Machine learning models to predict the response to anti-cancer therapy in metastatic melanoma patients.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e14071-e14071
Author(s):  
Romain Goussault ◽  
Cécile Frénard ◽  
Eve Maubec ◽  
Philippe Muller ◽  
Ludovic Martin ◽  
...  
Keyword(s):  
Machine Learning ◽  
Targeted Therapy ◽  
Random Forest ◽  
Learning Models ◽  
Stage Iiic ◽  
Test Set ◽  
Metastatic Relapse ◽  
Class 1 ◽  
Melanoma Patients ◽  
Machine Learning Models

e14071 Background: Machine learning methods are new artificial intelligence tools with promising applications in healthcare. We developed and validated 4 machine learning models to predict the response to immunotherapy and targeted therapy in stage IIIc or IV melanoma patients. Methods: This work was conducted on data from 10 centers participating in the French network for Research and Clinical Investigation on Melanoma (RIC-Mel), launched in 2012. Thus, 935 patients, corresponding to 1978 systemic treatments have been extracted from RIC-Mel database. The following data were considered: age, sex, Breslow, melanoma type, ulceration, spontaneous regression, mitotic index, number of invaded lymph nodes, extracapsular extension, mutational status, melanoma stage, number of metastasis sites, lines of treatments, and time between first melanoma excision and metastatic relapse. Treatment response: complete response, partial response, stable disease, defined as class 1 and progressive disease as class 2. We split this cohort/database into a training set (80%) and test set (20%). The algorithm performances were evaluated on the test set by the percentage of treatments correctly classified in class 1 or 2. Four machine learning algorithms (linear model, random forest, XGBoost and LightGBM) were compared in terms of performance and interpretation for both types of treatments. Results: The accuracies of the best models for immunotherapy (LightGBM) and targeted therapy (random forest) were respectively 66% and 65%. The most significant variables for building the models were respectively: stage (IIIc or IV), response to previous treatments lines, age, number of metastasis sites and time between first melanoma excision and metastatic relapse. Conclusions: We present here the first machine learning models to predict the response to immunotherapy and targeted therapy in stage IIIc or IV melanoma patients. The most predictive variables are coherent with the literature. Future development will include data from 18FDG-PET/CT imaging and other predictive markers recently identified, as circulating DNA to improve the models performance.

Document Preprocessing with TF-IDF to Improve the Polarity Classification Performance of Unstructured Sentiment Analysis

2020 ◽  
pp. 235-242
Author(s):  
Farrikh Alzami ◽  
Erika Devi Udayanti ◽  
Dwi Puji Prabowo ◽  
Rama Aria Megantara
Keyword(s):  
Machine Learning ◽  
Feature Extraction ◽  
Random Forest ◽  
Sentiment Analysis ◽  
Classification Performance ◽  
Document Preparation ◽  
Learning Models ◽  
Polarity Classification ◽  
Negative Sentiment ◽  
Machine Learning Models

Sentiment analysis in terms of polarity classification is very important in everyday life, with the existence of polarity, many people can find out whether the respected document has positive or negative sentiment so that it can help in choosing and making decisions. Sentiment analysis usually done manually. Therefore, an automatic sentiment analysis classification process is needed. However, it is rare to find studies that discuss extraction features and which learning models are suitable for unstructured sentiment analysis types with the Amazon food review case. This research explores some extraction features such as Word Bags, TF-IDF, Word2Vector, as well as a combination of TF-IDF and Word2Vector with several machine learning models such as Random Forest, SVM, KNN and Naïve Bayes to find out a combination of feature extraction and learning models that can help add variety to the analysis of polarity sentiments. By assisting with document preparation such as html tags and punctuation and special characters, using snowball stemming, TF-IDF results obtained with SVM are suitable for obtaining a polarity classification in unstructured sentiment analysis for the case of Amazon food review with a performance result of 87,3 percent.

scholarly journals Comparison of Resampling Algorithms to Address Class Imbalance when Developing Machine Learning Models to Predict Foodborne Pathogen Presence in Agricultural Water

2021 ◽  
Vol 9 ◽  
Author(s):  
Daniel Lowell Weller ◽  
Tanzy M. T. Love ◽  
Martin Wiedmann
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Predictive Models ◽  
Training Data ◽  
Agricultural Water ◽  
Learning Models ◽  
Safety Hazards ◽  
E Coli ◽  
Resampling Method ◽  
Machine Learning Models

