scholarly journals An Empirical Study of Different Approaches for Protein Classification

2014 ◽  
Vol 2014 ◽  
pp. 1-17 ◽  
Author(s):  
Loris Nanni ◽  
Alessandra Lumini ◽  
Sheryl Brahnam
Keyword(s):  
Tertiary Structure ◽  
State Of The Art ◽  
Support Vector ◽  
Protein Classification ◽  
Matrix Representations ◽  
New Methods ◽  
Multiple Datasets ◽  
Different Types ◽  
Scoring Matrix ◽  
Better Than

Many domains would benefit from reliable and efficient systems for automatic protein classification. An area of particular interest in recent studies on automatic protein classification is the exploration of new methods for extracting features from a protein that work well for specific problems. These methods, however, are not generalizable and have proven useful in only a few domains. Our goal is to evaluate several feature extraction approaches for representing proteins by testing them across multiple datasets. Different types of protein representations are evaluated: those starting from the position specific scoring matrix of the proteins (PSSM), those derived from the amino-acid sequence, two matrix representations, and features taken from the 3D tertiary structure of the protein. We also test new variants of proteins descriptors. We develop our system experimentally by comparing and combining different descriptors taken from the protein representations. Each descriptor is used to train a separate support vector machine (SVM), and the results are combined by sum rule. Some stand-alone descriptors work well on some datasets but not on others. Through fusion, the different descriptors provide a performance that works well across all tested datasets, in some cases performing better than the state-of-the-art.

scholarly journals Fighting Together against the Pandemic: Learning Multiple Models on Tomography Images for COVID-19 Diagnosis

AI ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 261-273
Author(s):  
Mario Manzo ◽  
Simone Pellino
Keyword(s):  
Network Architecture ◽  
State Of The Art ◽  
Ensemble Classification ◽  
Effective Vaccine ◽  
Rt Pcr ◽  
Neural Network Architecture ◽  
Experimental Phase ◽  
Different Types ◽  
Polymerase Chain ◽  
Better Than

COVID-19 has been a great challenge for humanity since the year 2020. The whole world has made a huge effort to find an effective vaccine in order to save those not yet infected. The alternative solution is early diagnosis, carried out through real-time polymerase chain reaction (RT-PCR) tests or thorax Computer Tomography (CT) scan images. Deep learning algorithms, specifically convolutional neural networks, represent a methodology for image analysis. They optimize the classification design task, which is essential for an automatic approach with different types of images, including medical. In this paper, we adopt a pretrained deep convolutional neural network architecture in order to diagnose COVID-19 disease from CT images. Our idea is inspired by what the whole of humanity is achieving, as the set of multiple contributions is better than any single one for the fight against the pandemic. First, we adapt, and subsequently retrain for our assumption, some neural architectures that have been adopted in other application domains. Secondly, we combine the knowledge extracted from images by the neural architectures in an ensemble classification context. Our experimental phase is performed on a CT image dataset, and the results obtained show the effectiveness of the proposed approach with respect to the state-of-the-art competitors.

scholarly journals Deep Learning Methods for Classification of Certain Abnormalities in Echocardiography

Electronics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 495
Author(s):  
Imayanmosha Wahlang ◽  
Arnab Kumar Maji ◽  
Goutam Saha ◽  
Prasun Chakrabarti ◽  
Michal Jasinski ◽  
...  
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Support Vector ◽  
Variational Autoencoder ◽  
Different Types ◽  
Static Images ◽  
Long Short Term Memory ◽  
2D And 3D ◽  
Better Than

This article experiments with deep learning methodologies in echocardiogram (echo), a promising and vigorously researched technique in the preponderance field. This paper involves two different kinds of classification in the echo. Firstly, classification into normal (absence of abnormalities) or abnormal (presence of abnormalities) has been done, using 2D echo images, 3D Doppler images, and videographic images. Secondly, based on different types of regurgitation, namely, Mitral Regurgitation (MR), Aortic Regurgitation (AR), Tricuspid Regurgitation (TR), and a combination of the three types of regurgitation are classified using videographic echo images. Two deep-learning methodologies are used for these purposes, a Recurrent Neural Network (RNN) based methodology (Long Short Term Memory (LSTM)) and an Autoencoder based methodology (Variational AutoEncoder (VAE)). The use of videographic images distinguished this work from the existing work using SVM (Support Vector Machine) and also application of deep-learning methodologies is the first of many in this particular field. It was found that deep-learning methodologies perform better than SVM methodology in normal or abnormal classification. Overall, VAE performs better in 2D and 3D Doppler images (static images) while LSTM performs better in the case of videographic images.

