scholarly journals Customized Efficient Neural Network for COVID-19 Infected Region Identification in CT Images

2021 ◽  
Vol 7 (8) ◽  
pp. 131
Author(s):  
Alessandro Stefano ◽  
Albert Comelli
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Dice Similarity Coefficient ◽  
Automated Identification ◽  
Accurate Identification ◽  
Computed Tomography Images ◽  
Volume Of Interest ◽  
Self Driving Cars ◽  
Learning Architectures ◽  
Deep Learning Model

Background: In the field of biomedical imaging, radiomics is a promising approach that aims to provide quantitative features from images. It is highly dependent on accurate identification and delineation of the volume of interest to avoid mistakes in the implementation of the texture-based prediction model. In this context, we present a customized deep learning approach aimed at addressing the real-time, and fully automated identification and segmentation of COVID-19 infected regions in computed tomography images. Methods: In a previous study, we adopted ENET, originally used for image segmentation tasks in self-driving cars, for whole parenchyma segmentation in patients with idiopathic pulmonary fibrosis which has several similarities to COVID-19 disease. To automatically identify and segment COVID-19 infected areas, a customized ENET, namely C-ENET, was implemented and its performance compared to the original ENET and some state-of-the-art deep learning architectures. Results: The experimental results demonstrate the effectiveness of our approach. Considering the performance obtained in terms of similarity of the result of the segmentation to the gold standard (dice similarity coefficient ~75%), our proposed methodology can be used for the identification and delineation of COVID-19 infected areas without any supervision of a radiologist, in order to obtain a volume of interest independent from the user. Conclusions: We demonstrated that the proposed customized deep learning model can be applied to rapidly identify, and segment COVID-19 infected regions to subsequently extract useful information for assessing disease severity through radiomics analyses.

scholarly journals Lung Segmentation on High-Resolution Computerized Tomography Images Using Deep Learning: A Preliminary Step for Radiomics Studies

2020 ◽  
Vol 6 (11) ◽  
pp. 125 ◽  
Author(s):  
Albert Comelli ◽  
Claudia Coronnello ◽  
Navdeep Dahiya ◽  
Viviana Benfante ◽  
Stefano Palmucci ◽  
...  
Keyword(s):  
Image Segmentation ◽  
Deep Learning ◽  
High Resolution ◽  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Dice Similarity Coefficient ◽  
Learning Models ◽  
High Resolution Computed Tomography ◽  
Computed Tomography Images ◽  
Self Driving Cars

Background: The aim of this work is to identify an automatic, accurate, and fast deep learning segmentation approach, applied to the parenchyma, using a very small dataset of high-resolution computed tomography images of patients with idiopathic pulmonary fibrosis. In this way, we aim to enhance the methodology performed by healthcare operators in radiomics studies where operator-independent segmentation methods must be used to correctly identify the target and, consequently, the texture-based prediction model. Methods: Two deep learning models were investigated: (i) U-Net, already used in many biomedical image segmentation tasks, and (ii) E-Net, used for image segmentation tasks in self-driving cars, where hardware availability is limited and accurate segmentation is critical for user safety. Our small image dataset is composed of 42 studies of patients with idiopathic pulmonary fibrosis, of which only 32 were used for the training phase. We compared the performance of the two models in terms of the similarity of their segmentation outcome with the gold standard and in terms of their resources’ requirements. Results: E-Net can be used to obtain accurate (dice similarity coefficient = 95.90%), fast (20.32 s), and clinically acceptable segmentation of the lung region. Conclusions: We demonstrated that deep learning models can be efficiently applied to rapidly segment and quantify the parenchyma of patients with pulmonary fibrosis, without any radiologist supervision, in order to produce user-independent results.

scholarly journals Bata-Unet: Deep Learning Model for Liver Segmentation

2020 ◽  
Vol 11 (5) ◽  
pp. 75-87
Author(s):  
Fatima Abdalbagi ◽  
Serestina Viriri ◽  
Mohammed Tajalsir Mohammed
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Similarity Coefficient ◽  
Dice Similarity Coefficient ◽  
Liver Segmentation ◽  
Batch Normalization ◽  
Learning Techniques ◽  
Proposed Model ◽  
Fully Automatic ◽  
Deep Learning Model

In computer vision, image segmentation is defined as process of a partition of an image in a number of regions with homogeneous features. The region of our interest here is the liver. Prior to the deep learning revolution traditional handcrafted features were used for liver segmentation but with deep learning the features are obtained automatically. There are many semiautomatic and fully automatic approaches have been proposed to improve the liver segmentation procedure some of them use deep learning techniques for Segmentation and other one use a Classical Based method for Segmentation. In this paper we aim to enhance our previous work which we were proposed a Batch Normalization After All - Convolutional Neural Network (BATA-Convnet) model to segment the liver, where the Dice is equal to 0.91% when implement our BATA Convnet using MICCA dataset and Dice is equal to 0.84% when implement it using 3D-IRCAD dataset. Here in this paper we propose BATA-Unet model for liver segmentation, it's based on Unet architecture as backbone but differ in we added a batch-normalization layer an after each convolution layer in both construction path and expanding path. The proposed method was able to achieve highest dice similarity coefficient than the previous work where for MICCA dataset Dice =0.97% and for 3D-IRCAD dataset =0.96%. Also our proposed model outperformed other state-of-the-art model when we compare it with them.

