scholarly journals Systems biology and machine learning approaches identify drug targets in diabetic nephropathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maryam Abedi ◽  
Hamid Reza Marateb ◽  
Mohammad Reza Mohebian ◽  
Seyed Hamid Aghaee-Bakhtiari ◽  
Seyed Mahdi Nassiri ◽  
...  
Keyword(s):  
Machine Learning ◽  
Diabetic Nephropathy ◽  
Drug Targets ◽  
High Performance ◽  
Learning Algorithm ◽  
Enrichment Analysis ◽  
Kidney Cortex ◽  
Learning Approaches ◽  
Microrna Target ◽  
Stage Renal Disease

AbstractDiabetic nephropathy (DN), the leading cause of end-stage renal disease, has become a massive global health burden. Despite considerable efforts, the underlying mechanisms have not yet been comprehensively understood. In this study, a systematic approach was utilized to identify the microRNA signature in DN and to introduce novel drug targets (DTs) in DN. Using microarray profiling followed by qPCR confirmation, 13 and 6 differentially expressed (DE) microRNAs were identified in the kidney cortex and medulla, respectively. The microRNA-target interaction networks for each anatomical compartment were constructed and central nodes were identified. Moreover, enrichment analysis was performed to identify key signaling pathways. To develop a strategy for DT prediction, the human proteome was annotated with 65 biochemical characteristics and 23 network topology parameters. Furthermore, all proteins targeted by at least one FDA-approved drug were identified. Next, mGMDH-AFS, a high-performance machine learning algorithm capable of tolerating massive imbalanced size of the classes, was developed to classify DT and non-DT proteins. The sensitivity, specificity, accuracy, and precision of the proposed method were 90%, 86%, 88%, and 89%, respectively. Moreover, it significantly outperformed the state-of-the-art (P-value ≤ 0.05) and showed very good diagnostic accuracy and high agreement between predicted and observed class labels. The cortex and medulla networks were then analyzed with this validated machine to identify potential DTs. Among the high-rank DT candidates are Egfr, Prkce, clic5, Kit, and Agtr1a which is a current well-known target in DN. In conclusion, a combination of experimental and computational approaches was exploited to provide a holistic insight into the disorder for introducing novel therapeutic targets.

scholarly journals An IoT-Focused Intrusion Detection System Approach Based on Preprocessing Characterization for Cybersecurity Datasets

Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 656
Author(s):  
Xavier Larriva-Novo ◽  
Víctor A. Villagrá ◽  
Mario Vega-Barbas ◽  
Diego Rivera ◽  
Mario Sanz Rodrigo
Keyword(s):  
Machine Learning ◽  
Intrusion Detection ◽  
High Performance ◽  
Learning Algorithm ◽  
Detection System ◽  
Machine Learning Algorithms ◽  
Statistical Characteristics ◽  
Detection Techniques ◽  
Traffic Characteristics ◽  
Benchmark Datasets

Security in IoT networks is currently mandatory, due to the high amount of data that has to be handled. These systems are vulnerable to several cybersecurity attacks, which are increasing in number and sophistication. Due to this reason, new intrusion detection techniques have to be developed, being as accurate as possible for these scenarios. Intrusion detection systems based on machine learning algorithms have already shown a high performance in terms of accuracy. This research proposes the study and evaluation of several preprocessing techniques based on traffic categorization for a machine learning neural network algorithm. This research uses for its evaluation two benchmark datasets, namely UGR16 and the UNSW-NB15, and one of the most used datasets, KDD99. The preprocessing techniques were evaluated in accordance with scalar and normalization functions. All of these preprocessing models were applied through different sets of characteristics based on a categorization composed by four groups of features: basic connection features, content characteristics, statistical characteristics and finally, a group which is composed by traffic-based features and connection direction-based traffic characteristics. The objective of this research is to evaluate this categorization by using various data preprocessing techniques to obtain the most accurate model. Our proposal shows that, by applying the categorization of network traffic and several preprocessing techniques, the accuracy can be enhanced by up to 45%. The preprocessing of a specific group of characteristics allows for greater accuracy, allowing the machine learning algorithm to correctly classify these parameters related to possible attacks.

scholarly journals Predicting Student’s Performance Using Machine Learning Algorithm

2021 ◽  
pp. 53-58
Author(s):  
Sheela Rani P ◽  
Dhivya S ◽  
Dharshini Priya M ◽  
Dharmila Chowdary A
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Prediction Model ◽  
Naive Bayes ◽  
Learning Algorithm ◽  
Naïve Bayes ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Learning Approaches ◽  
K Nearest Neighbors

