scholarly journals A New Ensemble Learning Framework for 3D Biomedical Image Segmentation

2019 ◽  
Vol 33 ◽  
pp. 5909-5916 ◽  
Author(s):  
Hao Zheng ◽  
Yizhe Zhang ◽  
Lin Yang ◽  
Peixian Liang ◽  
Zhuo Zhao ◽  
...  
Keyword(s):  
Image Segmentation ◽  
Ensemble Learning ◽  
State Of The Art ◽  
3D Models ◽  
Superior Performance ◽  
3D Image ◽  
Convolutional Network ◽  
Biomedical Image ◽  
Learning Framework ◽  
2D And 3D

3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the baselearners as multiple versions of “ground truths”. Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semisupervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.

scholarly journals PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Changyong Li ◽  
Yongxian Fan ◽  
Xiaodong Cai
Keyword(s):  
Image Segmentation ◽  
Deep Learning ◽  
State Of The Art ◽  
Experimental Results ◽  
Actual Situation ◽  
Controlled Experiments ◽  
Biomedical Image ◽  
Segmentation Methods ◽  
Art Performance

Abstract Background With the development of deep learning (DL), more and more methods based on deep learning are proposed and achieve state-of-the-art performance in biomedical image segmentation. However, these methods are usually complex and require the support of powerful computing resources. According to the actual situation, it is impractical that we use huge computing resources in clinical situations. Thus, it is significant to develop accurate DL based biomedical image segmentation methods which depend on resources-constraint computing. Results A lightweight and multiscale network called PyConvU-Net is proposed to potentially work with low-resources computing. Through strictly controlled experiments, PyConvU-Net predictions have a good performance on three biomedical image segmentation tasks with the fewest parameters. Conclusions Our experimental results preliminarily demonstrate the potential of proposed PyConvU-Net in biomedical image segmentation with resources-constraint computing.

scholarly journals Biomedical Image Segmentation via Representative Annotation

2019 ◽  
Vol 33 ◽  
pp. 5901-5908 ◽  
Author(s):  
Hao Zheng ◽  
Lin Yang ◽  
Jianxu Chen ◽  
Jun Han ◽  
Yizhe Zhang ◽  
...  
Keyword(s):  
Image Segmentation ◽  
Deep Learning ◽  
Active Learning ◽  
Iterative Process ◽  
Image Data ◽  
Manual Annotation ◽  
Convolutional Network ◽  
Biomedical Image ◽  
Image Patches ◽  
Representative Image

Deep learning has been applied successfully to many biomedical image segmentation tasks. However, due to the diversity and complexity of biomedical image data, manual annotation for training common deep learning models is very timeconsuming and labor-intensive, especially because normally only biomedical experts can annotate image data well. Human experts are often involved in a long and iterative process of annotation, as in active learning type annotation schemes. In this paper, we propose representative annotation (RA), a new deep learning framework for reducing annotation effort in biomedical image segmentation. RA uses unsupervised networks for feature extraction and selects representative image patches for annotation in the latent space of learned feature descriptors, which implicitly characterizes the underlying data while minimizing redundancy. A fully convolutional network (FCN) is then trained using the annotated selected image patches for image segmentation. Our RA scheme offers three compelling advantages: (1) It leverages the ability of deep neural networks to learn better representations of image data; (2) it performs one-shot selection for manual annotation and frees annotators from the iterative process of common active learning based annotation schemes; (3) it can be deployed to 3D images with simple extensions. We evaluate our RA approach using three datasets (two 2D and one 3D) and show our framework yields competitive segmentation results comparing with state-of-the-art methods.

scholarly journals Neural networks to learn protein sequence-function relationships from deep mutational scanning data

2020 ◽  
Author(s):  
Sam Gelman ◽  
Philip A. Romero ◽  
Anthony Gitter
Keyword(s):  
Protein Structure ◽  
Protein Sequence ◽  
Internal Representation ◽  
Superior Performance ◽  
Network Architectures ◽  
Convolutional Network ◽  
Learning Framework ◽  
And Function ◽  
Multiple Neural Network ◽  
Function Mapping

ABSTRACTThe mapping from protein sequence to function is highly complex, making it challenging to predict how sequence changes will affect a protein’s behavior and properties. We present a supervised deep learning framework to learn the sequence-function mapping from deep mutational scanning data and make predictions for new, uncharacterized sequence variants. We test multiple neural network architectures, including a graph convolutional network that incorporates protein structure, to explore how a network’s internal representation affects its ability to learn the sequence-function mapping. Our supervised learning approach displays superior performance over physics-based and unsupervised prediction methods. We find networks that capture nonlinear interactions and share parameters across sequence positions are important for learning the relationship between sequence and function. Further analysis of the trained models reveals the networks’ ability to learn biologically meaningful information about protein structure and mechanism. Our software is available from https://github.com/gitter-lab/nn4dms.

