Predicting survival in advanced cancers by applying machine learning to clinical narratives.

32 Background: We previously showed that a text mining approach can identify clinical prognostic factors from electronic medical records (EMR) in patients with advanced cancers (1). Here we further examine whether clinical narratives can be exploited to build prognostic tools by applying a machine-learning (ML) approach. Methods: A retrospective study of all patients with stage IV tumors was conducted at a single tertiary cancer centre. The text corpus was formed by extracting narratives from initial consultation letters authored by oncologists, and a feature learning pipeline (2) was then used to extract text features correlating to survival. Five classes of ML algorithms was then applied for survival prediction. Classification performance was assessed by stratified cross-validation and compared with Eastern Cooperative Oncology Group (ECOG) performance scores. Results: EMR were available for analysis in 4791 of 7043 patients from 2001-2017, and in 2211 of these cases ECOG performance scores were available. By applying ML on features extracted from EMR text, survival of patients at 2, 6, 12, 26, 52, and 80 weeks was predicted, with areas under the receiver operating characteristic (ROC) curve of 0.82, 0.80, 0.77, 0.72, 0.72, and 0.76 respectively. ML outperformed ECOG score in predicting patient prognosis between 12-16 weeks ( p < 0.05) and after 52 weeks ( p < 0.05), and was non-inferior at all other time points. Random forest was the best algorithm for the prognostic classification task. Feature filtering threshold was important to classification accuracy ( p < 0.001). Conclusions: In patients with advanced cancers, ML analysis of clinical narratives can be used to automate prognostication with greater accuracy than is currently obtainable from ECOG status. References: 1. Int Med J 2018; 48: S5: 8, 2. Sci Rep 2017; 7: 6918.

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Binary Spectrum Feature for Improved Classiﬁer Performance

10.36227/techrxiv.12993122 ◽

2020 ◽

Author(s):

Nalika Ulapane ◽

Karthick Thiyagarajan ◽

sarath kodagoda

Keyword(s):

Machine Learning ◽

Classification Performance ◽

Feature Reduction ◽

Sensor Data ◽

Machine Learning Techniques ◽

Support Vector ◽

Svm Classifier ◽

Monitoring Task ◽

Classifier Performance ◽

Spectrum Feature

<div>Classiﬁcation has become a vital task in modern machine learning and Artiﬁcial Intelligence applications, including smart sensing. Numerous machine learning techniques are available to perform classiﬁcation. Similarly, numerous practices, such as feature selection (i.e., selection of a subset of descriptor variables that optimally describe the output), are available to improve classiﬁer performance. In this paper, we consider the case of a given supervised learning classiﬁcation task that has to be performed making use of continuous-valued features. It is assumed that an optimal subset of features has already been selected. Therefore, no further feature reduction, or feature addition, is to be carried out. Then, we attempt to improve the classiﬁcation performance by passing the given feature set through a transformation that produces a new feature set which we have named the “Binary Spectrum”. Via a case study example done on some Pulsed Eddy Current sensor data captured from an infrastructure monitoring task, we demonstrate how the classiﬁcation accuracy of a Support Vector Machine (SVM) classiﬁer increases through the use of this Binary Spectrum feature, indicating the feature transformation’s potential for broader usage.</div><div><br></div>

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

Kinetik Game Technology Information System Computer Network Computing Electronics and Control ◽

10.22219/kinetik.v5i3.1066 ◽

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.

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Transformer Oil Quality Assessment Using Random Forest with Feature Engineering

Energies ◽

10.3390/en14071809 ◽

2021 ◽

Vol 14 (7) ◽

pp. 1809

Author(s):

Mohammed El Amine Senoussaoui ◽

Mostefa Brahami ◽

Issouf Fofana

Keyword(s):

Machine Learning ◽

Random Forest ◽

Oil Quality ◽

Principal Component ◽

Condition Assessment ◽

Classification Performance ◽

Transformer Oil ◽

Classification Model ◽

Insulation Degradation ◽

Transformer Oils

Machine learning is widely used as a panacea in many engineering applications including the condition assessment of power transformers. Most statistics attribute the main cause of transformer failure to insulation degradation. Thus, a new, simple, and effective machine-learning approach was proposed to monitor the condition of transformer oils based on some aging indicators. The proposed approach was used to compare the performance of two machine-learning classifiers: J48 decision tree and random forest. The service-aged transformer oils were classified into four groups: the oils that can be maintained in service, the oils that should be reconditioned or filtered, the oils that should be reclaimed, and the oils that must be discarded. From the two algorithms, random forest exhibited a better performance and high accuracy with only a small amount of data. Good performance was achieved through not only the application of the proposed algorithm but also the approach of data preprocessing. Before feeding the classification model, the available data were transformed using the simple k-means method. Subsequently, the obtained data were filtered through correlation-based feature selection (CFsSubset). The resulting features were again retransformed by conducting the principal component analysis and were passed through the CFsSubset filter. The transformation and filtration of the data improved the classification performance of the adopted algorithms, especially random forest. Another advantage of the proposed method is the decrease in the number of the datasets required for the condition assessment of transformer oils, which is valuable for transformer condition monitoring.

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Use of Machine Learning to Investigate the Quantitative Checklist for Autism in Toddlers (Q-CHAT) towards Early Autism Screening

Diagnostics ◽

10.3390/diagnostics11030574 ◽

2021 ◽

Vol 11 (3) ◽

pp. 574

Author(s):

Gennaro Tartarisco ◽

Giovanni Cicceri ◽

Davide Di Pietro ◽

Elisa Leonardi ◽

Stefania Aiello ◽

...

