scholarly journals Integrating Scientific Knowledge into Machine Learning using Interactive Decision Trees

2021 ◽  
Author(s):  
Georgios Sarailidis ◽  
Thorsten Wagener ◽  
Francesca Pianosi
Keyword(s):  
Machine Learning ◽  
Decision Trees ◽  
Scientific Knowledge ◽  
Large Data ◽  
High Dimensional ◽  
Machine Learning Method ◽  
Human In The Loop ◽  
Data Limitations ◽  
Visualization Techniques ◽  
Composite Variables

Decision Trees (DT) is a machine learning method that has been widely used in the environmental sciences to automatically extract patterns from complex and high dimensional data. However, like any data-based method, is hindered by data limitations and potentially physically unrealistic results. We develop interactive DT (iDT) that put the human in the loop and integrate the power of experts’ scientific knowledge with the power of the algorithms to automatically learn patterns from large data. We created a toolbox that contains methods and visualization techniques that allow users to interact with the DT. Users can create new composite variables, manually change the variable and threshold to split, manually prune and group variables based on physical meaning. We demonstrate with three case studies that iDT help experts incorporate their knowledge in the DT models achieving higher interpretability and realism in a physical sense.

scholarly journals Survey on Feature Transformation Techniques for Data Streams

2020 ◽  
Author(s):  
Maroua Bahri ◽  
Albert Bifet ◽  
Silviu Maniu ◽  
Heitor Murilo Gomes
Keyword(s):  
Machine Learning ◽  
Data Streams ◽  
Large Data ◽  
High Dimensional ◽  
Feature Transformation ◽  
Transformation Techniques ◽  
Computational Costs ◽  
The Past ◽  
Fundamental Challenge ◽  
Mining Algorithms

Mining high-dimensional data streams poses a fundamental challenge to machine learning as the presence of high numbers of attributes can remarkably degrade any mining task's performance. In the past several years, dimension reduction (DR) approaches have been successfully applied for different purposes (e.g., visualization). Due to their high-computational costs and numerous passes over large data, these approaches pose a hindrance when processing infinite data streams that are potentially high-dimensional. The latter increases the resource-usage of algorithms that could suffer from the curse of dimensionality. To cope with these issues, some techniques for incremental DR have been proposed. In this paper, we provide a survey on reduction approaches designed to handle data streams and highlight the key benefits of using these approaches for stream mining algorithms.

scholarly journals Methodology Proposal of ADHD Classification of Children Based on Cross Recurrence Plots

2021 ◽  
Author(s):  
Marco Aceves-Fernandez
Keyword(s):  
Machine Learning ◽  
Spectral Distribution ◽  
High Dimensional ◽  
Control Group ◽  
Machine Learning Method ◽  
Learning Method ◽  
Recurrence Plots ◽  
Eeg Signals ◽  
Power Spectral

Abstract Dealing with electroencephalogram signals (EEG) are often not easy. The lack of predicability and complexity of such non-stationary, noisy and high dimensional signals is challenging. Cross Recurrence Plots (CRP) have been used extensively to deal with detecting subtle changes in signals even when the noise is embedded in the signal. In this contribution, a total of 121 children performed visual attention experiments and a proposed methodology using CRP and a Welch Power Spectral Distribution have been used to classify then between those who have ADHD and the control group. Additional tools were presented to determine to which extent the proposed methodology is able to classify accurately and avoid misclassifications, thus demonstrating that this methodology is feasible to classify EEG signals from subjects with ADHD. Lastly, the results were compared with a baseline machine learning method to prove experimentally that this methodology is consistent and the results repeatable.

scholarly journals Explainable t-SNE for single-cell RNA-seq data analysis

2022 ◽  
Author(s):  
Henry Han ◽  
Tianyu Zhang ◽  
Mary Lauren Benton ◽  
Chun Li ◽  
Juan Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Data Analysis ◽  
Dimension Reduction ◽  
Single Cell ◽  
Method Development ◽  
Robustness Analysis ◽  
High Dimensional ◽  
Machine Learning Method ◽  
Learning Method

