Heterologous Machine Learning for the Identification of Antimicrobial Activity in Human-Targeted Drugs

The emergence of microbes resistant to common antibiotics represent a current treat to human health. It has been recently recognized that non-antibiotic labeled drugs may promote antibiotic-resistance mechanisms in the human microbiome by presenting a secondary antibiotic activity; hence, the development of computer-assisted procedures to identify antibiotic activity in human-targeted compounds may assist in preventing the emergence of resistant microbes. In this regard, it is worth noting that while most antibiotics used to treat human infectious diseases are non-peptidic compounds, most known antimicrobials nowadays are peptides, therefore all computer-based models aimed to predict antimicrobials either use small datasets of non-peptidic compounds rendering predictions with poor reliability or they predict antimicrobial peptides that are not currently used in humans. Here we report a machine-learning-based approach trained to identify gut antimicrobial compounds; a unique aspect of our model is the use of heterologous training sets, in which peptide and non-peptide antimicrobial compounds were used to increase the size of the training data set. Our results show that combining peptide and non-peptide antimicrobial compounds rendered the best classification of gut antimicrobial compounds. Furthermore, this classification model was tested on the latest human-approved drugs expecting to identify antibiotics with broad-spectrum activity and our results show that the model rendered predictions consistent with current knowledge about broad-spectrum antibiotics. Therefore, heterologous machine learning rendered an efficient computational approach to classify antimicrobial compounds.

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Relevant Features of Polypharmacologic Human-Target Antimicrobials Discovered by Machine-Learning Techniques

Pharmaceuticals ◽

10.3390/ph13090204 ◽

2020 ◽

Vol 13 (9) ◽

pp. 204

Author(s):

Rodrigo A. Nava Lara ◽

Jesús A. Beltrán ◽

Carlos A. Brizuela ◽

Gabriel Del Rio

Keyword(s):

Machine Learning ◽

Broad Spectrum ◽

Human Microbiome ◽

Antibiotic Activity ◽

Machine Learning Techniques ◽

Learning Approach ◽

Broad Spectrum Antibiotic ◽

Approach Training ◽

Learning Techniques ◽

Machine Learning Approach

Polypharmacologic human-targeted antimicrobials (polyHAM) are potentially useful in the treatment of complex human diseases where the microbiome is important (e.g., diabetes, hypertension). We previously reported a machine-learning approach to identify polyHAM from FDA-approved human targeted drugs using a heterologous approach (training with peptides and non-peptide compounds). Here we discover that polyHAM are more likely to be found among antimicrobials displaying a broad-spectrum antibiotic activity and that topological, but not chemical features, are most informative to classify this activity. A heterologous machine-learning approach was trained with broad-spectrum antimicrobials and tested with human metabolites; these metabolites were labeled as antimicrobials or non-antimicrobials based on a naïve text-mining approach. Human metabolites are not commonly recognized as antimicrobials yet circulate in the human body where microbes are found and our heterologous model was able to classify those with antimicrobial activity. These results provide the basis to develop applications aimed to design human diets that purposely alter metabolic compounds proportions as a way to control human microbiome.

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Comparative Analysis of Machine Learning Techniques Using Predictive Modeling

Recent Advances in Computer Science and Communications ◽

10.2174/2666255813999200904164539 ◽

2020 ◽

Vol 13 ◽

Author(s):

Ritu Khandelwal ◽

Hemlata Goyal ◽

Rajveer Singh Shekhawat

Keyword(s):

