Assessment of Neuronal Damage in Brain Slice Cultures Using Machine Learning Based on Spatial Features

Neuronal damage presents a major health issue necessitating extensive research to identify mechanisms of neuronal cell death and potential therapeutic targets. Commonly used models are slice cultures out of different brain regions extracted from mice or rats, excitotoxically, ischemic, or traumatically lesioned and subsequently treated with potential neuroprotective agents. Thereby cell death is regularly assessed by measuring the propidium iodide (PI) uptake or counting of PI-positive nuclei. The applied methods have a limited applicability, either in terms of objectivity and time consumption or regarding its applicability. Consequently, new tools for analysis are needed. Here, we present a framework to mimic manual counting using machine learning algorithms as tools for semantic segmentation of PI-positive dead cells in hippocampal slice cultures. Therefore, we trained a support vector machine (SVM) to classify images into either “high” or “low” neuronal damage and used naïve Bayes, discriminant analysis, random forest, and a multilayer perceptron (MLP) as classifiers for segmentation of dead cells. In our final models, pixel-wise accuracies of up to 0.97 were achieved using the MLP classifier. Furthermore, a SVM-based post-processing step was introduced to differentiate between false-positive and false-negative detections using morphological features. As only very few false-positive objects and thus training data remained when using the final model, this approach only mildly improved the results. A final object splitting step using Hough transformations was used to account for overlap, leading to a recall of up to 97.6% of the manually assigned PI-positive dead cells. Taken together, we present an analysis tool that can help to objectively and reproducibly analyze neuronal damage in brain-derived slice cultures, taking advantage of the morphology of pycnotic cells for segmentation, object splitting, and identification of false positives.

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Drill-Core Mineral Abundance Estimation Using Hyperspectral and High-Resolution Mineralogical Data

Remote Sensing ◽

10.3390/rs12071218 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1218

Author(s):

Laura Tuşa ◽

Mahdi Khodadadzadeh ◽

Cecilia Contreras ◽

Kasra Rafiezadeh Shahi ◽

Margret Fuchs ◽

...

Keyword(s):

Machine Learning ◽

High Resolution ◽

Ore Deposits ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Drill Core ◽

Data Types ◽

Mineralogical Characterization ◽

Core Samples

Due to the extensive drilling performed every year in exploration campaigns for the discovery and evaluation of ore deposits, drill-core mapping is becoming an essential step. While valuable mineralogical information is extracted during core logging by on-site geologists, the process is time consuming and dependent on the observer and individual background. Hyperspectral short-wave infrared (SWIR) data is used in the mining industry as a tool to complement traditional logging techniques and to provide a rapid and non-invasive analytical method for mineralogical characterization. Additionally, Scanning Electron Microscopy-based image analyses using a Mineral Liberation Analyser (SEM-MLA) provide exhaustive high-resolution mineralogical maps, but can only be performed on small areas of the drill-cores. We propose to use machine learning algorithms to combine the two data types and upscale the quantitative SEM-MLA mineralogical data to drill-core scale. This way, quasi-quantitative maps over entire drill-core samples are obtained. Our upscaling approach increases result transparency and reproducibility by employing physical-based data acquisition (hyperspectral imaging) combined with mathematical models (machine learning). The procedure is tested on 5 drill-core samples with varying training data using random forests, support vector machines and neural network regression models. The obtained mineral abundance maps are further used for the extraction of mineralogical parameters such as mineral association.