scholarly journals Contact Lens Classification by Using Segmented Lens Boundary Features

2018 ◽  
Vol 11 (3) ◽  
pp. 1129
Author(s):  
Nur Ariffin Mohd Zin ◽  
Hishammuddin Asmuni ◽  
Haza Nuzly Abdul Hamed ◽  
Razib M. Othman ◽  
Shahreen Kasim ◽  
...  
Keyword(s):  
Support Vector Machines ◽  
Contact Lens ◽  
State Of The Art ◽  
Classification Method ◽  
Support Vector ◽  
Local Descriptors ◽  
Iris Image ◽  
Vector Machines ◽  
False Reject Rate ◽  
Better Than

Recent studies have shown that the wearing of soft lens may lead to performance degradation with the increase of false reject rate. However, detecting the presence of soft lens is a non-trivial task as its texture that almost indiscernible. In this work, we proposed a classification method to identify the existence of soft lens in iris image. Our proposed method starts with segmenting the lens boundary on top of the sclera region. Then, the segmented boundary is used as features and extracted by local descriptors. These features are then trained and classified using Support Vector Machines. This method was tested on Notre Dame Cosmetic Contact Lens 2013 database. Experiment showed that the proposed method performed better than state of the art methods.

scholarly journals Zoomqa: Residue-Level Single-Model QA Support Vector Machine Utilizing Sequential and 3D Structural Features

2021 ◽  
Author(s):  
Kyle Hippe ◽  
Cade Lilley ◽  
William Berkenpas ◽  
Kiyomi Kishaba ◽  
Renzhi Cao
Keyword(s):  
Protein Complex ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
State Of The Art ◽  
Chemical Properties ◽  
Structural Features ◽  
Residue Level ◽  
Support Vector ◽  
Single Model

ABSTRACTMotivationThe Estimation of Model Accuracy problem is a cornerstone problem in the field of Bioinformatics. When predictions are made for proteins of which we do not know the native structure, we run into an issue to tell how good a tertiary structure prediction is, especially the protein binding regions, which are useful for drug discovery. Currently, most methods only evaluate the overall quality of a protein decoy, and few can work on residue level and protein complex. Here we introduce ZoomQA, a novel, single-model method for assessing the accuracy of a tertiary protein structure / complex prediction at residue level. ZoomQA differs from others by considering the change in chemical and physical features of a fragment structure (a portion of a protein within a radius r of the target amino acid) as the radius of contact increases. Fourteen physical and chemical properties of amino acids are used to build a comprehensive representation of every residue within a protein and grades their placement within the protein as a whole. Moreover, ZoomQA can evaluate the quality of protein complex, which is unique.ResultsWe benchmark ZoomQA on CASP14, it outperforms other state of the art local QA methods and rivals state of the art QA methods in global prediction metrics. Our experiment shows the efficacy of these new features, and shows our method is able to match the performance of other state-of-the-art methods without the use of homology searching against database or PSSM matrix.Availabilityhttp://[email protected]

scholarly journals Toward a General-Purpose Heterogeneous Ensemble for Pattern Classification

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Loris Nanni ◽  
Sheryl Brahnam ◽  
Stefano Ghidoni ◽  
Alessandra Lumini
Keyword(s):  
State Of The Art ◽  
Parameter Tuning ◽  
General Purpose ◽  
Extensive Study ◽  
Support Vector ◽  
Svm Classifier ◽  
Random Subspace ◽  
Sum Rule ◽  
Multiple Datasets ◽  
Heterogeneous Ensemble

We perform an extensive study of the performance of different classification approaches on twenty-five datasets (fourteen image datasets and eleven UCI data mining datasets). The aim is to find General-Purpose (GP) heterogeneous ensembles (requiring little to no parameter tuning) that perform competitively across multiple datasets. The state-of-the-art classifiers examined in this study include the support vector machine, Gaussian process classifiers, random subspace of adaboost, random subspace of rotation boosting, and deep learning classifiers. We demonstrate that a heterogeneous ensemble based on the simple fusion by sum rule of different classifiers performs consistently well across all twenty-five datasets. The most important result of our investigation is demonstrating that some very recent approaches, including the heterogeneous ensemble we propose in this paper, are capable of outperforming an SVM classifier (implemented with LibSVM), even when both kernel selection and SVM parameters are carefully tuned for each dataset.

scholarly journals Undercatch Adjustments for Tipping-Bucket Gauge Measurements of Solid Precipitation

