Protein–protein interactions (PPIs) are involved in an extensive variety of biological procedures, including cell-to-cell interactions, and metabolic and developmental control. PPIs are becoming one of the most important aims of system biology. PPIs act as a fundamental part in predicting the protein function of the target protein and the drug ability of molecules. An abundance of work has been performed to develop methods to computationally predict PPIs as this supplements laboratory trials and offers a cost-effective way of predicting the most likely set of interactions at the entire proteome scale. This article presents an innovative feature representation method (CAA-PPI) to extract features from protein sequences using two different encoding strategies followed by an ensemble learning method. The random forest methodwas used as a classifier for PPI prediction. CAA-PPI considers the role of the trigram and bond of a given amino acid with its nearby ones. The proposed PPI model achieved more than a 98% prediction accuracy with one encoding scheme and more than a 95% prediction accuracy with another encoding scheme for the two diverse PPI datasets, i.e., H. pylori and Yeast. Further, investigations were performed to compare the CAA-PPI approach with existing sequence-based methods and revealed the proficiency of the proposed method with both encoding strategies. To further assess the practical prediction competence, a blind test was implemented on five other species’ datasets independent of the training set, and the obtained results ascertained the productivity of CAA-PPI with both encoding schemes.
{"title":"CAA-PPI: A Computational Feature Design to Predict Protein–Protein Interactions Using Different Encoding Strategies","authors":"Bhawna Mewara, Gunjan Sahni, Soniya Lalwani, Rajesh Kumar","doi":"10.3390/ai4020020","DOIUrl":"https://doi.org/10.3390/ai4020020","url":null,"abstract":"Protein–protein interactions (PPIs) are involved in an extensive variety of biological procedures, including cell-to-cell interactions, and metabolic and developmental control. PPIs are becoming one of the most important aims of system biology. PPIs act as a fundamental part in predicting the protein function of the target protein and the drug ability of molecules. An abundance of work has been performed to develop methods to computationally predict PPIs as this supplements laboratory trials and offers a cost-effective way of predicting the most likely set of interactions at the entire proteome scale. This article presents an innovative feature representation method (CAA-PPI) to extract features from protein sequences using two different encoding strategies followed by an ensemble learning method. The random forest methodwas used as a classifier for PPI prediction. CAA-PPI considers the role of the trigram and bond of a given amino acid with its nearby ones. The proposed PPI model achieved more than a 98% prediction accuracy with one encoding scheme and more than a 95% prediction accuracy with another encoding scheme for the two diverse PPI datasets, i.e., H. pylori and Yeast. Further, investigations were performed to compare the CAA-PPI approach with existing sequence-based methods and revealed the proficiency of the proposed method with both encoding strategies. To further assess the practical prediction competence, a blind test was implemented on five other species’ datasets independent of the training set, and the obtained results ascertained the productivity of CAA-PPI with both encoding schemes.","PeriodicalId":93633,"journal":{"name":"AI (Basel, Switzerland)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136000603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Riad Ibadulla, Thomas M. Chen, Constantino Carlos Reyes-Aldasoro
This paper describes the transformation of a traditional in silico classification network into an optical fully convolutional neural network with high-resolution feature maps and kernels. When using the free-space 4f system to accelerate the inference speed of neural networks, higher resolutions of feature maps and kernels can be used without the loss in frame rate. We present FatNet for the classification of images, which is more compatible with free-space acceleration than standard convolutional classifiers. It neglects the standard combination of convolutional feature extraction and classifier dense layers by performing both in one fully convolutional network. This approach takes full advantage of the parallelism in the 4f free-space system and performs fewer conversions between electronics and optics by reducing the number of channels and increasing the resolution, making this network faster in optics than off-the-shelf networks. To demonstrate the capabilities of FatNet, it was trained with the CIFAR100 dataset on GPU and the simulator of the 4f system. A comparison of the results against ResNet-18 shows 8.2 times fewer convolution operations at the cost of only 6% lower accuracy. This demonstrates that the optical implementation of FatNet results in significantly faster inference than the optical implementation of the original ResNet-18. These are promising results for the approach of training deep learning with high-resolution kernels in the direction toward the upcoming optics era.