Single-cell RNA (scRNA-seq) sequencing technologies trigger the study of individual cell gene expression and reveal the diversity within cell populations. To measure cell-to-cell similarity based on their transcription and gene expression, many dimension reduction methods are employed to retrieve the corresponding low-dimensional embeddings of input scRNA-seq data to conduct clustering. However, the methods lack explainability and may not perform well with scRNA-seq data because they are often migrated from other fields and not customized for high-dimensional sparse scRNA-seq data. In this study, we propose an explainable t-SNE: cell-driven t-SNE (c-TSNE) that fuses the cell differences reflected from biologically meaningful distance metrics for input scRNA-seq data. Our study shows that the proposed method not only enhances the interpretation of the original t-SNE visualization for scRNA-seq data but also demonstrates favorable single cell segregation performance on benchmark datasets compared to the state-of-the-art peers. The robustness analysis shows that the proposed cell-driven t-SNE demonstrates robustness to dropout and noise in dimension reduction and clustering. It provides a novel and practical way to investigate the interpretability of t-SNE in scRNA-seq data analysis. Unlike the general assumption that the explainanbility of a machine learning method needs to compromise with the learning efficiency, the proposed explainable t-SNE improves both clustering efficiency and explainanbility in scRNA-seq analysis. More importantly, our work suggests that widely used t-SNE can be easily misused in the existing scRNA-seq analysis, because its default Euclidean distance can bring biases or meaningless results in cell difference evaluation for high-dimensional sparse scRNA-seq data. To the best of our knowledge, it is the first explainable t-SNE proposed in scRNA-seq analysis and will inspire other explainable machine learning method development in the field.

Speech Organ Contour Extraction Using Real-Time MRI and Machine Learning Method

2019 ◽  
Author(s):  
Hironori Takemoto ◽  
Tsubasa Goto ◽  
Yuya Hagihara ◽  
Sayaka Hamanaka ◽  
Tatsuya Kitamura ◽  
...  
Keyword(s):  
Machine Learning ◽  
Real Time ◽  
Machine Learning Method ◽  
Learning Method ◽  
Contour Extraction

In silico Prediction of Inhibitory Constant of Thrombin Inhibitors Using Machine Learning

2019 ◽  
Vol 21 (9) ◽  
pp. 662-669 ◽  
Author(s):  
Junnan Zhao ◽  
Lu Zhu ◽  
Weineng Zhou ◽  
Lingfeng Yin ◽  
Yuchen Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Regression Tree ◽  
Large Data ◽  
Thrombin Inhibitors ◽  
Coagulation Cascade ◽  
Gradient Boosting ◽  
Support Vector ◽  
Data Set ◽  
Descriptor Selection

Background: Thrombin is the central protease of the vertebrate blood coagulation cascade, which is closely related to cardiovascular diseases. The inhibitory constant Ki is the most significant property of thrombin inhibitors. Method: This study was carried out to predict Ki values of thrombin inhibitors based on a large data set by using machine learning methods. Taking advantage of finding non-intuitive regularities on high-dimensional datasets, machine learning can be used to build effective predictive models. A total of 6554 descriptors for each compound were collected and an efficient descriptor selection method was chosen to find the appropriate descriptors. Four different methods including multiple linear regression (MLR), K Nearest Neighbors (KNN), Gradient Boosting Regression Tree (GBRT) and Support Vector Machine (SVM) were implemented to build prediction models with these selected descriptors. Results: The SVM model was the best one among these methods with R2=0.84, MSE=0.55 for the training set and R2=0.83, MSE=0.56 for the test set. Several validation methods such as yrandomization test and applicability domain evaluation, were adopted to assess the robustness and generalization ability of the model. The final model shows excellent stability and predictive ability and can be employed for rapid estimation of the inhibitory constant, which is full of help for designing novel thrombin inhibitors.