BEHRT-HF: an interpretable transformer-based, deep learning model for prediction of incident heart failure

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Rao ◽  
Y Li ◽  
R Ramakrishnan ◽  
A Hassaine ◽  
D Canoy ◽  
...  
Keyword(s):  
Heart Failure ◽  
Deep Learning ◽  
State Of The Art ◽  
Failure Prediction ◽  
Predictive Performance ◽  
Learning Model ◽  
Learning Framework ◽  
Incident Heart Failure ◽  
Ablation Study ◽  
Deep Learning Model

Abstract Background/Introduction Predicting incident heart failure has been challenging. Deep learning models when applied to rich electronic health records (EHR) offer some theoretical advantages. However, empirical evidence for their superior performance is limited and they remain commonly uninterpretable, hampering their wider use in medical practice. Purpose We developed a deep learning framework for more accurate and yet interpretable prediction of incident heart failure. Methods We used longitudinally linked EHR from practices across England, involving 100,071 patients, 13% of whom had been diagnosed with incident heart failure during follow-up. We investigated the predictive performance of a novel transformer deep learning model, “Transformer for Heart Failure” (BEHRT-HF), and validated it using both an external held-out dataset and an internal five-fold cross-validation mechanism using area under receiver operating characteristic (AUROC) and area under the precision recall curve (AUPRC). Predictor groups included all outpatient and inpatient diagnoses within their temporal context, medications, age, and calendar year for each encounter. By treating diagnoses as anchors, we alternatively removed different modalities (ablation study) to understand the importance of individual modalities to the performance of incident heart failure prediction. Using perturbation-based techniques, we investigated the importance of associations between selected predictors and heart failure to improve model interpretability. Results BEHRT-HF achieved high accuracy with AUROC 0.932 and AUPRC 0.695 for external validation, and AUROC 0.933 (95% CI: 0.928, 0.938) and AUPRC 0.700 (95% CI: 0.682, 0.718) for internal validation. Compared to the state-of-the-art recurrent deep learning model, RETAIN-EX, BEHRT-HF outperformed it by 0.079 and 0.030 in terms of AUPRC and AUROC. Ablation study showed that medications were strong predictors, and calendar year was more important than age. Utilising perturbation, we identified and ranked the intensity of associations between diagnoses and heart failure. For instance, the method showed that established risk factors including myocardial infarction, atrial fibrillation and flutter, and hypertension all strongly associated with the heart failure prediction. Additionally, when population was stratified into different age groups, incident occurrence of a given disease had generally a higher contribution to heart failure prediction in younger ages than when diagnosed later in life. Conclusions Our state-of-the-art deep learning framework outperforms the predictive performance of existing models whilst enabling a data-driven way of exploring the relative contribution of a range of risk factors in the context of other temporal information. Funding Acknowledgement Type of funding source: Private grant(s) and/or Sponsorship. Main funding source(s): National Institute for Health Research, Oxford Martin School, Oxford Biomedical Research Centre

scholarly journals IMG-22. A DEEP LEARNING MODEL FOR AUTOMATIC POSTERIOR FOSSA PEDIATRIC BRAIN TUMOR SEGMENTATION: A MULTI-INSTITUTIONAL STUDY

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii359-iii359
Author(s):  
Lydia Tam ◽  
Edward Lee ◽  
Michelle Han ◽  
Jason Wright ◽  
Leo Chen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Posterior Fossa ◽  
Ground Truth ◽  
Learning Model ◽  
Tumor Segmentation ◽  
Dice Similarity Coefficient ◽  
Study Cohort ◽  
Navigation Systems ◽  
Tumor Types ◽  
Deep Learning Model

