scholarly journals Learning to count: A deep learning framework for graphlet count estimation

2020 ◽  
pp. 1-38
Author(s):  
Xutong Liu ◽  
Yu-Zhen Janice Chen ◽  
John C. S. Lui ◽  
Konstantin Avrachenkov
Keyword(s):  
Deep Learning ◽  
Real World ◽  
Sampling Methods ◽  
Structural Information ◽  
Estimation Procedure ◽  
Enumeration Algorithm ◽  
Underlying Distribution ◽  
Learning Framework ◽  
Counting Procedure ◽  
Count Estimation

Abstract Graphlet counting is a widely explored problem in network analysis and has been successfully applied to a variety of applications in many domains, most notatbly bioinformatics, social science, and infrastructure network studies. Efficiently computing graphlet counts remains challenging due to the combinatorial explosion, where a naive enumeration algorithm needs O(Nk) time for k-node graphlets in a network of size N. Recently, many works introduced carefully designed combinatorial and sampling methods with encouraging results. However, the existing methods ignore the fact that graphlet counts and the graph structural information are correlated. They always consider a graph as a new input and repeat the tedious counting procedure on a regular basis even if it is similar or exactly isomorphic to previously studied graphs. This provides an opportunity to speed up the graphlet count estimation procedure by exploiting this correlation via learning methods. In this paper, we raise a novel graphlet count learning (GCL) problem: given a set of historical graphs with known graphlet counts, how to learn to estimate/predict graphlet count for unseen graphs coming from the same (or similar) underlying distribution. We develop a deep learning framework which contains two convolutional neural network models and a series of data preprocessing techniques to solve the GCL problem. Extensive experiments are conducted on three types of synthetic random graphs and three types of real-world graphs for all 3-, 4-, and 5-node graphlets to demonstrate the accuracy, efficiency, and generalizability of our framework. Compared with state-of-the-art exact/sampling methods, our framework shows great potential, which can offer up to two orders of magnitude speedup on synthetic graphs and achieve on par speed on real-world graphs with competitive accuracy.

Deep Multi-Instance Multi-Label Learning for Image Annotation

2017 ◽  
Vol 32 (03) ◽  
pp. 1859005 ◽  
Author(s):  
Hai-Feng Guo ◽  
Lixin Han ◽  
Shoubao Su ◽  
Zhou-Bao Sun
Keyword(s):  
Neural Network ◽  
Social Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Real World ◽  
Supervised Classification ◽  
Image Annotation ◽  
Learning Framework ◽  
Recent Advancement ◽  
Real World Datasets

Multi-Instance Multi-Label learning (MIML) is a popular framework for supervised classification where an example is described by multiple instances and associated with multiple labels. Previous MIML approaches have focused on predicting labels for instances. The idea of tackling the problem is to identify its equivalence in the traditional supervised learning framework. Motivated by the recent advancement in deep learning, in this paper, we still consider the problem of predicting labels and attempt to model deep learning in MIML learning framework. The proposed approach enables us to train deep convolutional neural network with images from social networks where images are well labeled, even labeled with several labels or uncorrelated labels. Experiments on real-world datasets demonstrate the effectiveness of our proposed approach.

scholarly journals LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure

2021 ◽  
Author(s):  
Zichen Wang ◽  
Steven A. Combs ◽  
Ryan Brand ◽  
Miguel Romero Calvo ◽  
Panpan Xu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Structural Information ◽  
Language Model ◽  
Amino Acid Sequences ◽  
Property Prediction ◽  
Learning Framework ◽  
Protein Property ◽  
Protein Functions ◽  
Protease Stability ◽  
Prediction Problems

AbstractProteins perform many essential functions in biological systems and can be successfully developed as bio-therapeutics. It is invaluable to be able to predict their properties based on a proposed sequence and structure. In this study, we developed a novel generalizable deep learning framework, LM-GVP, composed of a protein Language Model (LM) and Graph Neural Network (GNN) to leverage information from both 1D amino acid sequences and 3D structures of proteins. Our approach outperformed the state-of-the-art protein LMs on a variety of property prediction tasks including fluorescence, protease stability, and protein functions from Gene Ontology (GO). We also illustrated insights into how a GNN prediction head can guide the protein LM to better leverage structural information. We envision that our deep learning framework will be generalizable to many protein property prediction problems to greatly accelerate protein engineering and drug development.

A Deep Learning Framework for Prediction of Retinal Disorders

2020 ◽  
Author(s):  
Raniyaharini R ◽  
Madhumitha K ◽  
Mishaa S ◽  
Virajaravi R
Keyword(s):  
Deep Learning ◽  
Learning Framework ◽  
Retinal Disorders

COVID-19 pneumonia diagnosis using a simple 2D deep learning framework with a single chest CT image (Preprint)

2020 ◽  
Author(s):  
Jinseok Lee
Keyword(s):  
Deep Learning ◽  
Diagnostic Performance ◽  
Ct Images ◽  
Chest Ct ◽  
University Hospital ◽  
Detection Accuracy ◽  
Ct Image ◽  
Test Dataset ◽  
Learning Framework ◽  
Testing Dataset

BACKGROUND The coronavirus disease (COVID-19) has explosively spread worldwide since the beginning of 2020. According to a multinational consensus statement from the Fleischner Society, computed tomography (CT) can be used as a relevant screening tool owing to its higher sensitivity for detecting early pneumonic changes. However, physicians are extremely busy fighting COVID-19 in this era of worldwide crisis. Thus, it is crucial to accelerate the development of an artificial intelligence (AI) diagnostic tool to support physicians. OBJECTIVE We aimed to quickly develop an AI technique to diagnose COVID-19 pneumonia and differentiate it from non-COVID pneumonia and non-pneumonia diseases on CT. METHODS A simple 2D deep learning framework, named fast-track COVID-19 classification network (FCONet), was developed to diagnose COVID-19 pneumonia based on a single chest CT image. FCONet was developed by transfer learning, using one of the four state-of-art pre-trained deep learning models (VGG16, ResNet50, InceptionV3, or Xception) as a backbone. For training and testing of FCONet, we collected 3,993 chest CT images of patients with COVID-19 pneumonia, other pneumonia, and non-pneumonia diseases from Wonkwang University Hospital, Chonnam National University Hospital, and the Italian Society of Medical and Interventional Radiology public database. These CT images were split into a training and a testing set at a ratio of 8:2. For the test dataset, the diagnostic performance to diagnose COVID-19 pneumonia was compared among the four pre-trained FCONet models. In addition, we tested the FCONet models on an additional external testing dataset extracted from the embedded low-quality chest CT images of COVID-19 pneumonia in recently published papers. RESULTS Of the four pre-trained models of FCONet, the ResNet50 showed excellent diagnostic performance (sensitivity 99.58%, specificity 100%, and accuracy 99.87%) and outperformed the other three pre-trained models in testing dataset. In additional external test dataset using low-quality CT images, the detection accuracy of the ResNet50 model was the highest (96.97%), followed by Xception, InceptionV3, and VGG16 (90.71%, 89.38%, and 87.12%, respectively). CONCLUSIONS The FCONet, a simple 2D deep learning framework based on a single chest CT image, provides excellent diagnostic performance in detecting COVID-19 pneumonia. Based on our testing dataset, the ResNet50-based FCONet might be the best model, as it outperformed other FCONet models based on VGG16, Xception, and InceptionV3.

Sign in / Sign up

Export Citation Format

Share Document