Machine Learning ◽

Comparative Analysis ◽

Data Science ◽

Training Data ◽

Machine Learning Techniques ◽

Future Trends ◽

Data Set ◽

Learning Stage ◽

Learning Techniques ◽

Different Types

Introduction: Machine learning is an intelligent technology that works as a bridge between businesses and data science. With the involvement of data science, the business goal focuses on findings to get valuable insights on available data. The large part of Indian Cinema is Bollywood which is a multi-million dollar industry. This paper attempts to predict whether the upcoming Bollywood Movie would be Blockbuster, Superhit, Hit, Average or Flop. For this Machine Learning techniques (classification and prediction) will be applied. To make classifier or prediction model first step is the learning stage in which we need to give the training data set to train the model by applying some technique or algorithm and after that different rules are generated which helps to make a model and predict future trends in different types of organizations. Methods: All the techniques related to classification and Prediction such as Support Vector Machine(SVM), Random Forest, Decision Tree, Naïve Bayes, Logistic Regression, Adaboost, and KNN will be applied and try to find out efficient and effective results. All these functionalities can be applied with GUI Based workflows available with various categories such as data, Visualize, Model, and Evaluate. Result: To make classifier or prediction model first step is learning stage in which we need to give the training data set to train the model by applying some technique or algorithm and after that different rules are generated which helps to make a model and predict future trends in different types of organizations Conclusion: This paper focuses on Comparative Analysis that would be performed based on different parameters such as Accuracy, Confusion Matrix to identify the best possible model for predicting the movie Success. By using Advertisement Propaganda, they can plan for the best time to release the movie according to the predicted success rate to gain higher benefits. Discussion: Data Mining is the process of discovering different patterns from large data sets and from that various relationships are also discovered to solve various problems that come in business and helps to predict the forthcoming trends. This Prediction can help Production Houses for Advertisement Propaganda and also they can plan their costs and by assuring these factors they can make the movie more profitable.

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Building Damage Detection from Post-Event Aerial Imagery Using Single Shot Multibox Detector

Applied Sciences ◽

10.3390/app9061128 ◽

2019 ◽

Vol 9 (6) ◽

pp. 1128 ◽

Cited By ~ 12

Author(s):

Yundong Li ◽

Wei Hu ◽

Han Dong ◽

Xueyan Zhang

Keyword(s):

Machine Learning ◽

Data Augmentation ◽

Hurricane Sandy ◽

Training Data ◽

Aerial Images ◽

Detection Methods ◽

Single Shot ◽

Data Set ◽

Augmentation Strategies ◽

Post Disaster

Using aerial cameras, satellite remote sensing or unmanned aerial vehicles (UAV) equipped with cameras can facilitate search and rescue tasks after disasters. The traditional manual interpretation of huge aerial images is inefficient and could be replaced by machine learning-based methods combined with image processing techniques. Given the development of machine learning, researchers find that convolutional neural networks can effectively extract features from images. Some target detection methods based on deep learning, such as the single-shot multibox detector (SSD) algorithm, can achieve better results than traditional methods. However, the impressive performance of machine learning-based methods results from the numerous labeled samples. Given the complexity of post-disaster scenarios, obtaining many samples in the aftermath of disasters is difficult. To address this issue, a damaged building assessment method using SSD with pretraining and data augmentation is proposed in the current study and highlights the following aspects. (1) Objects can be detected and classified into undamaged buildings, damaged buildings, and ruins. (2) A convolution auto-encoder (CAE) that consists of VGG16 is constructed and trained using unlabeled post-disaster images. As a transfer learning strategy, the weights of the SSD model are initialized using the weights of the CAE counterpart. (3) Data augmentation strategies, such as image mirroring, rotation, Gaussian blur, and Gaussian noise processing, are utilized to augment the training data set. As a case study, aerial images of Hurricane Sandy in 2012 were maximized to validate the proposed method’s effectiveness. Experiments show that the pretraining strategy can improve of 10% in terms of overall accuracy compared with the SSD trained from scratch. These experiments also demonstrate that using data augmentation strategies can improve mAP and mF1 by 72% and 20%, respectively. Finally, the experiment is further verified by another dataset of Hurricane Irma, and it is concluded that the paper method is feasible.

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Nowcasting heavy precipitation over the Netherlands using a 13-year radar archive: a machine learning approach

10.5194/egusphere-egu21-12814 ◽

2021 ◽

Author(s):

Eva van der Kooij ◽

Marc Schleiss ◽

Riccardo Taormina ◽

Francesco Fioranelli ◽

Dorien Lugt ◽

...

