Abstract 2452: Patient segmentation using machine-learning based literature and genomic data synthesis uncovers novel cohorts of NSCLC and mesothelioma patients

2019 ◽  
Author(s):  
Enrique Garcia-Rivera ◽  
Aaron S. Mansfield ◽  
Karthik Murugadoss ◽  
Murali Aravamudan
Keyword(s):  
Machine Learning ◽  
Genomic Data ◽  
Data Synthesis ◽  
Patient Segmentation

scholarly journals Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Finlay Maguire ◽  
Muhammad Attiq Rehman ◽  
Catherine Carrillo ◽  
Moussa S. Diarra ◽  
Robert G. Beiko
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Antimicrobial Resistance ◽  
Broiler Chicken ◽  
Genomic Data ◽  
Set Covering ◽  
Learning Models ◽  
Commercial Chicken ◽  
The Impact ◽  
Machine Learning Models

ABSTRACT Nontyphoidal Salmonella (NTS) is a leading global cause of bacterial foodborne morbidity and mortality. Our ability to treat severe NTS infections has been impaired by increasing antimicrobial resistance (AMR). To understand and mitigate the global health crisis AMR represents, we need to link the observed resistance phenotypes with their underlying genomic mechanisms. Broiler chickens represent a key reservoir and vector for NTS infections, but isolates from this setting have been characterized in only very low numbers relative to clinical isolates. In this study, we sequenced and assembled 97 genomes encompassing 7 serotypes isolated from broiler chicken in farms in British Columbia between 2005 and 2008. Through application of machine learning (ML) models to predict the observed AMR phenotype from this genomic data, we were able to generate highly (0.92 to 0.99) precise logistic regression models using known AMR gene annotations as features for 7 antibiotics (amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, and tetracycline). Similarly, we also trained “reference-free” k-mer-based set-covering machine phenotypic prediction models (0.91 to 1.0 precision) for these antibiotics. By combining the inferred k-mers and logistic regression weights, we identified the primary drivers of AMR for the 7 studied antibiotics in these isolates. With our research representing one of the largest studies of a diverse set of NTS isolates from broiler chicken, we can thus confirm that the AmpC-like CMY-2 β-lactamase is a primary driver of β-lactam resistance and that the phosphotransferases APH(6)-Id and APH(3″-Ib) are the principal drivers of streptomycin resistance in this important ecosystem. IMPORTANCE Antimicrobial resistance (AMR) represents an existential threat to the function of modern medicine. Genomics and machine learning methods are being increasingly used to analyze and predict AMR. This type of surveillance is very important to try to reduce the impact of AMR. Machine learning models are typically trained using genomic data, but the aspects of the genomes that they use to make predictions are rarely analyzed. In this work, we showed how, by using different types of machine learning models and performing this analysis, it is possible to identify the key genes underlying AMR in nontyphoidal Salmonella (NTS). NTS is among the leading cause of foodborne illness globally; however, AMR in NTS has not been heavily studied within the food chain itself. Therefore, in this work we performed a broad-scale analysis of the AMR in NTS isolates from commercial chicken farms and identified some priority AMR genes for surveillance.

scholarly journals CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kanggeun Lee ◽  
Hyoung-oh Jeong ◽  
Semin Lee ◽  
Won-Ki Jeong
Keyword(s):  
Machine Learning ◽  
Prediction Model ◽  
Genomic Data ◽  
The Cancer Genome Atlas ◽  
Cancer Type ◽  
Machine Learning Classifiers ◽  
Learning Classifiers ◽  
Somatic Alterations ◽  
The Impact ◽  
Type Classification

AbstractWith recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alterations detected from sequencing analyses. However, the ever-increasing size and complexity of the data make the classification task extremely challenging. In this study, we evaluate the contributions of various input features, such as mutation profiles, mutation rates, mutation spectra and signatures, and somatic copy number alterations that can be derived from genomic data, and further utilize them for accurate cancer type classification. We introduce a novel ensemble of machine learning classifiers, called CPEM (Cancer Predictor using an Ensemble Model), which is tested on 7,002 samples representing over 31 different cancer types collected from The Cancer Genome Atlas (TCGA) database. We first systematically examined the impact of the input features. Features known to be associated with specific cancers had relatively high importance in our initial prediction model. We further investigated various machine learning classifiers and feature selection methods to derive the ensemble-based cancer type prediction model achieving up to 84% classification accuracy in the nested 10-fold cross-validation. Finally, we narrowed down the target cancers to the six most common types and achieved up to 94% accuracy.

scholarly journals Prediction of condition-specific regulatory genes using machine learning

2020 ◽  
Vol 48 (11) ◽  
pp. e62-e62 ◽  
Author(s):  
Qi Song ◽  
Jiyoung Lee ◽  
Shamima Akter ◽  
Matthew Rogers ◽  
Ruth Grene ◽  
...  
Keyword(s):  
Machine Learning ◽  
Transcription Factors ◽  
Single Cell ◽  
Control Cell ◽  
Genomic Data ◽  
Regulatory Genes ◽  
Genomic Research ◽  
Open Chromatin ◽  
Data Set ◽  
Better Than

Abstract Recent advances in genomic technologies have generated data on large-scale protein–DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5–25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.

scholarly journals Identification of Natural Selection in Genomic Data with Deep Convolutional Neural Network

2021 ◽  
Author(s):  
Arnaud Nguembang Fadja ◽  
Fabrizio Riguzzi ◽  
Giorgio Bertorelle ◽  
Emiliano Trucchi
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Natural Selection ◽  
Convolutional Neural Network ◽  
Simulated Data ◽  
Genomic Data ◽  
Relevant Information ◽  
Supervised Machine Learning ◽  
Selection Processes ◽  
Adaptive Processes