Abstract BACKGROUND Brain tumors are the most common solid malignancies in childhood, many of which develop in the posterior fossa (PF). Manual tumor measurements are frequently required to optimize registration into surgical navigation systems or for surveillance of nonresectable tumors after therapy. With recent advances in artificial intelligence (AI), automated MRI-based tumor segmentation is now feasible without requiring manual measurements. Our goal was to create a deep learning model for automated PF tumor segmentation that can register into navigation systems and provide volume output. METHODS 720 pre-surgical MRI scans from five pediatric centers were divided into training, validation, and testing datasets. The study cohort comprised of four PF tumor types: medulloblastoma, diffuse midline glioma, ependymoma, and brainstem or cerebellar pilocytic astrocytoma. Manual segmentation of the tumors by an attending neuroradiologist served as “ground truth” labels for model training and evaluation. We used 2D Unet, an encoder-decoder convolutional neural network architecture, with a pre-trained ResNet50 encoder. We assessed ventricle segmentation accuracy on a held-out test set using Dice similarity coefficient (0–1) and compared ventricular volume calculation between manual and model-derived segmentations using linear regression. RESULTS Compared to the ground truth expert human segmentation, overall Dice score for model performance accuracy was 0.83 for automatic delineation of the 4 tumor types. CONCLUSIONS In this multi-institutional study, we present a deep learning algorithm that automatically delineates PF tumors and outputs volumetric information. Our results demonstrate applied AI that is clinically applicable, potentially augmenting radiologists, neuro-oncologists, and neurosurgeons for tumor evaluation, surveillance, and surgical planning.

scholarly journals A computationally efficient approach to segmentation of the aorta and coronary arteries using deep learning

2021 ◽  
Author(s):  
Wing Keung Cheung ◽  
Robert Bell ◽  
Arjun Nair ◽  
Leon Menezies ◽  
Riyaz Patel ◽  
...  
Keyword(s):  
Deep Learning ◽  
Coronary Arteries ◽  
Automatic Segmentation ◽  
Three Dimensional ◽  
Regions Of Interest ◽  
Dice Similarity Coefficient ◽  
Processing Unit ◽  
Two Dimensional ◽  
Computed Tomography Images ◽  
Graphical Processing

AbstractA fully automatic two-dimensional Unet model is proposed to segment aorta and coronary arteries in computed tomography images. Two models are trained to segment two regions of interest, (1) the aorta and the coronary arteries or (2) the coronary arteries alone. Our method achieves 91.20% and 88.80% dice similarity coefficient accuracy on regions of interest 1 and 2 respectively. Compared with a semi-automatic segmentation method, our model performs better when segmenting the coronary arteries alone. The performance of the proposed method is comparable to existing published two-dimensional or three-dimensional deep learning models. Furthermore, the algorithmic and graphical processing unit memory efficiencies are maintained such that the model can be deployed within hospital computer networks where graphical processing units are typically not available.

Fauce

2021 ◽  
Vol 14 (11) ◽  
pp. 1950-1963
Author(s):  
Jie Liu ◽  
Wenqian Dong ◽  
Qingqing Zhou ◽  
Dong Li
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
The State ◽  
Light Weight ◽  
Critical Problem ◽  
Estimation Errors ◽  
Cardinality Estimation ◽  
Complex Queries ◽  
Uncertainty Information ◽  
Deep Learning Model

Cardinality estimation is a fundamental and critical problem in databases. Recently, many estimators based on deep learning have been proposed to solve this problem and they have achieved promising results. However, these estimators struggle to provide accurate results for complex queries, due to not capturing real inter-column and inter-table correlations. Furthermore, none of these estimators contain the uncertainty information about their estimations. In this paper, we present a join cardinality estimator called Fauce. Fauce learns the correlations across all columns and all tables in the database. It also contains the uncertainty information of each estimation. Among all studied learned estimators, our results are promising: (1) Fauce is a light-weight estimator, it has 10× faster inference speed than the state of the art estimator; (2) Fauce is robust to the complex queries, it provides 1.3×--6.7× smaller estimation errors for complex queries compared with the state of the art estimator; (3) To the best of our knowledge, Fauce is the first estimator that incorporates uncertainty information for cardinality estimation into a deep learning model.

Deep Learning Model for Imbalanced Multi-label Surface Defect Classification

2021 ◽  
Author(s):  
Yang Liu ◽  
Yachao Yuan ◽  
Jing Liu
Keyword(s):  
Deep Learning ◽  
Surface Defect ◽  
State Of The Art ◽  
Steel Production ◽  
Learning Model ◽  
The State ◽  
Low Latency ◽  
Defect Classification ◽  
Key Techniques ◽  
Deep Learning Model

Abstract Automatic defect classification is vital to ensure product quality, especially for steel production. In the real world, the amount of collected samples with labels is limited due to high labor costs, and the gathered dataset is usually imbalanced, making accurate steel defect classification very challenging. In this paper, a novel deep learning model for imbalanced multi-label surface defect classification, named ImDeep, is proposed. It can be deployed easily in steel production lines to identify different defect types on the steel's surface. ImDeep incorporates three key techniques, i.e., Imbalanced Sampler, Fussy-FusionNet, and Transfer Learning. It improves the model's classification performance with multi-label and reduces the model's complexity over small datasets with low latency. The performance of different fusion strategies and three key techniques of ImDeep is verified. Simulation results prove that ImDeep accomplishes better performance than the state-of-the-art over the public dataset with varied sizes. Specifically, ImDeep achieves about 97% accuracy of steel surface defect classification over a small imbalanced dataset with a low latency, which improves about 10% compared with that of the state-of-the-art.