Machine learning is a new analysis discipline that uses knowledge to boost learning, optimizing the training method and developing the atmosphere within which learning happens. There square measure 2 sorts of machine learning approaches like supervised and unsupervised approach that square measure accustomed extract the knowledge that helps the decision-makers in future to require correct intervention. This paper introduces an issue that influences students' tutorial performance prediction model that uses a supervised variety of machine learning algorithms like support vector machine , KNN(k-nearest neighbors), Naïve Bayes and supplying regression and logistic regression. The results supported by various algorithms are compared and it is shown that the support vector machine and Naïve Bayes performs well by achieving improved accuracy as compared to other algorithms. The final prediction model during this paper may have fairly high prediction accuracy .The objective is not just to predict future performance of students but also provide the best technique for finding the most impactful features that influence student’s while studying.

scholarly journals Environmental Sound Recognition on Embedded Systems: From FPGAs to TPUs

Electronics ◽  
2021 ◽  
Vol 10 (21) ◽  
pp. 2622
Author(s):  
Jurgen Vandendriessche ◽  
Nick Wouters ◽  
Bruno da Silva ◽  
Mimoun Lamrini ◽  
Mohamed Yassin Chkouri ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Machine Learning Techniques ◽  
Sound Recognition ◽  
Learning Approaches ◽  
Environmental Sound ◽  
Embedded Devices ◽  
Power Efficient ◽  
Computationally Intensive ◽  
Environmental Sound Recognition

In recent years, Environmental Sound Recognition (ESR) has become a relevant capability for urban monitoring applications. The techniques for automated sound recognition often rely on machine learning approaches, which have increased in complexity in order to achieve higher accuracy. Nonetheless, such machine learning techniques often have to be deployed on resource and power-constrained embedded devices, which has become a challenge with the adoption of deep learning approaches based on Convolutional Neural Networks (CNNs). Field-Programmable Gate Arrays (FPGAs) are power efficient and highly suitable for computationally intensive algorithms like CNNs. By fully exploiting their parallel nature, they have the potential to accelerate the inference time as compared to other embedded devices. Similarly, dedicated architectures to accelerate Artificial Intelligence (AI) such as Tensor Processing Units (TPUs) promise to deliver high accuracy while achieving high performance. In this work, we evaluate existing tool flows to deploy CNN models on FPGAs as well as on TPU platforms. We propose and adjust several CNN-based sound classifiers to be embedded on such hardware accelerators. The results demonstrate the maturity of the existing tools and how FPGAs can be exploited to outperform TPUs.

A Novel Machine Learning Sepsis Prediction Algorithm for Intended ICU Use (NAVOY Sepsis): A Proof-of-Concept Study (Preprint)

2021 ◽  
Author(s):  
Inger Persson ◽  
Andreas Östling ◽  
Martin Arlbrandt ◽  
Joakim Söderberg ◽  
David Becedas
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Learning Algorithm ◽  
Scoring Systems ◽  
High Accuracy ◽  
Prediction Algorithm ◽  
Massachusetts Institute Of Technology ◽  
Operating Characteristics ◽  
Mortality And Morbidity ◽  
Institute Of Technology

BACKGROUND Despite decades of research, sepsis remains a leading cause of mortality and morbidity in ICUs worldwide. The key to effective management and patient outcome is early detection, where no prospectively validated machine learning prediction algorithm is available for clinical use in Europe today. OBJECTIVE To develop a high-performance machine learning sepsis prediction algorithm based on routinely collected ICU data, designed to be implemented in Europe. METHODS The machine learning algorithm is developed using Convolutional Neural Network, based on the Massachusetts Institute of Technology Lab for Computational Physiology MIMIC-III Clinical Database, focusing on ICU patients aged 18 years or older. Twenty variables are used for prediction, on an hourly basis. Onset of sepsis is defined in accordance with the international Sepsis-3 criteria. RESULTS The developed algorithm NAVOY Sepsis uses 4 hours of input and can with high accuracy predict patients with high risk of developing sepsis in the coming hours. The prediction performance is superior to that of existing sepsis early warning scoring systems, and competes well with previously published prediction algorithms designed to predict sepsis onset in accordance with the Sepsis-3 criteria, as measured by the area under the receiver operating characteristics curve (AUROC) and the area under the precision-recall curve (AUPRC). NAVOY Sepsis yields AUROC = 0.90 and AUPRC = 0.62 for predictions up to 3 hours before sepsis onset. The predictive performance is externally validated on hold-out test data, where NAVOY Sepsis is confirmed to predict sepsis with high accuracy. CONCLUSIONS An algorithm with excellent predictive properties has been developed, based on variables routinely collected at ICUs. This algorithm is to be further validated in an ongoing prospective randomized clinical trial and will be CE marked as Software as a Medical Device, designed for commercial use in European ICUs.

