scholarly journals HippUnfold: Automated hippocampal unfolding, morphometry, and subfield segmentation

2021 ◽  
Author(s):  
Jordan DeKraker ◽  
Roy AM Haast ◽  
Mohamed D Yousif ◽  
Bradley Karat ◽  
Stefan Köhler ◽  
...  
Keyword(s):  
Feature Extraction ◽  
Deep Learning ◽  
Construct Validity ◽  
State Of The Art ◽  
Laminar Structure ◽  
Topological Constraints ◽  
Hippocampal Subfields ◽  
Micro Scale ◽  
Subject Specific ◽  
Topological Framework

AbstractThe archicortical hippocampus differs, like the neocortex, in its folding patterns between individuals. Here, we present an automated and robust BIDS-App, HippUnfold, for defining and indexing subject-specific hippocampal folding in MRI, analogous to popular tools used in neocortical reconstruction. This is critical for inter-individual alignment, with topology as the basis for homology. This topological framework enables qualitatively new analyses of morphological and laminar structure in the hippocampus or hippocampal subfields, and is critical for the advancement of neuroimaging analyses at a meso- or micro-scale. HippUnfold uses state-of-the-art deep learning combined with previously developed topological constraints on hippocampal tissue. It is designed to work with commonly employed sub-millimetric MRI acquisitions, with extensibility to microscopic resolutions as well. In this paper we illustrate the power of HippUnfold in feature extraction, and its construct validity compared to several extant hippocampal subfield analysis methods.

scholarly journals A Mobile Percussograph for Medical Examination of the Torso

2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Kayode P Ayodele ◽  
Femi J Olugbon ◽  
Oluwadare Ogunlade ◽  
Olawale B Akinwale ◽  
Oluwasegun T Akinniyi ◽  
...  
Keyword(s):  
Feature Extraction ◽  
Classification Accuracy ◽  
State Of The Art ◽  
General Purpose ◽  
Decay Rates ◽  
Observer Agreement ◽  
Cross Entropy ◽  
Specific Test ◽  
B Spline ◽  
Subject Specific

Medical percussion is a free, low-risk procedure used by physicians during physical examination of patients. Although it is very useful procedure, a downside to manual percussion is that its results are subjective, with typically low inter-observer agreement. Not much work has been done, however, to create automated and reliable percussion devices or percussograph. This paper reports the development of a mobile percussograph. A spring-loaded solenoid was used as the plessor generating mechanical impact for application to a subject’s skin. Generated signals were amplified and digitized at a rate of 22.1 kHz. Thereafter, Frequency B-Spline (FBSP) base wavelet transform at 512 scales was used for feature extraction. Spectrographs generated from the wavelet coefficients were used for training a MobileNet network with 17 inverted layers for a 3-way classification.  Training employed a cross entropy loss function and the Adam optimization algorithm. Learning rate was 0.001, and first and second moment decay rates were 0.9 and 0.999 respectively. Subject-specific test accuracies of 92.9 %, 93.7 %, and 96.4 % were obtained for three subjects, while the cross-subject classification accuracy was 95.0 %. As this is the first reported general purpose mobile percussograph reported in the literature, these results are state-of-the-art. This study has established the viability of implementing mobile percussography in a standard, repeatable and accurate manner, which can lead to faster and more reliable medical percussion globally.Keywords— MobileNet, Percussion, Percussograph, Percussography, Wavelets

scholarly journals Automating Morphological Profiling with Generic Deep Convolutional Networks

2016 ◽  
Author(s):  
Nick Pawlowski ◽  
Juan C Caicedo ◽  
Shantanu Singh ◽  
Anne E Carpenter ◽  
Amos Storkey
Keyword(s):  
Computer Vision ◽  
Feature Extraction ◽  
Deep Learning ◽  
Processing Speed ◽  
State Of The Art ◽  
Learning Models ◽  
Convolutional Networks ◽  
Automated Processing ◽  
Classical Computer ◽  
Microscopy Images

AbstractMorphological profiling aims to create signatures of genes, chemicals and diseases from microscopy images. Current approaches use classical computer vision-based segmentation and feature extraction. Deep learning models achieve state-of-the-art performance in many computer vision tasks such as classification and segmentation. We propose to transfer activation features of generic deep convolutional networks to extract features for morphological profiling. Our approach surpasses currently used methods in terms of accuracy and processing speed. Furthermore, it enables fully automated processing of microscopy images without need for single cell identification.