Keyword(s):

Machine Learning ◽

High Performance ◽

Behavioral Science ◽

Autistic Traits ◽

Classification Performance ◽

Recursive Feature Elimination ◽

Diagnostic Tools ◽

Support Vector ◽

K Nearest Neighbors ◽

Autism Screening

In the past two decades, several screening instruments were developed to detect toddlers who may be autistic both in clinical and unselected samples. Among others, the Quantitative CHecklist for Autism in Toddlers (Q-CHAT) is a quantitative and normally distributed measure of autistic traits that demonstrates good psychometric properties in different settings and cultures. Recently, machine learning (ML) has been applied to behavioral science to improve the classification performance of autism screening and diagnostic tools, but mainly in children, adolescents, and adults. In this study, we used ML to investigate the accuracy and reliability of the Q-CHAT in discriminating young autistic children from those without. Five different ML algorithms (random forest (RF), naïve Bayes (NB), support vector machine (SVM), logistic regression (LR), and K-nearest neighbors (KNN)) were applied to investigate the complete set of Q-CHAT items. Our results showed that ML achieved an overall accuracy of 90%, and the SVM was the most effective, being able to classify autism with 95% accuracy. Furthermore, using the SVM–recursive feature elimination (RFE) approach, we selected a subset of 14 items ensuring 91% accuracy, while 83% accuracy was obtained from the 3 best discriminating items in common to ours and the previously reported Q-CHAT-10. This evidence confirms the high performance and cross-cultural validity of the Q-CHAT, and supports the application of ML to create shorter and faster versions of the instrument, maintaining high classification accuracy, to be used as a quick, easy, and high-performance tool in primary-care settings.

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Machine-Learning-Based Radiomics MRI Model for Survival Prediction of Recurrent Glioblastomas Treated with Bevacizumab

Diagnostics ◽

10.3390/diagnostics11071263 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1263

Author(s):

Samy Ammari ◽

Raoul Sallé de Chou ◽

Tarek Assi ◽

Mehdi Touat ◽

Emilie Chouzenoux ◽

...

Keyword(s):

Machine Learning ◽

Therapeutic Option ◽

Binary Classification ◽

Progression Free Survival ◽

Recurrent Glioblastoma ◽

Machine Learning Algorithms ◽

Survival Prediction ◽

Classification Models ◽

Angiogenic Therapy ◽

Recurrent Gbm

Anti-angiogenic therapy with bevacizumab is a widely used therapeutic option for recurrent glioblastoma (GBM). Nevertheless, the therapeutic response remains highly heterogeneous among GBM patients with discordant outcomes. Recent data have shown that radiomics, an advanced recent imaging analysis method, can help to predict both prognosis and therapy in a multitude of solid tumours. The objective of this study was to identify novel biomarkers, extracted from MRI and clinical data, which could predict overall survival (OS) and progression-free survival (PFS) in GBM patients treated with bevacizumab using machine-learning algorithms. In a cohort of 194 recurrent GBM patients (age range 18–80), radiomics data from pre-treatment T2 FLAIR and gadolinium-injected MRI images along with clinical features were analysed. Binary classification models for OS at 9, 12, and 15 months were evaluated. Our classification models successfully stratified the OS. The AUCs were equal to 0.78, 0.85, and 0.76 on the test sets (0.79, 0.82, and 0.87 on the training sets) for the 9-, 12-, and 15-month endpoints, respectively. Regressions yielded a C-index of 0.64 (0.74) for OS and 0.57 (0.69) for PFS. These results suggest that radiomics could assist in the elaboration of a predictive model for treatment selection in recurrent GBM patients.

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Screening the genome for HCC-specific CpG methylation signatures as biomarkers for diagnosis and prognosis evaluation

BMC Medical Genomics ◽

10.1186/s12920-021-01015-9 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Rui-kun Zhang ◽

Jia-lin Liu

Keyword(s):

Cox Regression ◽

Malignant Tumors ◽

Gene Expression Omnibus ◽

The Cancer Genome Atlas ◽

Survival Prediction ◽

Training Set ◽

Cpg Sites ◽

Diagnosis And Prognosis ◽

Patient Prognosis ◽

Prognosis Evaluation

Abstract Background Hepatocellular carcinoma (HCC) is one of the most common and invasive malignant tumors in the world. The change in DNA methylation is a key event in HCC. Methods Methylation datasets for HCC and 17 other types of cancer were downloaded from The Cancer Genome Atlas (TCGA). The CpG sites with large differences in methylation between tumor tissues and paracancerous tissues were identified. We used the HCC methylation dataset downloaded from the TCGA as the training set and removed the overlapping sites among all cancer datasets to ensure that only CpG sites specific to HCC remained. Logistic regression analysis was performed to select specific biomarkers that can be used to diagnose HCC, and two datasets—GSE157341 and GSE54503—downloaded from GEO as validation sets were used to validate our model. We also used a Cox regression model to select CpG sites related to patient prognosis. Results We identified 6 HCC-specific methylated CpG sites as biomarkers for HCC diagnosis. In the training set, the area under the receiver operating characteristic (ROC) curve (AUC) for the model containing all these sites was 0.971. The AUCs were 0.8802 and 0.9711 for the two validation sets from the GEO database. In addition, 3 other CpG sites were analyzed and used to create a risk scoring model for patient prognosis and survival prediction. Conclusions Through the analysis of HCC methylation datasets from the TCGA and Gene Expression Omnibus (GEO) databases, potential biomarkers for HCC diagnosis and prognosis evaluation were ascertained.

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