Machine Learning to Design an Auto-tuning System for the Best Compressed Format Detection for Parallel Sparse Computations

2021 ◽  
Author(s):  
Olfa Hamdi-Larbi ◽  
Ichrak Mehrez ◽  
Thomas Dufaud
Keyword(s):  
Machine Learning ◽  
Numerical Method ◽  
High Performance ◽  
Programming Model ◽  
Learning Algorithm ◽  
Sparse Matrix ◽  
Sparse Matrices ◽  
Matrix Compression ◽  
Target Architecture ◽  
Parallel Programming Model

Many applications in scientific computing process very large sparse matrices on parallel architectures. The presented work in this paper is a part of a project where our general aim is to develop an auto-tuner system for the selection of the best matrix compression format in the context of high-performance computing. The target smart system can automatically select the best compression format for a given sparse matrix, a numerical method processing this matrix, a parallel programming model and a target architecture. Hence, this paper describes the design and implementation of the proposed concept. We consider a case study consisting of a numerical method reduced to the sparse matrix vector product (SpMV), some compression formats, the data parallel as a programming model and, a distributed multi-core platform as a target architecture. This study allows extracting a set of important novel metrics and parameters which are relative to the considered programming model. Our metrics are used as input to a machine-learning algorithm to predict the best matrix compression format. An experimental study targeting a distributed multi-core platform and processing random and real-world matrices shows that our system can improve in average up to 7% the accuracy of the machine learning.

Precipitation Estimates from MSG SEVIRI Daytime, Nighttime, and Twilight Data with Random Forests

2014 ◽  
Vol 53 (11) ◽  
pp. 2457-2480 ◽  
Author(s):  
Meike Kühnlein ◽  
Tim Appelhans ◽  
Boris Thies ◽  
Thomas Nauß
Keyword(s):  
Machine Learning ◽  
Random Forests ◽  
Learning Algorithm ◽  
Radar Data ◽  
Convective Precipitation ◽  
General Tendency ◽  
Learning Approaches ◽  
Rain Area ◽  
Individual Step ◽  
Performance Patterns

AbstractA new rainfall retrieval technique for determining rainfall rates in a continuous manner (day, twilight, and night) resulting in a 24-h estimation applicable to midlatitudes is presented. The approach is based on satellite-derived information on cloud-top height, cloud-top temperature, cloud phase, and cloud water path retrieved from Meteosat Second Generation (MSG) Spinning Enhanced Visible and Infrared Imager (SEVIRI) data and uses the random forests (RF) machine-learning algorithm. The technique is realized in three steps: (i) precipitating cloud areas are identified, (ii) the areas are separated into convective and advective-stratiform precipitating areas, and (iii) rainfall rates are assigned separately to the convective and advective-stratiform precipitating areas. Validation studies were carried out for each individual step as well as for the overall procedure using collocated ground-based radar data. Regarding each individual step, the models for rain area and convective precipitation detection produce good results. Both retrieval steps show a general tendency toward elevated prediction skill during summer months and daytime. The RF models for rainfall-rate assignment exhibit similar performance patterns, yet it is noteworthy how well the model is able to predict rainfall rates during nighttime and twilight. The performance of the overall procedure shows a very promising potential to estimate rainfall rates at high temporal and spatial resolutions in an automated manner. The near-real-time continuous applicability of the technique with acceptable prediction performances at 3–8-hourly intervals is particularly remarkable. This provides a very promising basis for future investigations into precipitation estimation based on machine-learning approaches and MSG SEVIRI data.

scholarly journals A Ligand-Based Virtual Screening Method Using Direct Quantification of Generalization Ability

Molecules ◽  
2019 ◽  
Vol 24 (13) ◽  
pp. 2414
Author(s):  
Weixing Dai ◽  
Dianjing Guo
Keyword(s):  
Machine Learning ◽  
Virtual Screening ◽  
Learning Algorithm ◽  
Screening Method ◽  
Chemical Characteristic ◽  
High Dimensional ◽  
Learning Approaches ◽  
Generalization Ability ◽  
Model Interpretation ◽  
Screening Accuracy