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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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Automatic Grading of Stroke Symptoms for Rapid Assessment Using Optimized Machine Learning and 4-Limb Kinematics: Clinical Validation Study (Preprint)

10.2196/preprints.20641 ◽

2020 ◽

Author(s):

Eunjeong Park ◽

Kijeong Lee ◽

Taehwa Han ◽

Hyo Suk Nam

Keyword(s):

Machine Learning ◽

Medical Staff ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Grading System ◽

Operating Characteristics ◽

Stroke Patients ◽

Motor Weakness ◽

Automatic Grading

BACKGROUND Subtle abnormal motor signs are indications of serious neurological diseases. Although neurological deficits require fast initiation of treatment in a restricted time, it is difficult for nonspecialists to detect and objectively assess the symptoms. In the clinical environment, diagnoses and decisions are based on clinical grading methods, including the National Institutes of Health Stroke Scale (NIHSS) score or the Medical Research Council (MRC) score, which have been used to measure motor weakness. Objective grading in various environments is necessitated for consistent agreement among patients, caregivers, paramedics, and medical staff to facilitate rapid diagnoses and dispatches to appropriate medical centers. OBJECTIVE In this study, we aimed to develop an autonomous grading system for stroke patients. We investigated the feasibility of our new system to assess motor weakness and grade NIHSS and MRC scores of 4 limbs, similar to the clinical examinations performed by medical staff. METHODS We implemented an automatic grading system composed of a measuring unit with wearable sensors and a grading unit with optimized machine learning. Inertial sensors were attached to measure subtle weaknesses caused by paralysis of upper and lower limbs. We collected 60 instances of data with kinematic features of motor disorders from neurological examination and demographic information of stroke patients with NIHSS 0 or 1 and MRC 7, 8, or 9 grades in a stroke unit. Training data with 240 instances were generated using a synthetic minority oversampling technique to complement the imbalanced number of data between classes and low number of training data. We trained 2 representative machine learning algorithms, an ensemble and a support vector machine (SVM), to implement auto-NIHSS and auto-MRC grading. The optimized algorithms performed a 5-fold cross-validation and were searched by Bayes optimization in 30 trials. The trained model was tested with the 60 original hold-out instances for performance evaluation in accuracy, sensitivity, specificity, and area under the receiver operating characteristics curve (AUC). RESULTS The proposed system can grade NIHSS scores with an accuracy of 83.3% and an AUC of 0.912 using an optimized ensemble algorithm, and it can grade with an accuracy of 80.0% and an AUC of 0.860 using an optimized SVM algorithm. The auto-MRC grading achieved an accuracy of 76.7% and a mean AUC of 0.870 in SVM classification and an accuracy of 78.3% and a mean AUC of 0.877 in ensemble classification. CONCLUSIONS The automatic grading system quantifies proximal weakness in real time and assesses symptoms through automatic grading. The pilot outcomes demonstrated the feasibility of remote monitoring of motor weakness caused by stroke. The system can facilitate consistent grading with instant assessment and expedite dispatches to appropriate hospitals and treatment initiation by sharing auto-MRC and auto-NIHSS scores between prehospital and hospital responses as an objective observation.

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Android Malware Detection using Machine Learning

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.b1011.0982s1219 ◽

2020 ◽

Vol 8 (2S12) ◽

pp. 65-70

Keyword(s):

Machine Learning ◽

Nearest Neighbor ◽

Machine Learning Algorithms ◽

Training Data ◽

Machine Learning Techniques ◽

Support Vector ◽

K Nearest Neighbor ◽

User Interest ◽

Android Malware ◽

Android Malware Detection

Machine Learning is empowering many aspects of day-to-day lives from filtering the content on social networks to suggestions of products that we may be looking for. This technology focuses on taking objects as image input to find new observations or show items based on user interest. The major discussion here is the Machine Learning techniques where we use supervised learning where the computer learns by the input data/training data and predict result based on experience. We also discuss the machine learning algorithms: Naïve Bayes Classifier, K-Nearest Neighbor, Random Forest, Decision Tress, Boosted Trees, Support Vector Machine, and use these classifiers on a dataset Malgenome and Drebin which are the Android Malware Dataset. Android is an operating system that is gaining popularity these days and with a rise in demand of these devices the rise in Android Malware. The traditional techniques methods which were used to detect malware was unable to detect unknown applications. We have run this dataset on different machine learning classifiers and have recorded the results. The experiment result provides a comparative analysis that is based on performance, accuracy, and cost.