Digging for the truth: the case for active annotation in evaluating the credibility of online medical information (Preprint)

2020 ◽  
Author(s):  
Mikołaj Morzy ◽  
Bartłomiej Balcerzak ◽  
Adam Wierzbicki ◽  
Adam Wierzbicki
Keyword(s):  
Machine Learning ◽  
Medical Information ◽  
Representation Learning ◽  
Training Dataset ◽  
Highly Qualified ◽  
Human In The Loop ◽  
Annotation Process ◽  
Comprehensive Framework ◽  
Online Sources ◽  
The Web

BACKGROUND With the rapidly accelerating spread of dissemination of false medical information on the Web, the task of establishing the credibility of online sources of medical information becomes a pressing necessity. The sheer number of websites offering questionable medical information presented as reliable and actionable suggestions with possibly harmful effects poses an additional requirement for potential solutions, as they have to scale to the size of the problem. Machine learning is one such solution which, when properly deployed, can be an effective tool in fighting medical disinformation on the Web. OBJECTIVE We present a comprehensive framework for designing and curating of machine learning training datasets for online medical information credibility assessment. We show how the annotation process should be constructed and what pitfalls should be avoided. Our main objective is to provide researchers from medical and computer science communities with guidelines on how to construct datasets for machine learning models for various areas of medical information wars. METHODS The key component of our approach is the active annotation process. We begin by outlining the annotation protocol for the curation of high-quality training dataset, which then can be augmented and rapidly extended by employing the human-in-the-loop paradigm to machine learning training. To circumvent the cold start problem of insufficient gold standard annotations, we propose a pre-processing pipeline consisting of representation learning, clustering, and re-ranking of sentences for the acceleration of the training process and the optimization of human resources involved in the annotation. RESULTS We collect over 10 000 annotations of sentences related to selected subjects (psychiatry, cholesterol, autism, antibiotics, vaccines, steroids, birth methods, food allergy testing) for less than $7 000 employing 9 highly qualified annotators (certified medical professionals) and we release this dataset to the general public. We develop an active annotation framework for more efficient annotation of non-credible medical statements. The results of the qualitative analysis support our claims of the efficacy of the presented method. CONCLUSIONS A set of very diverse incentives is driving the widespread dissemination of medical disinformation on the Web. An effective strategy of countering this spread is to use machine learning for automatically establishing the credibility of online medical information. This, however, requires a thoughtful design of the training pipeline. In this paper we present a comprehensive framework of active annotation. In addition, we publish a large curated dataset of medical statements labelled as credible, non-credible, or neutral.

scholarly journals Classification of Brainwaves for Sleep Stages by High-Dimensional FFT Features from EEG Signals

2020 ◽  
Vol 10 (5) ◽  
pp. 1797 ◽  
Author(s):  
Mera Kartika Delimayanti ◽  
Bedy Purnama ◽  
Ngoc Giang Nguyen ◽  
Mohammad Reza Faisal ◽  
Kunti Robiatul Mahmudah ◽  
...  
Keyword(s):  
Machine Learning ◽  
Sleep Stage ◽  
Machine Learning Algorithms ◽  
High Dimensional ◽  
Sleep Stages ◽  
Eeg Signals ◽  
Stage Classification ◽  
Sleep Stage Classification ◽  
Low Dimensional

Manual classification of sleep stage is a time-consuming but necessary step in the diagnosis and treatment of sleep disorders, and its automation has been an area of active study. The previous works have shown that low dimensional fast Fourier transform (FFT) features and many machine learning algorithms have been applied. In this paper, we demonstrate utilization of features extracted from EEG signals via FFT to improve the performance of automated sleep stage classification through machine learning methods. Unlike previous works using FFT, we incorporated thousands of FFT features in order to classify the sleep stages into 2–6 classes. Using the expanded version of Sleep-EDF dataset with 61 recordings, our method outperformed other state-of-the art methods. This result indicates that high dimensional FFT features in combination with a simple feature selection is effective for the improvement of automated sleep stage classification.

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