scholarly journals Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system

2020 ◽  
Author(s):  
Manolo F. Perez ◽  
Isabel A. S. Bonatelli ◽  
Monique Romeiro-Brito ◽  
Fernando F. Franco ◽  
Nigel P. Taylor ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Species Delimitation ◽  
Approximate Bayesian Computation ◽  
Learning Algorithm ◽  
Bayesian Computation ◽  
Cryptic Diversity ◽  
Test Species ◽  
Approximate Bayesian

AbstractDelimiting species boundaries is a major goal in evolutionary biology. An increasing body of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihood, and machine learning approaches, are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species with a sky-island distribution and taxonomic uncertainty. To validate our proposed method, we also applied the same strategy on sequence data from widely accepted species from the genus Drosophila. The results show that our CNN approach has high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than the ABC procedure. For Pilosocereus, the delimitation hypothesis based on a splitter taxonomic arrangement without migration showed the highest probability in both CNN and ABC approaches. The splits observed within P. aurisetus agree with previous taxonomic conjectures considering more taxonomic entities within currently accepted species. Our results highlight the cryptic diversity within P. aurisetus and show that CNNs are a promising approach for distinguishing divergent and complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC. Keywords: Species delimitation, fragmented systems, recent diversification, deep learning, Convolutional Neural Networks, Approximate Bayesian Computation

scholarly journals MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Yang-Ming Lin ◽  
Ching-Tai Chen ◽  
Jia-Ming Chang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Large Scale ◽  
Learning Algorithm ◽  
Pearson Correlation ◽  
Tandem Mass ◽  
Spectral Library ◽  
Deep Convolutional Neural Networks ◽  
Library Search

Abstract Background Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An accurate tandem mass spectrum prediction tool is thus crucial in expanding the peptide space and increasing the coverage of spectral library search. Results We propose MS2CNN, a non-linear regression model based on deep convolutional neural networks, a deep learning algorithm. The features for our model are amino acid composition, predicted secondary structure, and physical-chemical features such as isoelectric point, aromaticity, helicity, hydrophobicity, and basicity. MS2CNN was trained with five-fold cross validation on a three-way data split on the large-scale human HCD MS2 dataset of Orbitrap LC-MS/MS downloaded from the National Institute of Standards and Technology. It was then evaluated on a publicly available independent test dataset of human HeLa cell lysate from LC-MS experiments. On average, our model shows better cosine similarity and Pearson correlation coefficient (0.690 and 0.632) than MS2PIP (0.647 and 0.601) and is comparable with pDeep (0.692 and 0.642). Notably, for the more complex MS2 spectra of 3+ peptides, MS2PIP is significantly better than both MS2PIP and pDeep. Conclusions We showed that MS2CNN outperforms MS2PIP for 2+ and 3+ peptides and pDeep for 3+ peptides. This implies that MS2CNN, the proposed convolutional neural network model, generates highly accurate MS2 spectra for LC-MS/MS experiments using Orbitrap machines, which can be of great help in protein and peptide identifications. The results suggest that incorporating more data for deep learning model may improve performance.

scholarly journals Detecting The Speaker Language Using CNN Deep Learning Algorithm

2022 ◽  
pp. 43-52
Author(s):  
Fawziya M. Rammo ◽  
Mohammed N. Al-Hamdani
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Open Source ◽  
Convolutional Neural Networks ◽  
Learning Algorithm ◽  
Language Models ◽  
Mel Frequency Cepstral Coefficients ◽  
Deep Learning Algorithm ◽  
Time Frames

Many languages identification (LID) systems rely on language models that use machine learning (ML) approaches, LID systems utilize rather long recording periods to achieve satisfactory accuracy. This study aims to extract enough information from short recording intervals in order to successfully classify the spoken languages under test. The classification process is based on frames of (2-18) seconds where most of the previous LID systems were based on much longer time frames (from 3 seconds to 2 minutes). This research defined and implemented many low-level features using MFCC (Mel-frequency cepstral coefficients), containing speech files in five languages (English. French, German, Italian, Spanish), from voxforge.org an open-source corpus that consists of user-submitted audio clips in various languages, is the source of data used in this paper. A CNN (convolutional Neural Networks) algorithm applied in this paper for classification and the result was perfect, binary language classification had an accuracy of 100%, and five languages classification with six languages had an accuracy of 99.8%.