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A Comparison of Machine Learning Algorithms for the Segmentation and Classification of Snow Micro Penetrometer Profiles on Arctic Sea Ice

10.5194/egusphere-egu21-15637 ◽

2021 ◽

Author(s):

Julia Kaltenborn ◽

Viviane Clay ◽

Amy R. Macfarlane ◽

Joshua Michael Lloyd King ◽

Martin Schneebeli

Keyword(s):

Machine Learning ◽

Sea Ice ◽

Arctic Sea Ice ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Snow Layer ◽

Arctic Sea ◽

Execution Speed

Snow-layer classification is an essential diagnostic task for a wide variety of cryospheric science and climate research applications. Traditionally, these measurements are made in snow pits, requiring trained operators and a substantial time commitment. The SnowMicroPen (SMP), a portable high-resolution snow penetrometer, has been demonstrated as a capable tool for rapid snow grain classification and layer type segmentation through statistical inversion of its mechanical signal. The manual classification of the SMP profiles requires time and training and becomes infeasible for large datasets.Here, we introduce a novel set of SMP measurements collected during the MOSAiC expedition and apply Machine Learning (ML) algorithms to automatically classify and segment SMP profiles of snow on Arctic sea ice. To this end, different supervised and unsupervised ML methods, including Random Forests, Support Vector Machines, Artificial Neural Networks, and k-means Clustering, are compared. A subsequent segmentation of the classified data results in distinct layers and snow grain markers for the SMP profiles. The models are trained with the dataset by King et al. (2020) and the MOSAiC SMP dataset. The MOSAiC dataset is a unique and extensive dataset characterizing seasonal and spatial variation of snow on the central Arctic sea-ice.We will test and compare the different algorithms and evaluate the algorithms&#8217; effectiveness based on the need for initial dataset labeling, execution speed, and ease of implementation. In particular, we will compare supervised to unsupervised methods, which are distinguished by their need for labeled training data.The implementation of different ML algorithms for SMP profile classification could provide a fast and automatic grain type classification and snow layer segmentation. Based on the gained knowledge from the algorithms&#8217; comparison, a tool can be built to provide scientists from different fields with an immediate SMP profile classification and segmentation.&#160;&#160;King, J., Howell, S., Brady, M., Toose, P., Derksen, C., Haas, C., & Beckers, J. (2020). Local-scale variability of snow density on Arctic sea ice. The Cryosphere, 14(12), 4323-4339, https://doi.org/10.5194/tc-14-4323-2020.

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Identification of Leukemia Subtypes from Microscopic Images Using Convolutional Neural Network

Diagnostics ◽

10.3390/diagnostics9030104 ◽

2019 ◽

Vol 9 (3) ◽

pp. 104 ◽

Cited By ~ 11

Author(s):

Ahmed ◽

Yigit ◽

Isik ◽

Alpkocak

Keyword(s):

Machine Learning ◽

Data Augmentation ◽

Nearest Neighbor ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

K Nearest Neighbor ◽

Data Set ◽

Leukemia Data

Leukemia is a fatal cancer and has two main types: Acute and chronic. Each type has two more subtypes: Lymphoid and myeloid. Hence, in total, there are four subtypes of leukemia. This study proposes a new approach for diagnosis of all subtypes of leukemia from microscopic blood cell images using convolutional neural networks (CNN), which requires a large training data set. Therefore, we also investigated the effects of data augmentation for an increasing number of training samples synthetically. We used two publicly available leukemia data sources: ALL-IDB and ASH Image Bank. Next, we applied seven different image transformation techniques as data augmentation. We designed a CNN architecture capable of recognizing all subtypes of leukemia. Besides, we also explored other well-known machine learning algorithms such as naive Bayes, support vector machine, k-nearest neighbor, and decision tree. To evaluate our approach, we set up a set of experiments and used 5-fold cross-validation. The results we obtained from experiments showed that our CNN model performance has 88.25% and 81.74% accuracy, in leukemia versus healthy and multiclass classification of all subtypes, respectively. Finally, we also showed that the CNN model has a better performance than other wellknown machine learning algorithms.