scholarly journals A Deep Feature Extraction Method for HEp-2 Cell Image Classification

Electronics ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 20 ◽  
Author(s):  
Caleb Vununu ◽  
Suk-Hwan Lee ◽  
Ki-Ryong Kwon
Keyword(s):  
Feature Extraction ◽  
Deep Learning ◽  
Extraction Method ◽  
State Of The Art ◽  
Feature Learning ◽  
Cell Types ◽  
Feature Representation ◽  
Feature Extraction Method ◽  
Cell Image ◽  
Art Methods

The automated and accurate classification of the images portraying the Human Epithelial cells of type 2 (HEp-2) represents one of the most important steps in the diagnosis procedure of many autoimmune diseases. The extreme intra-class variations of the HEp-2 cell images datasets drastically complicates the classification task. We propose in this work a classification framework that, unlike most of the state-of-the-art methods, uses a deep learning-based feature extraction method in a strictly unsupervised way. We propose a deep learning-based hybrid feature learning with two levels of deep convolutional autoencoders. The first level takes the original cell images as the inputs and learns to reconstruct them, in order to capture the features related to the global shape of the cells, and the second network takes the gradients of the images, in order to encode the localized changes in intensity (gray variations) that characterize each cell type. A final feature vector is constructed by combining the latent representations extracted from the two networks, giving a highly discriminative feature representation. The created features will be fed to a nonlinear classifier whose output will represent the type of the cell image. We have tested the discriminability of the proposed features on two of the most popular HEp-2 cell classification datasets, the SNPHEp-2 and ICPR 2016 datasets. The results show that the proposed features manage to capture the distinctive characteristics of the different cell types while performing at least as well as the actual deep learning-based state-of-the-art methods in terms of discrimination.

Smart teaching mode based on particle swarm image recognition and human-computer interaction deep learning

2020 ◽  
Vol 39 (4) ◽  
pp. 5699-5711
Author(s):  
Shirong Long ◽  
Xuekong Zhao
Keyword(s):  
Feature Extraction ◽  
Particle Swarm Optimization ◽  
Deep Learning ◽  
Real Time ◽  
Image Recognition ◽  
Particle Swarm ◽  
Learning Technology ◽  
Search Performance ◽  
Swarm Optimization ◽  
Teaching Mode

The smart teaching mode overcomes the shortcomings of traditional teaching online and offline, but there are certain deficiencies in the real-time feature extraction of teachers and students. In view of this, this study uses the particle swarm image recognition and deep learning technology to process the intelligent classroom video teaching image and extracts the classroom task features in real time and sends them to the teacher. In order to overcome the shortcomings of the premature convergence of the standard particle swarm optimization algorithm, an improved strategy for multiple particle swarm optimization algorithms is proposed. In order to improve the premature problem in the search performance algorithm of PSO algorithm, this paper combines the algorithm with the useful attributes of other algorithms to improve the particle diversity in the algorithm, enhance the global search ability of the particle, and achieve effective feature extraction. The research indicates that the method proposed in this paper has certain practical effects and can provide theoretical reference for subsequent related research.

Levenshtein Augmentation Improves Performance of SMILES Based Deep-Learning Synthesis Prediction

2020 ◽  
Author(s):  
Dean Sumner ◽  
Jiazhen He ◽  
Amol Thakkar ◽  
Ola Engkvist ◽  
Esben Jannik Bjerrum
Keyword(s):  
Neural Networks ◽  
Pattern Recognition ◽  
Deep Learning ◽  
Recurrent Neural Networks ◽  
Data Augmentation ◽  
State Of The Art ◽  
Sequence Similarity ◽  
Learning Models ◽  
Underlying Network

<p>SMILES randomization, a form of data augmentation, has previously been shown to increase the performance of deep learning models compared to non-augmented baselines. Here, we propose a novel data augmentation method we call “Levenshtein augmentation” which considers local SMILES sub-sequence similarity between reactants and their respective products when creating training pairs. The performance of Levenshtein augmentation was tested using two state of the art models - transformer and sequence-to-sequence based recurrent neural networks with attention. Levenshtein augmentation demonstrated an increase performance over non-augmented, and conventionally SMILES randomization augmented data when used for training of baseline models. Furthermore, Levenshtein augmentation seemingly results in what we define as <i>attentional gain </i>– an enhancement in the pattern recognition capabilities of the underlying network to molecular motifs.</p>

Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Ferdinand Filip ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
State Of The Art ◽  
Science Methods ◽  
Learning Models ◽  
Diverse Range ◽  
Hybrid Machine ◽  
Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

Deep Learning for text in limted data settings

2020 ◽  
Author(s):  
Pathikkumar Patel ◽  
Bhargav Lad ◽  
Jinan Fiaidhi
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Transfer Learning ◽  
Text Classification ◽  
State Of The Art ◽  
Time Series Forecasting ◽  
Text Data ◽  
Performance Levels

During the last few years, RNN models have been extensively used and they have proven to be better for sequence and text data. RNNs have achieved state-of-the-art performance levels in several applications such as text classification, sequence to sequence modelling and time series forecasting. In this article we will review different Machine Learning and Deep Learning based approaches for text data and look at the results obtained from these methods. This work also explores the use of transfer learning in NLP and how it affects the performance of models on a specific application of sentiment analysis.

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

Multi Disease-Prediction Framework Using Hybrid Deep Learning: An Optimal Prediction Model (Preprint)

2020 ◽  
Author(s):  
Anusha Ampavathi ◽  
Vijaya Saradhi T
Keyword(s):  
Feature Extraction ◽  
Big Data ◽  
Deep Learning ◽  
Weight Function ◽  
Optimization Algorithm ◽  
Large Scale ◽  
Heuristic Algorithms ◽  
Disease Prediction ◽  
Health Care Decisions ◽  
Proposed Model

UNSTRUCTURED Big data and its approaches are generally helpful for healthcare and biomedical sectors for predicting the disease. For trivial symptoms, the difficulty is to meet the doctors at any time in the hospital. Thus, big data provides essential data regarding the diseases on the basis of the patient’s symptoms. For several medical organizations, disease prediction is important for making the best feasible health care decisions. Conversely, the conventional medical care model offers input as structured that requires more accurate and consistent prediction. This paper is planned to develop the multi-disease prediction using the improvised deep learning concept. Here, the different datasets pertain to “Diabetes, Hepatitis, lung cancer, liver tumor, heart disease, Parkinson’s disease, and Alzheimer’s disease”, from the benchmark UCI repository is gathered for conducting the experiment. The proposed model involves three phases (a) Data normalization (b) Weighted normalized feature extraction, and (c) prediction. Initially, the dataset is normalized in order to make the attribute's range at a certain level. Further, weighted feature extraction is performed, in which a weight function is multiplied with each attribute value for making large scale deviation. Here, the weight function is optimized using the combination of two meta-heuristic algorithms termed as Jaya Algorithm-based Multi-Verse Optimization algorithm (JA-MVO). The optimally extracted features are subjected to the hybrid deep learning algorithms like “Deep Belief Network (DBN) and Recurrent Neural Network (RNN)”. As a modification to hybrid deep learning architecture, the weight of both DBN and RNN is optimized using the same hybrid optimization algorithm. Further, the comparative evaluation of the proposed prediction over the existing models certifies its effectiveness through various performance measures.

scholarly journals Deep Learning for Transient Image Reconstruction from ToF Data

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 1962
Author(s):  
Enrico Buratto ◽  
Adriano Simonetto ◽  
Gianluca Agresti ◽  
Henrik Schäfer ◽  
Pietro Zanuttigh
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Light Response ◽  
Real Data ◽  
Depth Image ◽  
Learning Approach ◽  
Multiple Reflections ◽  
Noisy Input ◽  
Novel Approach ◽  
Incoming Light

In this work, we propose a novel approach for correcting multi-path interference (MPI) in Time-of-Flight (ToF) cameras by estimating the direct and global components of the incoming light. MPI is an error source linked to the multiple reflections of light inside a scene; each sensor pixel receives information coming from different light paths which generally leads to an overestimation of the depth. We introduce a novel deep learning approach, which estimates the structure of the time-dependent scene impulse response and from it recovers a depth image with a reduced amount of MPI. The model consists of two main blocks: a predictive model that learns a compact encoded representation of the backscattering vector from the noisy input data and a fixed backscattering model which translates the encoded representation into the high dimensional light response. Experimental results on real data show the effectiveness of the proposed approach, which reaches state-of-the-art performances.

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