scholarly journals Using Slit-Lamp Images for Deep Learning-Based Identification of Bacterial and Fungal Keratitis: Model Development and Validation with Different Convolutional Neural Networks

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1246
Author(s):  
Ning Hung ◽  
Andy Kuan-Yu Shih ◽  
Chihung Lin ◽  
Ming-Tse Kuo ◽  
Yih-Shiou Hwang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Diagnostic Accuracy ◽  
Convolutional Neural Networks ◽  
Learning Algorithm ◽  
Model Performance ◽  
Fungal Keratitis ◽  
Classification Model ◽  
Slit Lamp ◽  
Deep Learning Algorithm

In this study, we aimed to develop a deep learning model for identifying bacterial keratitis (BK) and fungal keratitis (FK) by using slit-lamp images. We retrospectively collected slit-lamp images of patients with culture-proven microbial keratitis between 1 January 2010 and 31 December 2019 from two medical centers in Taiwan. We constructed a deep learning algorithm consisting of a segmentation model for cropping cornea images and a classification model that applies different convolutional neural networks (CNNs) to differentiate between FK and BK. The CNNs included DenseNet121, DenseNet161, DenseNet169, DenseNet201, EfficientNetB3, InceptionV3, ResNet101, and ResNet50. The model performance was evaluated and presented as the area under the curve (AUC) of the receiver operating characteristic curves. A gradient-weighted class activation mapping technique was used to plot the heat map of the model. By using 1330 images from 580 patients, the deep learning algorithm achieved the highest average accuracy of 80.0%. Using different CNNs, the diagnostic accuracy for BK ranged from 79.6% to 95.9%, and that for FK ranged from 26.3% to 65.8%. The CNN of DenseNet161 showed the best model performance, with an AUC of 0.85 for both BK and FK. The heat maps revealed that the model was able to identify the corneal infiltrations. The model showed a better diagnostic accuracy than the previously reported diagnostic performance of both general ophthalmologists and corneal specialists.

scholarly journals Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation

2020 ◽  
Author(s):  
Théophile Sanchez ◽  
Jean Cury ◽  
Guillaume Charpiat ◽  
Flora Jay
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Deep Learning ◽  
Population Size ◽  
Effective Population Size ◽  
Approximate Bayesian Computation ◽  
Summary Statistics ◽  
Effective Population ◽  
The Past ◽  
Approximate Bayesian

AbstractFor the past decades, simulation-based likelihood-free inference methods have enabled researchers to address numerous population genetics problems. As the richness and amount of simulated and real genetic data keep increasing, the field has a strong opportunity to tackle tasks that current methods hardly solve. However, high data dimensionality forces most methods to summarize large genomic datasets into a relatively small number of handcrafted features (summary statistics). Here we propose an alternative to summary statistics, based on the automatic extraction of relevant information using deep learning techniques. Specifically, we design artificial neural networks (ANNs) that take as input single nucleotide polymorphic sites (SNPs) found in individuals sampled from a single population and infer the past effective population size history. First, we provide guidelines to construct artificial neural networks that comply with the intrinsic properties of SNP data such as invariance to permutation of haplotypes, long scale interactions between SNPs and variable genomic length. Thanks to a Bayesian hyperparameter optimization procedure, we evaluate the performance of multiple networks and compare them to well established methods like Approximate Bayesian Computation (ABC). Even without the expert knowledge of summary statistics, our approach compares fairly well to an ABC based on handcrafted features. Furthermore we show that combining deep learning and ABC can improve performance while taking advantage of both frameworks. Finally, we apply our approach to reconstruct the effective population size history of cattle breed populations.

scholarly journals Convolutional Neural Networks(CNN) based Eye-Gaze Tracking System using Machine Learning Algorithm

2021 ◽  
Vol 5 (2) ◽  
pp. 36-40
Author(s):  
Prakash Kanade ◽  
Fortune David ◽  
Sunay Kanade
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
User Interfaces ◽  
Data Science ◽  
Learning Algorithm ◽  
Tracking System ◽  
Eye Gaze ◽  
Classification Systems ◽  
Gaze Tracking