2020 ◽  
Vol 21 (6) ◽  
pp. 1193-1205 ◽  
Author(s):  
John Kochendorfer ◽  
Michael E. Earle ◽  
Daniel Hodyss ◽  
Audrey Reverdin ◽  
Yves-Alain Roulet ◽  
...  
Keyword(s):  
Transfer Functions ◽  
Test Results ◽  
Monitoring Networks ◽  
New Approach ◽  
Solid Precipitation ◽  
New Methods ◽  
Different Types ◽  
Precipitation Records ◽  
Better Than

AbstractHeated tipping-bucket (TB) gauges are used broadly in national weather monitoring networks, but their performance for the measurement of solid precipitation has not been well characterized. Manufacturer-provided TB gauges were evaluated at five test sites during the World Meteorological Organization Solid Precipitation Intercomparison Experiment (WMO-SPICE), with most gauge types tested at more than one site. The test results were used to develop and evaluate adjustments for the undercatch of solid precipitation by heated TB gauges. New methods were also developed to address challenges specific to measurements from heated TB gauges. Tipping-bucket transfer functions were created specifically to minimize the sum of errors over the course of the adjusted multiseasonal accumulation. This was based on the hypothesis that the best transfer function produces the most accurate long-term precipitation records, rather than accurate catch efficiency measurements or accurate daily or hourly precipitation measurements. Using this new approach, an adjustment function derived from multiple gauges was developed that performed better than traditional gauge-specific and multigauge catch efficiency derived adjustments. Because this new multigauge adjustment was developed using six different types of gauges tested at five different sites, it may be applicable to solid precipitation measurements from unshielded heated TB gauges that were not evaluated in WMO-SPICE. In addition, this new method of optimizing transfer functions may be useful for other types of precipitation gauges, as it has many practical advantages over the traditional catch efficiency methods used to derive undercatch adjustments.

scholarly journals A New End-to-End Multi-Dimensional CNN Framework for Land Cover/Land Use Change Detection in Multi-Source Remote Sensing Datasets

2020 ◽  
Vol 12 (12) ◽  
pp. 2010 ◽  
Author(s):  
Seyd Teymoor Seydi ◽  
Mahdi Hasanlou ◽  
Meisam Amani
Keyword(s):  
Remote Sensing ◽  
Change Detection ◽  
State Of The Art ◽  
Polarimetric Synthetic Aperture Radar ◽  
Different Types ◽  
Benchmark Datasets ◽  
Convolution Kernels ◽  
2D And 3D ◽  
Accuracy Indices ◽  
Better Than

The diversity of change detection (CD) methods and the limitations in generalizing these techniques using different types of remote sensing datasets over various study areas have been a challenge for CD applications. Additionally, most CD methods have been implemented in two intensive and time-consuming steps: (a) predicting change areas, and (b) decision on predicted areas. In this study, a novel CD framework based on the convolutional neural network (CNN) is proposed to not only address the aforementioned problems but also to considerably improve the level of accuracy. The proposed CNN-based CD network contains three parallel channels: the first and second channels, respectively, extract deep features on the original first- and second-time imagery and the third channel focuses on the extraction of change deep features based on differencing and staking deep features. Additionally, each channel includes three types of convolution kernels: 1D-, 2D-, and 3D-dilated-convolution. The effectiveness and reliability of the proposed CD method are evaluated using three different types of remote sensing benchmark datasets (i.e., multispectral, hyperspectral, and Polarimetric Synthetic Aperture RADAR (PolSAR)). The results of the CD maps are also evaluated both visually and statistically by calculating nine different accuracy indices. Moreover, the results of the CD using the proposed method are compared to those of several state-of-the-art CD algorithms. All the results prove that the proposed method outperforms the other remote sensing CD techniques. For instance, considering different scenarios, the Overall Accuracies (OAs) and Kappa Coefficients (KCs) of the proposed CD method are better than 95.89% and 0.805, respectively, and the Miss Detection (MD) and the False Alarm (FA) rates are lower than 12% and 3%, respectively.

scholarly journals A Study on Ranking Fusion Approaches for the Retrieval of Medical Publications

Information ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 103
Author(s):  
Teofan Clipa ◽  
Giorgio Maria Di Nunzio
Keyword(s):  
Statistical Analysis ◽  
Relevance Feedback ◽  
Query Expansion ◽  
State Of The Art ◽  
Word Embeddings ◽  
Medical Topic ◽  
Medical Publication ◽  
Different Types ◽  
Text Preprocessing ◽  
Better Than

