box of the promoter, which may be the main source of its regulating downstream gene expression.

Learning representations of Web entities for entity resolution

2019 ◽  
Vol 15 (3) ◽  
pp. 346-358
Author(s):  
Luciano Barbosa
Keyword(s):  
Deep Learning ◽  
Dimensional Space ◽  
Entity Resolution ◽  
Data Sets ◽  
Content Type ◽  
Learning Framework ◽  
Document Frequency ◽  
Deep Learning Network ◽  
Low Dimensional ◽  
Vector Representations

Purpose Matching instances of the same entity, a task known as entity resolution, is a key step in the process of data integration. This paper aims to propose a deep learning network that learns different representations of Web entities for entity resolution. Design/methodology/approach To match Web entities, the proposed network learns the following representations of entities: embeddings, which are vector representations of the words in the entities in a low-dimensional space; convolutional vectors from a convolutional layer, which capture short-distance patterns in word sequences in the entities; and bag-of-word vectors, created by a bow layer that learns weights for words in the vocabulary based on the task at hand. Given a pair of entities, the similarity between their learned representations is used as a feature to a binary classifier that identifies a possible match. In addition to those features, the classifier also uses a modification of inverse document frequency for pairs, which identifies discriminative words in pairs of entities. Findings The proposed approach was evaluated in two commercial and two academic entity resolution benchmarking data sets. The results have shown that the proposed strategy outperforms previous approaches in the commercial data sets, which are more challenging, and have similar results to its competitors in the academic data sets. Originality/value No previous work has used a single deep learning framework to learn different representations of Web entities for entity resolution.

Classification of remote sensed images using random forests and deep learning framework

2016 ◽  
Author(s):  
S. Piramanayagam ◽  
W. Schwartzkopf ◽  
F. W. Koehler ◽  
E. Saber
Keyword(s):  
Deep Learning ◽  
Random Forests ◽  
Learning Framework

scholarly journals A Multitask Deep-Learning System to Classify Diabetic Macular Edema for Different Optical Coherence Tomography Devices: A Multicenter Analysis

2021 ◽  
Author(s):  
Fangyao Tang ◽  
Xi Wang ◽  
An-ran Ran ◽  
Carmen KM Chan ◽  
Mary Ho ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Deep Learning ◽  
Macular Edema ◽  
Diabetic Macular Edema ◽  
Vision Loss ◽  
Three Dimensional ◽  
Learning System ◽  
Optical Coherence ◽  
Automated Classification

<a><b>Objective:</b></a> Diabetic macular edema (DME) is the primary cause of vision loss among individuals with diabetes mellitus (DM). We developed, validated, and tested a deep-learning (DL) system for classifying DME using images from three common commercially available optical coherence tomography (OCT) devices. <p><b>Research Design and Methods:</b> We trained and validated two versions of a multi-task convolution neural network (CNN) to classify DME (center-involved DME [CI-DME], non-CI-DME, or absence of DME) using three-dimensional (3D) volume-scans and two-dimensional (2D) B-scans respectively. For both 3D and 2D CNNs, we employed the residual network (ResNet) as the backbone. For the 3D CNN, we used a 3D version of ResNet-34 with the last fully connected layer removed as the feature extraction module. A total of 73,746 OCT images were used for training and primary validation. External testing was performed using 26,981 images across seven independent datasets from Singapore, Hong Kong, the US, China, and Australia. </p> <p><b>Results:</b> In classifying the presence or absence of DME, the DL system achieved area under the receiver operating characteristic curves (AUROCs) of 0.937 (95% CI 0.920–0.954), 0.958 (0.930–0.977), and 0.965 (0.948–0.977) for primary dataset obtained from Cirrus, Spectralis, and Triton OCTs respectively, in addition to AUROCs greater than 0.906 for the external datasets. For the further classification of the CI-DME and non-CI-DME subgroups, the AUROCs were 0.968 (0.940–0.995), 0.951 (0.898–0.982), and 0.975 (0.947–0.991) for the primary dataset and greater than 0.894 for the external datasets. </p> <p><b>Conclusion:</b> We demonstrated excellent performance with a DL system for the automated classification of DME, highlighting its potential as a promising second-line screening tool for patients with DM, which may potentially create a more effective triaging mechanism to eye clinics. </p>

scholarly journals Data Mining Techniques for Identification and Classification of Various Diseases in Plants

2019 ◽  
Vol 9 (2S) ◽  
pp. 676-680
Keyword(s):  
Neural Network ◽  
Data Mining ◽  
Nearest Neighbors ◽  
Crop Productivity ◽  
Vital Role ◽  
Support Vector ◽  
Data Sets ◽  
K Nearest Neighbors ◽  
Data Mining Techniques

Data mining is currently being used in various applications; In research community it plays a vital role. This paper specify about data mining techniques for the preprocessing and classification of various disease in plants. Since various plants has different diseases based on that each of them has different data sets and different objectives for knowledge discovery. Data Mining Techniques applied on plants that it helps in segmentation and classification of diseased plants, it avoids Oral Inspection and helps to increase in crop productivity. This paper provides various classification techniques Such as K-Nearest Neighbors, Support Vector Machine, Principle component Analysis, Neural Network. Thus among various techniques neural network is effective for disease detection in plants.

scholarly journals Data mining in web personalization using the blended deep learning model

2020 ◽  
Vol 20 (3) ◽  
pp. 1507
Author(s):  
Qusay Abdullah Abed ◽  
Osamah Mohammed Fadhil ◽  
Wathiq Laftah Al-Yaseen
Keyword(s):  
Data Mining ◽  
Deep Learning ◽  
Web Application ◽  
Large Data ◽  
Learning Model ◽  
Multidimensional Data ◽  
Data Sets ◽  
Web Personalization ◽  
Deep Learning Model ◽  
The Web

In general, multidimensional data (mobile application for example) contain a large number of unnecessary information. Web app users find it difficult to get the information needed quickly and effectively due to the sheer volume of data (big data produced per second). In this paper, we tend to study the data mining in web personalization using blended deep learning model. So, one of the effective solutions to this problem is web personalization. As well as, explore how this model helps to analyze and estimate the huge amounts of operations. Providing personalized recommendations to improve reliability depends on the web application using useful information in the web application. The results of this research are important for the training and testing of large data sets for a map of deep mixed learning based on the model of back-spread neural network. The HADOOP framework was used to perform a number of experiments in a different environment with a learning rate between -1 and +1. Also, using the number of techniques to evaluate the number of parameters, true positive cases are represent and fall into positive cases in this example to evaluate the proposed model.

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