Keyword(s):

Machine Learning ◽

The Netherlands ◽

Heavy Rainfall ◽

Predictive Performance ◽

Heavy Precipitation ◽

Early Warning Systems ◽

Training Data ◽

Short Term ◽

Data Set ◽

Radar Images

Accurate short-term forecasts, also known as nowcasts, of heavy precipitation are desirable for creating early warning systems for extreme weather and its consequences, e.g. urban flooding. In this research, we explore the use of machine learning for short-term prediction of heavy rainfall showers in the Netherlands.We assess the performance of a recurrent, convolutional neural network (TrajGRU) with lead times of 0 to 2 hours. The network is trained on a 13-year archive of radar images with 5-min temporal and 1-km spatial resolution from the precipitation radars of the Royal Netherlands Meteorological Institute (KNMI). We aim to train the model to predict the formation and dissipation of dynamic, heavy, localized rain events, a task for which traditional Lagrangian nowcasting methods still come up short.We report on different ways to optimize predictive performance for heavy rainfall intensities through several experiments. The large dataset available provides many possible configurations for training. To focus on heavy rainfall intensities, we use different subsets of this dataset through using different conditions for event selection and varying the ratio of light and heavy precipitation events present in the training data set and change the loss function used to train the model.To assess the performance of the model, we compare our method to current state-of-the-art Lagrangian nowcasting system from the pySTEPS library, like S-PROG, a deterministic approximation of an ensemble mean forecast. The results of the experiments are used to discuss the pros and cons of machine-learning based methods for precipitation nowcasting and possible ways to further increase performance.

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Synthetic Sonic Log Generation With Machine Learning: A Contest Summary From Five Methods

Petrophysics – The SPWLA Journal of Formation Evaluation and Reservoir Description ◽

10.30632/pjv62n4-2021a4 ◽

2021 ◽

Vol 62 (4) ◽

pp. 393-406

Author(s):

Yanxiang Yu ◽

◽

Chicheng Xu ◽

Siddharth Misra ◽

Weichang Li ◽

...

Keyword(s):

Machine Learning ◽

Test Data ◽

Short Term Memory ◽

Rock Physics ◽

Training Data ◽

Machine Learning Techniques ◽

Blind Test ◽

Data Set ◽

Benchmark Model ◽

Sonic Log

Compressional and shear sonic traveltime logs (DTC and DTS, respectively) are crucial for subsurface characterization and seismic-well tie. However, these two logs are often missing or incomplete in many oil and gas wells. Therefore, many petrophysical and geophysical workflows include sonic log synthetization or pseudo-log generation based on multivariate regression or rock physics relations. Started on March 1, 2020, and concluded on May 7, 2020, the SPWLA PDDA SIG hosted a contest aiming to predict the DTC and DTS logs from seven “easy-to-acquire” conventional logs using machine-learning methods (GitHub, 2020). In the contest, a total number of 20,525 data points with half-foot resolution from three wells was collected to train regression models using machine-learning techniques. Each data point had seven features, consisting of the conventional “easy-to-acquire” logs: caliper, neutron porosity, gamma ray (GR), deep resistivity, medium resistivity, photoelectric factor, and bulk density, respectively, as well as two sonic logs (DTC and DTS) as the target. The separate data set of 11,089 samples from a fourth well was then used as the blind test data set. The prediction performance of the model was evaluated using root mean square error (RMSE) as the metric, shown in the equation below: RMSE=sqrt(1/2*1/m* [∑_(i=1)^m▒〖(〖DTC〗_pred^i-〖DTC〗_true^i)〗^2 + 〖(〖DTS〗_pred^i-〖DTS〗_true^i)〗^2 ] In the benchmark model, (Yu et al., 2020), we used a Random Forest regressor and conducted minimal preprocessing to the training data set; an RMSE score of 17.93 was achieved on the test data set. The top five models from the contest, on average, beat the performance of our benchmark model by 27% in the RMSE score. In the paper, we will review these five solutions, including preprocess techniques and different machine-learning models, including neural network, long short-term memory (LSTM), and ensemble trees. We found that data cleaning and clustering were critical for improving the performance in all models.