Recent studies have shown that predictive models can supplement or provide alternatives to E. coli-testing for assessing the potential presence of food safety hazards in water used for produce production. However, these studies used balanced training data and focused on enteric pathogens. As such, research is needed to determine 1) if predictive models can be used to assess Listeria contamination of agricultural water, and 2) how resampling (to deal with imbalanced data) affects performance of these models. To address these knowledge gaps, this study developed models that predict nonpathogenic Listeria spp. (excluding L. monocytogenes) and L. monocytogenes presence in agricultural water using various combinations of learner (e.g., random forest, regression), feature type, and resampling method (none, oversampling, SMOTE). Four feature types were used in model training: microbial, physicochemical, spatial, and weather. “Full models” were trained using all four feature types, while “nested models” used between one and three types. In total, 45 full (15 learners*3 resampling approaches) and 108 nested (5 learners*9 feature sets*3 resampling approaches) models were trained per outcome. Model performance was compared against baseline models where E. coli concentration was the sole predictor. Overall, the machine learning models outperformed the baseline E. coli models, with random forests outperforming models built using other learners (e.g., rule-based learners). Resampling produced more accurate models than not resampling, with SMOTE models outperforming, on average, oversampling models. Regardless of resampling method, spatial and physicochemical water quality features drove accurate predictions for the nonpathogenic Listeria spp. and L. monocytogenes models, respectively. Overall, these findings 1) illustrate the need for alternatives to existing E. coli-based monitoring programs for assessing agricultural water for the presence of potential food safety hazards, and 2) suggest that predictive models may be one such alternative. Moreover, these findings provide a conceptual framework for how such models can be developed in the future with the ultimate aim of developing models that can be integrated into on-farm risk management programs. For example, future studies should consider using random forest learners, SMOTE resampling, and spatial features to develop models to predict the presence of foodborne pathogens, such as L. monocytogenes, in agricultural water when the training data is imbalanced.

scholarly journals Three machine learning models for the 2019 Solubility Challenge

ADMET & DMPK ◽  
2020 ◽  
Author(s):  
John Mitchell
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Gold Standard ◽  
Challenge Test ◽  
Wisdom Of Crowds ◽  
Learning Models ◽  
The Third ◽  
Aqueous Solubilities ◽  
Machine Learning Models ◽  
Better Than

<p class="ADMETabstracttext">We describe three machine learning models submitted to the 2019 Solubility Challenge. All are founded on tree-like classifiers, with one model being based on Random Forest and another on the related Extra Trees algorithm. The third model is a consensus predictor combining the former two with a Bagging classifier. We call this consensus classifier Vox Machinarum, and here discuss how it benefits from the Wisdom of Crowds. On the first 2019 Solubility Challenge test set of 100 low-variance intrinsic aqueous solubilities, Extra Trees is our best classifier. One the other, a high-variance set of 32 molecules, we find that Vox Machinarum and Random Forest both perform a little better than Extra Trees, and almost equally to one another. We also compare the gold standard solubilities from the 2019 Solubility Challenge with a set of literature-based solubilities for most of the same compounds.</p>

scholarly journals CPT Data Interpretation Employing Different Machine Learning Techniques

Geosciences ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 265
Author(s):  
Stefan Rauter ◽  
Franz Tschuchnigg
Keyword(s):  
Machine Learning ◽  
Grain Size ◽  
Random Forest ◽  
Classification Model ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Models ◽  
Cone Penetration ◽  
Tip Resistance ◽  
Machine Learning Models

The classification of soils into categories with a similar range of properties is a fundamental geotechnical engineering procedure. At present, this classification is based on various types of cost- and time-intensive laboratory and/or in situ tests. These soil investigations are essential for each individual construction site and have to be performed prior to the design of a project. Since Machine Learning could play a key role in reducing the costs and time needed for a suitable site investigation program, the basic ability of Machine Learning models to classify soils from Cone Penetration Tests (CPT) is evaluated. To find an appropriate classification model, 24 different Machine Learning models, based on three different algorithms, are built and trained on a dataset consisting of 1339 CPT. The applied algorithms are a Support Vector Machine, an Artificial Neural Network and a Random Forest. As input features, different combinations of direct cone penetration test data (tip resistance qc, sleeve friction fs, friction ratio Rf, depth d), combined with “defined”, thus, not directly measured data (total vertical stresses σv, effective vertical stresses σ’v and hydrostatic pore pressure u0), are used. Standard soil classes based on grain size distributions and soil classes based on soil behavior types according to Robertson are applied as targets. The different models are compared with respect to their prediction performance and the required learning time. The best results for all targets were obtained with models using a Random Forest classifier. For the soil classes based on grain size distribution, an accuracy of about 75%, and for soil classes according to Robertson, an accuracy of about 97–99%, was reached.

scholarly journals Mode Choice Prediction using Machine Learning Technique for A Door-to-Door Journey in Kuantan City