To avoid the rising number of car crash deaths, which are mostly caused by drivers' inattentiveness, a paradigm shift is expected. The knowledge of a driver's look area may provide useful details about his or her point of attention. Cars with accurate and low-cost gaze classification systems can increase driver safety. When drivers shift their eyes without turning their heads to look at objects, the margin of error in gaze detection increases. For new consumer electronic applications such as driver tracking systems and novel user interfaces, accurate and effective eye gaze prediction is critical. Such systems must be able to run efficiently in difficult, unconstrained conditions while using reduced power and expense. A deep learning-based gaze estimation technique has been considered to solve this issue, with an emphasis on WSN based Convolutional Neural Networks (CNN) based system. The proposed study proposes the following architecture, which is focused on data science: The first is a novel neural network model that is programmed to manipulate any possible visual feature, such as the states of both eyes and head location, as well as many augmentations; the second is a data fusion approach that incorporates several gaze datasets. However, due to different factors such as environment light shifts, reflections on glasses surface, and motion and optical blurring of the captured eye signal, the accuracy of detecting and classifying the pupil centre and corneal reflection centre depends on a car environment. This work also includes pre-trained models, network structures, and datasets for designing and developing CNN-based deep learning models for Eye-Gaze Tracking and Classification.

scholarly journals Assessment of the Degree of Building Damage Caused by Disaster Using Convolutional Neural Networks in Combination with Ordinal Regression

2019 ◽  
Vol 11 (23) ◽  
pp. 2858 ◽  
Author(s):  
Tianyu Ci ◽  
Zhen Liu ◽  
Ying Wang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Algorithm ◽  
Network Models ◽  
Building Damage ◽  
Ordinal Regression ◽  
Aerial Images ◽  
Deep Learning Algorithm ◽  
Ordinal Regression Model

We propose a new convolutional neural networks method in combination with ordinal regression aiming at assessing the degree of building damage caused by earthquakes with aerial imagery. The ordinal regression model and a deep learning algorithm are incorporated to make full use of the information to improve the accuracy of the assessment. A new loss function was introduced in this paper to combine convolutional neural networks and ordinal regression. Assessing the level of damage to buildings can be considered as equivalent to predicting the ordered labels of buildings to be assessed. In the existing research, the problem has usually been simplified as a problem of pure classification to be further studied and discussed, which ignores the ordinal relationship between different levels of damage, resulting in a waste of information. Data accumulated throughout history are used to build network models for assessing the level of damage, and models for assessing levels of damage to buildings based on deep learning are described in detail, including model construction, implementation methods, and the selection of hyperparameters, and verification is conducted by experiments. When categorizing the damage to buildings into four types, we apply the method proposed in this paper to aerial images acquired from the 2014 Ludian earthquake and achieve an overall accuracy of 77.39%; when categorizing damage to buildings into two types, the overall accuracy of the model is 93.95%, exceeding such values in similar types of theories and methods.

scholarly journals Automated object detection of mechanical fasteners using faster region based convolutional neural networks

2021 ◽  
Vol 11 (6) ◽  
pp. 5430
Author(s):  
M. Karthikeyan ◽  
T. S. Subashini
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Object Detection ◽  
Convolutional Neural Networks ◽  
Learning Algorithm ◽  
Region Of Interest ◽  
Vital Role ◽  
Robot Arm ◽  
Sensors And Actuators ◽  
Mechanical Fasteners

Mechanical fasteners are widely used in manufacturing of hardware and mechanical components such as automobiles, turbine & power generation and industries. Object detection method play a vital role to make a smart system for the society. Internet of things (IoT) leads to automation based on sensors and actuators not enough to build the systems due to limitations of sensors. Computer vision is the one which makes IoT too much smarter using deep learning techniques. Object detection is used to detect, recognize and localize the object in an image or a real time video. In industry revolution, robot arm is used to fit the fasteners to the automobile components. This system will helps the robot to detect the object of fasteners such as screw and nails accordingly to fit to the vehicle moved in the assembly line. Faster R-CNN deep learning algorithm is used to train the custom dataset and object detection is used to detect the fasteners. Region based convolutional neural networks (Faster R-CNN) uses a region proposed network (RPN) network to train the model efficiently and also with the help of Region of Interest able to localize the screw and nails objects with a mean average precision of 0.72 percent leads to accuracy of 95 percent object detection

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