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A Novel ECG Automatic Detection Using LongShort-Term Memory Network and Internet of Things Technology

Journal of Medical Imaging and Health Informatics ◽

10.1166/jmihi.2021.3684 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1592-1598

Author(s):

Xufei Liu

Keyword(s):

Machine Learning ◽

Cardiovascular Diseases ◽

Internet Of Things ◽

Network Structure ◽

Recognition Rate ◽

Classification Model ◽

Data Set ◽

Public Data ◽

Lstm Network ◽

Internet Of Things Technology

The early detection of cardiovascular diseases based on electrocardiogram (ECG) is very important for the timely treatment of cardiovascular patients, which increases the survival rate of patients. ECG is a visual representation that describes changes in cardiac bioelectricity and is the basis for detecting heart health. With the rise of edge machine learning and Internet of Things (IoT) technologies, small machine learning models have received attention. This study proposes an ECG automatic classification method based on Internet of Things technology and LSTM network to achieve early monitoring and early prevention of cardiovascular diseases. Specifically, this paper first proposes a single-layer bidirectional LSTM network structure. Make full use of the timing-dependent features of the sampling points before and after to automatically extract features. The network structure is more lightweight and the calculation complexity is lower. In order to verify the effectiveness of the proposed classification model, the relevant comparison algorithm is used to verify on the MIT-BIH public data set. Secondly, the model is embedded in a wearable device to automatically classify the collected ECG. Finally, when an abnormality is detected, the user is alerted by an alarm. The experimental results show that the proposed model has a simple structure and a high classification and recognition rate, which can meet the needs of wearable devices for monitoring ECG of patients.

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A sentiment analysis system for social media using machine learning techniques: Social enablement

Digital Scholarship in the Humanities ◽

10.1093/llc/fqy037 ◽

2018 ◽

Vol 34 (3) ◽

pp. 569-581 ◽

Cited By ~ 1

Author(s):

Sujata Rani ◽

Parteek Kumar

Keyword(s):

Machine Learning ◽

Social Media ◽

Sentiment Analysis ◽

Media Analysis ◽

Training Data ◽

Machine Learning Techniques ◽

Support Vector ◽

Analysis Tool ◽

Data Set ◽

Learning Techniques

Abstract In this article, an innovative approach to perform the sentiment analysis (SA) has been presented. The proposed system handles the issues of Romanized or abbreviated text and spelling variations in the text to perform the sentiment analysis. The training data set of 3,000 movie reviews and tweets has been manually labeled by native speakers of Hindi in three classes, i.e. positive, negative, and neutral. The system uses WEKA (Waikato Environment for Knowledge Analysis) tool to convert these string data into numerical matrices and applies three machine learning techniques, i.e. Naive Bayes (NB), J48, and support vector machine (SVM). The proposed system has been tested on 100 movie reviews and tweets, and it has been observed that SVM has performed best in comparison to other classifiers, and it has an accuracy of 68% for movie reviews and 82% in case of tweets. The results of the proposed system are very promising and can be used in emerging applications like SA of product reviews and social media analysis. Additionally, the proposed system can be used in other cultural/social benefits like predicting/fighting human riots.

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TermPicks: A century of Greenland glacier terminus data for use in machine learning applications

10.5194/tc-2021-311 ◽

2021 ◽

Author(s):

Sophie Goliber ◽

Taryn Black ◽

Ginny Catania ◽

James M. Lea ◽

Helene Olsen ◽

...

Keyword(s):

Machine Learning ◽

Greenland Ice Sheet ◽

Median Number ◽

Google Earth ◽

Training Data ◽

Machine Learning Techniques ◽

Data Set ◽

Outlet Glacier ◽

Glacier Terminus ◽

Median Error

Abstract. Marine-terminating outlet glacier terminus traces, mapped from satellite and aerial imagery, have been used extensively in understanding how outlet glaciers adjust to climate change variability over a range of time scales. Numerous studies have digitized termini manually, but this process is labor-intensive, and no consistent approach exists. A lack of coordination leads to duplication of efforts, particularly for Greenland, which is a major scientific research focus. At the same time, machine learning techniques are rapidly making progress in their ability to automate accurate extraction of glacier termini, with promising developments across a number of optical and SAR satellite sensors. These techniques rely on high quality, manually digitized terminus traces to be used as training data for robust automatic traces. Here we present a database of manually digitized terminus traces for machine learning and scientific applications. These data have been collected, cleaned, assigned with appropriate metadata including image scenes, and compiled so they can be easily accessed by scientists. The TermPicks data set includes 39,060 individual terminus traces for 278 glaciers with a mean and median number of traces per glacier of 136 ± 190 and 93, respectively. Across all glaciers, 32,567 dates have been picked, of which 4,467 have traces from more than one author (duplication of 14 %). We find a median error of ∼100 m among manually-traced termini. Most traces are obtained after 1999, when Landsat 7 was launched. We also provide an overview of an updated version of The Google Earth Engine Digitization Tool (GEEDiT), which has been developed specifically for future manual picking of the Greenland Ice Sheet.