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Rotor Unbalance Kind and Severity Identification by Current Signature Analysis with Adaptative Update to Multiclass Machine Learning Algorithms

Studies in Engineering and Technology ◽

10.11114/set.v8i1.5213 ◽

2021 ◽

Vol 8 (1) ◽

pp. 28

Author(s):

S. L. Ávila ◽

H. M. Schaberle ◽

S. Youssef ◽

F. S. Pacheco ◽

C. A. Penz

Keyword(s):

Machine Learning ◽

Machine Learning Algorithms ◽

Training Data ◽

Machine Learning Techniques ◽

Support Vector ◽

Signature Analysis ◽

Data Set ◽

Learning Techniques ◽

Environmental Variations ◽

Current Signature

The health of a rotating electric machine can be evaluated by monitoring electrical and mechanical parameters. As more information is available, it easier can become the diagnosis of the machine operational condition. We built a laboratory test bench to study rotor unbalance issues according to ISO standards. Using the electric stator current harmonic analysis, this paper presents a comparison study among Support-Vector Machines, Decision Tree classifies, and One-vs-One strategy to identify rotor unbalance kind and severity problem – a nonlinear multiclass task. Moreover, we propose a methodology to update the classifier for dealing better with changes produced by environmental variations and natural machinery usage. The adaptative update means to update the training data set with an amount of recent data, saving the entire original historical data. It is relevant for engineering maintenance. Our results show that the current signature analysis is appropriate to identify the type and severity of the rotor unbalance problem. Moreover, we show that machine learning techniques can be effective for an industrial application.

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A Novel GIS-Based Random Forest Machine Algorithm for the Spatial Prediction of Shallow Landslide Susceptibility

Forests ◽

10.3390/f11010118 ◽

2020 ◽

Vol 11 (1) ◽

pp. 118 ◽

Cited By ~ 6

Author(s):

Viet-Hung Dang ◽

Nhat-Duc Hoang ◽

Le-Mai-Duyen Nguyen ◽

Dieu Tien Bui ◽

Pijush Samui

Keyword(s):

Machine Learning ◽

Random Forest ◽

Landslide Susceptibility ◽

Spatial Prediction ◽

Shallow Landslide ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Conditioning Factors ◽

Susceptibility Modeling

This study developed and verified a new hybrid machine learning model, named random forest machine (RFM), for the spatial prediction of shallow landslides. RFM is a hybridization of two state-of-the-art machine learning algorithms, random forest classifier (RFC) and support vector machine (SVM), in which RFC is used to generate subsets from training data and SVM is used to build decision functions for these subsets. To construct and verify the hybrid RFM model, a shallow landslide database of the Lang Son area (northern Vietnam) was prepared. The database consisted of 101 shallow landslide polygons and 14 conditioning factors. The relevance of these factors for shallow landslide susceptibility modeling was assessed using the ReliefF method. Experimental results pointed out that the proposed RFM can help to achieve the desired prediction with an F1 score of roughly 0.96. The performance of the RFM was better than those of benchmark approaches, including the SVM, RFC, and logistic regression. Thus, the newly developed RFM is a promising tool to help local authorities in shallow landslide hazard mitigations.