scholarly journals Non-Local Context Encoder: Robust Biomedical Image Segmentation against Adversarial Attacks

2019 ◽  
Vol 33 ◽  
pp. 8417-8424 ◽  
Author(s):  
Xiang He ◽  
Sibei Yang ◽  
Guanbin Li ◽  
Haofeng Li ◽  
Huiyou Chang ◽  
...  
Keyword(s):  
Image Segmentation ◽  
State Of The Art ◽  
Contextual Information ◽  
Local Context ◽  
Deep Convolutional Neural Networks ◽  
Biomedical Image ◽  
Feature Representations ◽  
Segmentation Methods ◽  
Spatial Dependencies ◽  
Non Local

Recent progress in biomedical image segmentation based on deep convolutional neural networks (CNNs) has drawn much attention. However, its vulnerability towards adversarial samples cannot be overlooked. This paper is the first one that discovers that all the CNN-based state-of-the-art biomedical image segmentation models are sensitive to adversarial perturbations. This limits the deployment of these methods in safety-critical biomedical fields. In this paper, we discover that global spatial dependencies and global contextual information in a biomedical image can be exploited to defend against adversarial attacks. To this end, non-local context encoder (NLCE) is proposed to model short- and long-range spatial dependencies and encode global contexts for strengthening feature activations by channel-wise attention. The NLCE modules enhance the robustness and accuracy of the non-local context encoding network (NLCEN), which learns robust enhanced pyramid feature representations with NLCE modules, and then integrates the information across different levels. Experiments on both lung and skin lesion segmentation datasets have demonstrated that NLCEN outperforms any other state-of-the-art biomedical image segmentation methods against adversarial attacks. In addition, NLCE modules can be applied to improve the robustness of other CNN-based biomedical image segmentation methods.

scholarly journals CharTeC-Net: An Efficient and Lightweight Character-Based Convolutional Network for Text Classification

2020 ◽  
Vol 2020 ◽  
pp. 1-7 ◽  
Author(s):  
Aboubakar Nasser Samatin Njikam ◽  
Huan Zhao
Keyword(s):  
Text Classification ◽  
Building Block ◽  
Large Scale ◽  
State Of The Art ◽  
Building Blocks ◽  
Training Data ◽  
Superior Performance ◽  
Classification Problems ◽  
Computationally Efficient ◽  
Convolutional Network

This paper introduces an extremely lightweight (with just over around two hundred thousand parameters) and computationally efficient CNN architecture, named CharTeC-Net (Character-based Text Classification Network), for character-based text classification problems. This new architecture is composed of four building blocks for feature extraction. Each of these building blocks, except the last one, uses 1 × 1 pointwise convolutional layers to add more nonlinearity to the network and to increase the dimensions within each building block. In addition, shortcut connections are used in each building block to facilitate the flow of gradients over the network, but more importantly to ensure that the original signal present in the training data is shared across each building block. Experiments on eight standard large-scale text classification and sentiment analysis datasets demonstrate CharTeC-Net’s superior performance over baseline methods and yields competitive accuracy compared with state-of-the-art methods, although CharTeC-Net has only between 181,427 and 225,323 parameters and weighs less than 1 megabyte.

scholarly journals A Deep Learning Framework for Malware Classification

2020 ◽  
Vol 12 (1) ◽  
pp. 90-108
Author(s):  
Mahmoud Kalash ◽  
Mrigank Rochan ◽  
Noman Mohammed ◽  
Neil Bruce ◽  
Yang Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Learning Algorithms ◽  
Superior Performance ◽  
Traditional Learning ◽  
Security Threats ◽  
Learning Approaches ◽  
Learning Framework ◽  
Malware Classification ◽  
New Strategies

In this article, the authors propose a deep learning framework for malware classification. There has been a huge increase in the volume of malware in recent years which poses serious security threats to financial institutions, businesses, and individuals. In order to combat the proliferation of malware, new strategies are essential to quickly identify and classify malware samples. Nowadays, machine learning approaches are becoming popular for malware classification. However, most of these approaches are based on shallow learning algorithms (e.g. SVM). Recently, convolutional neural networks (CNNs), a deep learning approach, have shown superior performance compared to traditional learning algorithms, especially in tasks such as image classification. Inspired by this, the authors propose a CNN-based architecture to classify malware samples. They convert malware binaries to grayscale images and subsequently train a CNN for classification. Experiments on two challenging malware classification datasets, namely Malimg and Microsoft, demonstrate that their method outperforms competing state-of-the-art algorithms.

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