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Water Quality Prediction Using Statistical Tool and Machine Learning Algorithm

Waste Management ◽

10.4018/978-1-7998-1210-4.ch029 ◽

2020 ◽

pp. 609-623

Author(s):

Arun Kumar Beerala ◽

Gobinath R. ◽

Shyamala G. ◽

Siribommala Manvitha

Keyword(s):

Machine Learning ◽

Learning Algorithm ◽

Training Data ◽

Machine Learning Techniques ◽

Statistical Tool ◽

Data Set ◽

Water Quality Prediction ◽

Living Things ◽

Sampling Locations ◽

Different Seasons

Water is the most valuable natural resource for all living things and the ecosystem. The quality of groundwater is changed due to change in ecosystem, industrialisation, and urbanisation, etc. In the study, 60 samples were taken and analysed for various physio-chemical parameters. The sampling locations were located using global positioning system (GPS) and were taken for two consecutive years for two different seasons, monsoon (Nov-Dec) and post-monsoon (Jan-Mar). In 2016-2017 and 2017-2018 pH, EC, and TDS were obtained in the field. Hardness and Chloride are determined using titration method. Nitrate and Sulphate were determined using Spectrophotometer. Machine learning techniques were used to train the data set and to predict the unknown values. The dominant elements of groundwater are as follows: Ca2, Mg2 for cation and Cl-, SO42, NO3− for anions. The regression value for the training data set was found to be 0.90596, and for the entire network, it was found to be 0.81729. The best performance was observed as 0.0022605 at epoch 223.

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Exploiting Rules to Enhance Machine Learning in Extracting Information From Multi-Institutional Prostate Pathology Reports

JCO Clinical Cancer Informatics ◽

10.1200/cci.20.00028 ◽

2020 ◽

pp. 865-874

Author(s):

Enrico Santus ◽

Tal Schuster ◽

Amir M. Tahmasebi ◽

Clara Li ◽

Adam Yala ◽

...

Keyword(s):

Machine Learning ◽

Hybrid Systems ◽

High Performance ◽

Feature Model ◽

Training Data ◽

Gradient Boosting ◽

Support Vector ◽

Data Set ◽

Extreme Gradient Boosting ◽

Pathology Reports

PURPOSE Literature on clinical note mining has highlighted the superiority of machine learning (ML) over hand-crafted rules. Nevertheless, most studies assume the availability of large training sets, which is rarely the case. For this reason, in the clinical setting, rules are still common. We suggest 2 methods to leverage the knowledge encoded in pre-existing rules to inform ML decisions and obtain high performance, even with scarce annotations. METHODS We collected 501 prostate pathology reports from 6 American hospitals. Reports were split into 2,711 core segments, annotated with 20 attributes describing the histology, grade, extension, and location of tumors. The data set was split by institutions to generate a cross-institutional evaluation setting. We assessed 4 systems, namely a rule-based approach, an ML model, and 2 hybrid systems integrating the previous methods: a Rule as Feature model and a Classifier Confidence model. Several ML algorithms were tested, including logistic regression (LR), support vector machine (SVM), and eXtreme gradient boosting (XGB). RESULTS When training on data from a single institution, LR lags behind the rules by 3.5% (F1 score: 92.2% v 95.7%). Hybrid models, instead, obtain competitive results, with Classifier Confidence outperforming the rules by +0.5% (96.2%). When a larger amount of data from multiple institutions is used, LR improves by +1.5% over the rules (97.2%), whereas hybrid systems obtain +2.2% for Rule as Feature (97.7%) and +2.6% for Classifier Confidence (98.3%). Replacing LR with SVM or XGB yielded similar performance gains. CONCLUSION We developed methods to use pre-existing handcrafted rules to inform ML algorithms. These hybrid systems obtain better performance than either rules or ML models alone, even when training data are limited.

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