Machine learning plays an important role in ligand-based virtual screening. However, conventional machine learning approaches tend to be inefficient when dealing with such problems where the data are imbalanced and features describing the chemical characteristic of ligands are high-dimensional. We here describe a machine learning algorithm LBS (local beta screening) for ligand-based virtual screening. The unique characteristic of LBS is that it quantifies the generalization ability of screening directly by a refined loss function, and thus can assess the risk of over-fitting accurately and efficiently for imbalanced and high-dimensional data in ligand-based virtual screening without the help of resampling methods such as cross validation. The robustness of LBS was demonstrated by a simulation study and tests on real datasets, in which LBS outperformed conventional algorithms in terms of screening accuracy and model interpretation. LBS was then used for screening potential activators of HIV-1 integrase multimerization in an independent compound library, and the virtual screening result was experimentally validated. Of the 25 compounds tested, six were proved to be active. The most potent compound in experimental validation showed an EC50 value of 0.71 µM.

scholarly journals An Experimental Comparison between Deep Learning and Classical Machine Learning Approaches for Writer Identification in Medieval Documents

2020 ◽  
Vol 6 (9) ◽  
pp. 89
Author(s):  
Nicole Dalia Cilia ◽  
Claudio De Stefano ◽  
Francesco Fontanella ◽  
Claudio Marrocco ◽  
Mario Molinara ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
High Performance ◽  
Ad Hoc ◽  
Digital Images ◽  
Experimental Comparison ◽  
Learning Approaches ◽  
Test Bed ◽  
Ancient Manuscripts ◽  
Ancient Documents

In the framework of palaeography, the availability of both effective image analysis algorithms, and high-quality digital images has favored the development of new applications for the study of ancient manuscripts and has provided new tools for decision-making support systems. The quality of the results provided by such applications, however, is strongly influenced by the selection of effective features, which should be able to capture the distinctive aspects to which the paleography expert is interested in. This process is very difficult to generalize due to the enormous variability in the type of ancient documents, produced in different historical periods with different languages and styles. The effect is that it is very difficult to define standard techniques that are general enough to be effectively used in any case, and this is the reason why ad-hoc systems, generally designed according to paleographers’ suggestions, have been designed for the analysis of ancient manuscripts. In recent years, there has been a growing scientific interest in the use of techniques based on deep learning (DL) for the automatic processing of ancient documents. This interest is not only due to their capability of designing high-performance pattern recognition systems, but also to their ability of automatically extracting features from raw data, without using any a priori knowledge. Moving from these considerations, the aim of this study is to verify if DL-based approaches may actually represent a general methodology for automatically designing machine learning systems for palaeography applications. To this purpose, we compared the performance of a DL-based approach with that of a “classical” machine learning one, in a particularly unfavorable case for DL, namely that of highly standardized schools. The rationale of this choice is to compare the obtainable results even when context information is present and discriminating: this information is ignored by DL approaches, while it is used by machine learning methods, making the comparison more significant. The experimental results refer to the use of a large sets of digital images extracted from an entire 12th-century Bibles, the “Avila Bible”. This manuscript, produced by several scribes who worked in different periods and in different places, represents a severe test bed to evaluate the efficiency of scribe identification systems.

Intelligent Web Search through Adaptive Learning from Relevance Feedback

2011 ◽  
pp. 140-154
Author(s):  
Zhixiang Chen ◽  
Binhai Zhu ◽  
Xiannong Meng
Keyword(s):  
Machine Learning ◽  
Real Time ◽  
Adaptive Learning ◽  
Relevance Feedback ◽  
Search Engines ◽  
Web Search ◽  
Learning Algorithm ◽  
Future Research ◽  
Learning Approaches ◽  
Research Issues

In this chapter, machine-learning approaches to real-time intelligent Web search are discussed. The goal is to build an intelligent Web search system that can find the user’s desired information with as little relevance feedback from the user as possible. The system can achieve a significant search precision increase with a small number of iterations of user relevance feedback. A new machine-learning algorithm is designed as the core of the intelligent search component. This algorithm is applied to three different search engines with different emphases. This chapter presents the algorithm, the architectures, and the performances of these search engines. Future research issues regarding real-time intelligent Web search are also discussed.

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