A Probabilistic Deep Learning Approach for Twitter Sentiment Analysis

2020 ◽  
Vol 12 (2) ◽  
pp. 21-34
Author(s):  
Mostefai Abdelkader
Keyword(s):  
Deep Learning ◽  
Sentiment Analysis ◽  
State Of The Art ◽  
Learning Approach ◽  
Probabilistic Representation ◽  
Effective Manner ◽  
Textual Data ◽  
Positive Class ◽  
Negative Class ◽  
Deep Learning Model

In recent years, increasing attention is being paid to sentiment analysis on microblogging platforms such as Twitter. Sentiment analysis refers to the task of detecting whether a textual item (e.g., a tweet) contains an opinion about a topic. This paper proposes a probabilistic deep learning approach for sentiments analysis. The deep learning model used is a convolutional neural network (CNN). The main contribution of this approach is a new probabilistic representation of the text to be fed as input to the CNN. This representation is a matrix that stores for each word composing the message the probability that it belongs to a positive class and the probability that it belongs to a negative class. The proposed approach is evaluated on four well-known datasets HCR, OMD, STS-gold, and a dataset provided by the SemEval-2017 Workshop. The results of the experiments show that the proposed approach competes with the state-of-the-art sentiment analyzers and has the potential to detect sentiments from textual data in an effective manner.

scholarly journals Comparing Deep-Learning Architectures and Traditional Machine-Learning Approaches for Satire Identification in Spanish Tweets

Mathematics ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. 2075
Author(s):  
Óscar Apolinario-Arzube ◽  
José Antonio García-Díaz ◽  
José Medina-Moreira ◽  
Harry Luna-Aveiga ◽  
Rafael Valencia-García
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
User Interfaces ◽  
State Of The Art ◽  
Learning Approaches ◽  
Word Embeddings ◽  
Linguistic Features ◽  
Intended Meaning ◽  
Language User ◽  
Learning Architectures

Automatic satire identification can help to identify texts in which the intended meaning differs from the literal meaning, improving tasks such as sentiment analysis, fake news detection or natural-language user interfaces. Typically, satire identification is performed by training a supervised classifier for finding linguistic clues that can determine whether a text is satirical or not. For this, the state-of-the-art relies on neural networks fed with word embeddings that are capable of learning interesting characteristics regarding the way humans communicate. However, as far as our knowledge goes, there are no comprehensive studies that evaluate these techniques in Spanish in the satire identification domain. Consequently, in this work we evaluate several deep-learning architectures with Spanish pre-trained word-embeddings and compare the results with strong baselines based on term-counting features. This evaluation is performed with two datasets that contain satirical and non-satirical tweets written in two Spanish variants: European Spanish and Mexican Spanish. Our experimentation revealed that term-counting features achieved similar results to deep-learning approaches based on word-embeddings, both outperforming previous results based on linguistic features. Our results suggest that term-counting features and traditional machine learning models provide competitive results regarding automatic satire identification, slightly outperforming state-of-the-art models.

scholarly journals Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines

2019 ◽  
Author(s):  
Ngoc Hieu Tran ◽  
Rui Qiao ◽  
Lei Xin ◽  
Xin Chen ◽  
Baozhen Shan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Deep Learning ◽  
De Novo ◽  
Mass Spectrometry Data ◽  
Main Role ◽  
Accurate Identification ◽  
Identification Rate ◽  
Cell Responses ◽  
First Time ◽  
Deep Learning Model

AbstractTumor-specific neoantigens play the main role for developing personal vaccines in cancer immunotherapy. We propose, for the first time, a personalized de novo sequencing workflow to identify HLA-I and HLA-II neoantigens directly and solely from mass spectrometry data. Our workflow trains a personal deep learning model on the immunopeptidome of an individual patient and then uses it to predict mutated neoantigens of that patient. This personalized learning and mass spectrometry-based approach enables comprehensive and accurate identification of neoantigens. We applied the workflow to datasets of five melanoma patients and substantially improved the accuracy and identification rate of de novo HLA peptides by 14.3% and 38.9%, respectively. This subsequently led to the identification of 10,440 HLA-I and 1,585 HLA-II new peptides that were not presented in existing databases. Most importantly, our workflow successfully discovered 17 neoantigens of both HLA-I and HLA-II, including those with validated T cell responses and those novel neoantigens that had not been reported in previous studies.

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