In this work, we compare and analyze a variety of approaches in the task of medical publication retrieval and, in particular, for the Technology Assisted Review (TAR) task. This problem consists in the process of collecting articles that summarize all evidence that has been published regarding a certain medical topic. This task requires long search sessions by experts in the field of medicine. For this reason, semi-automatic approaches are essential for supporting these types of searches when the amount of data exceeds the limits of users. In this paper, we use state-of-the-art models and weighting schemes with different types of preprocessing as well as query expansion (QE) and relevance feedback (RF) approaches in order to study the best combination for this particular task. We also tested word embeddings representation of documents and queries in addition to three different ranking fusion approaches to see if the merged runs perform better than the single models. In order to make our results reproducible, we have used the collection provided by the Conference and Labs Evaluation Forum (CLEF) eHealth tasks. Query expansion and relevance feedback greatly improve the performance while the fusion of different rankings does not perform well in this task. The statistical analysis showed that, in general, the performance of the system does not depend much on the type of text preprocessing but on which weighting scheme is applied.

scholarly journals Global processing provides malignancy evidence complementary to the information captured by humans or machines following detailed mammogram inspection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ziba Gandomkar ◽  
Somphone Siviengphanom ◽  
Ernest U. Ekpo ◽  
Mo’ayyad Suleiman ◽  
Seyedamir Tavakoli Taba‬ ◽  
...  
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Repeated Measure ◽  
Support Vector ◽  
Computer Algorithms ◽  
Viewing Condition ◽  
Image Presentation ◽  
Average Reader ◽  
Leave One Out ◽  
Better Than

AbstractThe information captured by the gist signal, which refers to radiologists’ first impression arising from an initial global image processing, is poorly understood. We examined whether the gist signal can provide complementary information to data captured by radiologists (experiment 1), or computer algorithms (experiment 2) based on detailed mammogram inspection. In the first experiment, 19 radiologists assessed a case set twice, once based on a half-second image presentation (i.e., gist signal) and once in the usual viewing condition. Their performances in two viewing conditions were compared using repeated measure correlation (rm-corr). The cancer cases (19 cases × 19 readers) exhibited non-significant trend with rm-corr = 0.012 (p = 0.82, CI: −0.09, 0.12). For normal cases (41 cases × 19 readers), a weak correlation of rm-corr = 0.238 (p < 0.001, CI: 0.17, 0.30) was found. In the second experiment, we combined the abnormality score from a state-of-the-art deep learning-based tool (DL) with the radiological gist signal using a support vector machine (SVM). To obtain the gist signal, 53 radiologists assessed images based on half-second image presentation. The SVM performance for each radiologist and an average reader, whose gist responses were the mean abnormality scores given by all 53 readers to each image was assessed using leave-one-out cross-validation. For the average reader, the AUC for gist, DL, and the SVM, were 0.76 (CI: 0.62–0.86), 0.79 (CI: 0.63–0.89), and 0.88 (CI: 0.79–0.94). For all readers with a gist AUC significantly better than chance-level, the SVM outperformed DL. The gist signal provided malignancy evidence with no or weak associations with the information captured by humans in normal radiologic reporting, which involves detailed mammogram inspection. Adding gist signal to a state-of-the-art deep learning-based tool improved its performance for the breast cancer detection.

A Universal Steganalysis Algorithm for JPEG Image Based on Selective SVMs Ensemble

2012 ◽  
Vol 532-533 ◽  
pp. 1548-1552 ◽  
Author(s):  
Da Ya Chen ◽  
Shang Ping Zhong
Keyword(s):  
Detection Rate ◽  
Ensemble Classifier ◽  
Support Vector ◽  
Jpeg Image ◽  
Different Types ◽  
Universal Steganalysis ◽  
Ensemble Algorithm ◽  
Embedding Rate ◽  
Steganalysis Method ◽  
Better Than

Universal steganalysis include feature extraction and steganalyzer design. Most universal steganalysis use Support Vector Machine (SVM) as steganalyzer. However, most SVM-based universal steganalysis are not to be very much effective at lower embedding rates. The reason why selective SVMs ensemble improve the generalization ability was analyzed, and an algorithm to select a part of individual SVMs according to their difference to build the ensemble classifier was proposed, which based on the selected ensemble theory-Many could be better than all. In this paper, the selective SVMs ensemble algorithm was used to construct a strong steganalyzer to improve the performance of steganographic detection. The twenty five experiments on the benchmark with 2000 different types of images show that: for popular steganography methods, and under different conditions of embedding rate, the average detection rate of proposed steganalysis method outperforms the maximum average detection rate for the steganalysis method based on single SVM with improving by 3.05%-12.05%; and for the steganalysis method based on BaggingSVM with improving by 0.2%-1.3%.

Sign in / Sign up

Export Citation Format

Share Document