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Spatial–Temporal Analysis of Land Cover Change at the Bento Rodrigues Dam Disaster Area Using Machine Learning Techniques

Remote Sensing ◽

10.3390/rs11212548 ◽

2019 ◽

Vol 11 (21) ◽

pp. 2548

Author(s):

Dong Luo ◽

Douglas G. Goodin ◽

Marcellus M. Caldas

Keyword(s):

Machine Learning ◽

Support Vector Machine ◽

Land Cover ◽

Decision Tree ◽

Machine Learning Algorithms ◽

Training Data ◽

Machine Learning Techniques ◽

Support Vector ◽

Disaster Area ◽

Mine Sites

Disasters are an unpredictable way to change land use and land cover. Improving the accuracy of mapping a disaster area at different time is an essential step to analyze the relationship between human activity and environment. The goals of this study were to test the performance of different processing procedures and examine the effect of adding normalized difference vegetation index (NDVI) as an additional classification feature for mapping land cover changes due to a disaster. Using Landsat ETM+ and OLI images of the Bento Rodrigues mine tailing disaster area, we created two datasets, one with six bands, and the other one with six bands plus the NDVI. We used support vector machine (SVM) and decision tree (DT) algorithms to build classifier models and validated models performance using 10-fold cross-validation, resulting in accuracies higher than 90%. The processed results indicated that the accuracy could reach or exceed 80%, and the support vector machine had a better performance than the decision tree. We also calculated each land cover type’s sensitivity (true positive rate) and found that Agriculture, Forest and Mine sites had higher values but Bareland and Water had lower values. Then, we visualized land cover maps in 2000 and 2017 and found out the Mine sites areas have been expanded about twice of the size, but Forest decreased 12.43%. Our findings showed that it is feasible to create a training data pool and use machine learning algorithms to classify a different year’s Landsat products and NDVI can improve the vegetation covered land classification. Furthermore, this approach can provide a venue to analyze land pattern change in a disaster area over time.

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Aligning text mining and machine learning algorithms with best practices for study selection in systematic literature reviews

Systematic Reviews ◽

10.1186/s13643-020-01520-5 ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

E. Popoff ◽

M. Besada ◽

J. P. Jansen ◽

S. Cope ◽

S. Kanters

Keyword(s):

Machine Learning ◽

Text Mining ◽

Sensitivity And Specificity ◽

Full Text ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Study Selection ◽

Literature Reviews

Abstract Background Despite existing research on text mining and machine learning for title and abstract screening, the role of machine learning within systematic literature reviews (SLRs) for health technology assessment (HTA) remains unclear given lack of extensive testing and of guidance from HTA agencies. We sought to address two knowledge gaps: to extend ML algorithms to provide a reason for exclusion—to align with current practices—and to determine optimal parameter settings for feature-set generation and ML algorithms. Methods We used abstract and full-text selection data from five large SLRs (n = 3089 to 12,769 abstracts) across a variety of disease areas. Each SLR was split into training and test sets. We developed a multi-step algorithm to categorize each citation into the following categories: included; excluded for each PICOS criterion; or unclassified. We used a bag-of-words approach for feature-set generation and compared machine learning algorithms using support vector machines (SVMs), naïve Bayes (NB), and bagged classification and regression trees (CART) for classification. We also compared alternative training set strategies: using full data versus downsampling (i.e., reducing excludes to balance includes/excludes because machine learning algorithms perform better with balanced data), and using inclusion/exclusion decisions from abstract versus full-text screening. Performance comparisons were in terms of specificity, sensitivity, accuracy, and matching the reason for exclusion. Results The best-fitting model (optimized sensitivity and specificity) was based on the SVM algorithm using training data based on full-text decisions, downsampling, and excluding words occurring fewer than five times. The sensitivity and specificity of this model ranged from 94 to 100%, and 54 to 89%, respectively, across the five SLRs. On average, 75% of excluded citations were excluded with a reason and 83% of these citations matched the reviewers’ original reason for exclusion. Sensitivity significantly improved when both downsampling and abstract decisions were used. Conclusions ML algorithms can improve the efficiency of the SLR process and the proposed algorithms could reduce the workload of a second reviewer by identifying exclusions with a relevant PICOS reason, thus aligning with HTA guidance. Downsampling can be used to improve study selection, and improvements using full-text exclusions have implications for a learn-as-you-go approach.

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