Mekatronika ◽  
2020 ◽  
Vol 2 (1) ◽  
pp. 73-78
Author(s):  
Nur Fahriza Mohd Ali ◽  
Ahmad Farhan Mohd Sadullah ◽  
Anwar P.P. Abdul Majeed ◽  
Mohd Azraai Mohd Razman ◽  
Rabiu Muazu Musa
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Mode Choice ◽  
Learning Models ◽  
Machine Learning Technique ◽  
Travel Mode Choice ◽  
Testing Data ◽  
Learning Technique ◽  
The City ◽  
Machine Learning Models

A door-to-door journey in a public transportation system is a notable concept that is practically being promoted among users to consider public transport as an important alternative. The door-to-door journey will integrate the travel segments starting from home to destination, including all visible amenities. Users’ preferences on the time travel of these key segments are necessary to be understood. In this case, Machine Learning technique has been seen as a robust computational advancement to forecast their travel mode choice. However, the most convenient model as the best predictor is still questionable. To address this issue, we employed some pre-eminent machine learning models, specifically Random Forest (RF), Naïve Bayes (NB), Logistic Regression (LR), k-Nearest Neighbor (kNN) as well as Support Vector Machine (SVM), to compare their travel mode choice prediction performance of users in the city of Kuantan. The data collection was conducted in Kuantan City via Revealed/Stated Preferences (RPSP) Survey between 8:00 AM to 5:00 PM on weekdays. The data collected was split into a ratio of 80:20 for training and testing before evaluating them between the aforesaid models. The results depicted that the Random Forest could provide satisfactory classification accuracies for both training and testing data up to 68.3% and 61.3%, respectively, compared to the other evaluated machine learning models. In summary, Random Forest provides a good result in the training and testing data and is considered as the best predictor in this research to forecast users’ mode choice in the city of Kuantan.

scholarly journals Application of Natural Language Processing with Supervised Machine Learning Techniques to Predict the Overall Drugs Performance

2020 ◽  
Vol 11 (40) ◽  
pp. 8-23
Author(s):  
Pius MARTHIN ◽  
Duygu İÇEN
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Random Forest ◽  
Semantic Analysis ◽  
Classification Tree ◽  
Supervised Machine Learning ◽  
Training Dataset ◽  
Support Vector ◽  
Learning Models ◽  
Machine Learning Models

Online product reviews have become a valuable source of information which facilitate customer decision with respect to a particular product. With the wealthy information regarding user's satisfaction and experiences about a particular drug, pharmaceutical companies make the use of online drug reviews to improve the quality of their products. Machine learning has enabled scientists to train more efficient models which facilitate decision making in various fields. In this manuscript we applied a drug review dataset used by (Gräβer, Kallumadi, Malberg,& Zaunseder, 2018), available freely from machine learning repository website of the University of California Irvine (UCI) to identify best machine learning model which provide a better prediction of the overall drug performance with respect to users' reviews. Apart from several manipulations done to improve model accuracy, all necessary procedures required for text analysis were followed including text cleaning and transformation of texts to numeric format for easy training machine learning models. Prior to modeling, we obtained overall sentiment scores for the reviews. Customer's reviews were summarized and visualized using a bar plot and word cloud to explore the most frequent terms. Due to scalability issues, we were able to use only the sample of the dataset. We randomly sampled 15000 observations from the 161297 training dataset and 10000 observations were randomly sampled from the 53766 testing dataset. Several machine learning models were trained using 10 folds cross-validation performed under stratified random sampling. The trained models include Classification and Regression Trees (CART), classification tree by C5.0, logistic regression (GLM), Multivariate Adaptive Regression Spline (MARS), Support vector machine (SVM) with both radial and linear kernels and a classification tree using random forest (Random Forest). Model selection was done through a comparison of accuracies and computational efficiency. Support vector machine (SVM) with linear kernel was significantly best with an accuracy of 83% compared to the rest. Using only a small portion of the dataset, we managed to attain reasonable accuracy in our models by applying the TF-IDF transformation and Latent Semantic Analysis (LSA) technique to our TDM.

scholarly journals Forest Fire Prediction using Machine Learning Models based on DC, Wind and RH

2020 ◽  
Vol 8 (6S) ◽  
pp. 142-143
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Forest Fire ◽  
Random Forest Algorithm ◽  
Learning Models ◽  
Learning Classifier ◽  
Machine Learning Models ◽  
Classifier Algorithms

The paper points out forest fire prediction using machine learning models on the basis of viz. DC, Wind, RH out of the several machine learning classifier algorithms, It is relevant that random forest algorithm generates optimum accuracy(99.61%).

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