{"title":"FatNet: High-Resolution Kernels for Classification Using Fully Convolutional Optical Neural Networks","authors":"Riad Ibadulla, Thomas M. Chen, Constantino Carlos Reyes-Aldasoro","doi":"10.3390/ai4020018","DOIUrl":"https://doi.org/10.3390/ai4020018","url":null,"abstract":"This paper describes the transformation of a traditional in silico classification network into an optical fully convolutional neural network with high-resolution feature maps and kernels. When using the free-space 4f system to accelerate the inference speed of neural networks, higher resolutions of feature maps and kernels can be used without the loss in frame rate. We present FatNet for the classification of images, which is more compatible with free-space acceleration than standard convolutional classifiers. It neglects the standard combination of convolutional feature extraction and classifier dense layers by performing both in one fully convolutional network. This approach takes full advantage of the parallelism in the 4f free-space system and performs fewer conversions between electronics and optics by reducing the number of channels and increasing the resolution, making this network faster in optics than off-the-shelf networks. To demonstrate the capabilities of FatNet, it was trained with the CIFAR100 dataset on GPU and the simulator of the 4f system. A comparison of the results against ResNet-18 shows 8.2 times fewer convolution operations at the cost of only 6% lower accuracy. This demonstrates that the optical implementation of FatNet results in significantly faster inference than the optical implementation of the original ResNet-18. These are promising results for the approach of training deep learning with high-resolution kernels in the direction toward the upcoming optics era.","PeriodicalId":93633,"journal":{"name":"AI (Basel, Switzerland)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136329582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Laith R Sultan, Theodore W Cary, Maryam Al-Hasani, Mrigendra B Karmacharya, Santosh S Venkatesh, Charles-Antoine Assenmacher, Enrico Radaelli, Chandra M Sehgal
Machine learning for medical imaging not only requires sufficient amounts of data for training and testing but also that the data be independent. It is common to see highly interdependent data whenever there are inherent correlations between observations. This is especially to be expected for sequential imaging data taken from time series. In this study, we evaluate the use of statistical measures to test the independence of sequential ultrasound image data taken from the same case. A total of 1180 B-mode liver ultrasound images with 5903 regions of interests were analyzed. The ultrasound images were taken from two liver disease groups, fibrosis and steatosis, as well as normal cases. Computer-extracted texture features were then used to train a machine learning (ML) model for computer-aided diagnosis. The experiment resulted in high two-category diagnosis using logistic regression, with AUC of 0.928 and high performance of multicategory classification, using random forest ML, with AUC of 0.917. To evaluate the image region independence for machine learning, Jenson–Shannon (JS) divergence was used. JS distributions showed that images of normal liver were independent from each other, while the images from the two disease pathologies were not independent. To guarantee the generalizability of machine learning models, and to prevent data leakage, multiple frames of image data acquired of the same object should be tested for independence before machine learning. Such tests can be applied to real-world medical image problems to determine if images from the same subject can be used for training.
{"title":"Can Sequential Images from the Same Object Be Used for Training Machine Learning Models? A Case Study for Detecting Liver Disease by Ultrasound Radiomics.","authors":"Laith R Sultan, Theodore W Cary, Maryam Al-Hasani, Mrigendra B Karmacharya, Santosh S Venkatesh, Charles-Antoine Assenmacher, Enrico Radaelli, Chandra M Sehgal","doi":"10.3390/ai3030043","DOIUrl":"https://doi.org/10.3390/ai3030043","url":null,"abstract":"Machine learning for medical imaging not only requires sufficient amounts of data for training and testing but also that the data be independent. It is common to see highly interdependent data whenever there are inherent correlations between observations. This is especially to be expected for sequential imaging data taken from time series. In this study, we evaluate the use of statistical measures to test the independence of sequential ultrasound image data taken from the same case. A total of 1180 B-mode liver ultrasound images with 5903 regions of interests were analyzed. The ultrasound images were taken from two liver disease groups, fibrosis and steatosis, as well as normal cases. Computer-extracted texture features were then used to train a machine learning (ML) model for computer-aided diagnosis. The experiment resulted in high two-category diagnosis using logistic regression, with AUC of 0.928 and high performance of multicategory classification, using random forest ML, with AUC of 0.917. To evaluate the image region independence for machine learning, Jenson–Shannon (JS) divergence was used. JS distributions showed that images of normal liver were independent from each other, while the images from the two disease pathologies were not independent. To guarantee the generalizability of machine learning models, and to prevent data leakage, multiple frames of image data acquired of the same object should be tested for independence before machine learning. Such tests can be applied to real-world medical image problems to determine if images from the same subject can be used for training.","PeriodicalId":93633,"journal":{"name":"AI (Basel, Switzerland)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9511699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40378366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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