Abstract Background: With the increase in the size of genomic datasets describing variability in populations, extracting relevant information becomes increasingly useful as well as complex. Recently, computational methodologies such as Supervised Machine Learning and specifically Convolutional Neural Networks have been proposed to order to make inferences on demographic and adaptive processes using genomic data, Even though it was already shown to be powerful and efficient in different fields of investigation, Supervised Machine Learning has still to be explored as to unfold its enormous potential in evolutionary genomics. Results: The paper proposes a method based on Supervised Machine Learning for classifying genomic data, represented as windows of genomic sequences from a sample of individuals belonging to the same population. A Convolutional Neural Network is used to test whether a genomic window shows the signature of natural selection. Experiments performed on simulated data show that the proposed model can accurately predict neutral and selection processes on genomic data with more than 99% accuracy.

scholarly journals GeNets: A unified web platform for network-based analyses of genomic data

2018 ◽  
Author(s):  
Taibo Li ◽  
April Kim ◽  
Joseph Rosenbluh ◽  
Heiko Horn ◽  
Liraz Greenfeld ◽  
...  
Keyword(s):  
Machine Learning ◽  
Functional Genomics ◽  
Rna Sequencing ◽  
Signal To Noise Ratio ◽  
Genomic Data ◽  
Learning Model ◽  
Signal To Noise ◽  
Machine Learning Model ◽  
Optimal Network ◽  
Web Platform

Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to quantitatively compare the signal-to-noise ratio of different networks, the biology they describe, and to identify the optimal network to interpret a particular genetic dataset. Via GeNets users can train a machine-learning model (Quack) to make such comparisons; and they can execute, store, and share analyses of genetic and RNA sequencing datasets.

scholarly journals Deep learning for predicting disease status using genomic data

2018 ◽  
Author(s):  
Qianfan Wu ◽  
Adel Boueiz ◽  
Alican Bozkurt ◽  
Arya Masoomi ◽  
Allan Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Rapid Development ◽  
Learning Algorithms ◽  
Genomic Data ◽  
Disease Status ◽  
Machine Learning Algorithms ◽  
High Dimensional ◽  
Learning Approach ◽  
Low Dimensional

Predicting disease status for a complex human disease using genomic data is an important, yet challenging, step in personalized medicine. Among many challenges, the so-called curse of dimensionality problem results in unsatisfied performances of many state-of-art machine learning algorithms. A major recent advance in machine learning is the rapid development of deep learning algorithms that can efficiently extract meaningful features from high-dimensional and complex datasets through a stacked and hierarchical learning process. Deep learning has shown breakthrough performance in several areas including image recognition, natural language processing, and speech recognition. However, the performance of deep learning in predicting disease status using genomic datasets is still not well studied. In this article, we performed a review on the four relevant articles that we found through our thorough literature review. All four articles used auto-encoders to project high-dimensional genomic data to a low dimensional space and then applied the state-of-the-art machine learning algorithms to predict disease status based on the low-dimensional representations. This deep learning approach outperformed existing prediction approaches, such as prediction based on probe-wise screening and prediction based on principal component analysis. The limitations of the current deep learning approach and possible improvements were also discussed.

scholarly journals Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

2019 ◽  
Author(s):  
Marina Esteban ◽  
María Peña-Chilet ◽  
Carlos Loucera ◽  
Joaquín Dopazo
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Fanconi Anemia ◽  
Rare Diseases ◽  
Predictive Models ◽  
Mechanistic Model ◽  
Genomic Data ◽  
Potential Effect ◽  
Mechanistic Models ◽  
Related Cell

AbstractBackgroundIn spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensionality, given the disbalance between samples and candidate genes. And this is especially dramatic in scenarios in which the availability of samples is difficult, such as the case of rare diseases.ResultsThe application of multi-output regression machine learning methodologies to predict the potential effect of external proteins over the signaling circuits that trigger Fanconi anemia related cell functionalities, inferred with a mechanistic model, allowed us to detect over 20 potential therapeutic targets.ConclusionsThe use of artificial intelligence methods for the prediction of potentially causal relationships between proteins of interest and cell activities related with disease-related phenotypes opens promising avenues for the systematic search of new targets in rare diseases.

scholarly journals A Review of Tabular Data Synthesis Using GANs on an IDS Dataset

Information ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 375
Author(s):  
Stavroula Bourou ◽  
Andreas El Saer ◽  
Terpsichori-Helen Velivassaki ◽  
Artemis Voulkidis ◽  
Theodore Zahariadis
Keyword(s):  
Machine Learning ◽  
Defense Mechanism ◽  
Learning Tools ◽  
Data Generation ◽  
Tabular Data ◽  
Network Systems ◽  
Generative Adversarial Network ◽  
Data Synthesis ◽  
Detection Systems ◽  
Adversarial Network

Recent technological innovations along with the vast amount of available data worldwide have led to the rise of cyberattacks against network systems. Intrusion Detection Systems (IDS) play a crucial role as a defense mechanism in networks against adversarial attackers. Machine Learning methods provide various cybersecurity tools. However, these methods require plenty of data to be trained efficiently, which may be hard to collect or to use due to privacy reasons. One of the most notable Machine Learning tools is the Generative Adversarial Network (GAN), and it has great potential for tabular data synthesis. In this work, we start by briefly presenting the most popular GAN architectures, VanillaGAN, WGAN, and WGAN-GP. Focusing on tabular data generation, CTGAN, CopulaGAN, and TableGAN models are used for the creation of synthetic IDS data. Specifically, the models are trained and evaluated on an NSL-KDD dataset, considering the limitations and requirements that this procedure needs. Finally, based on certain quantitative and qualitative methods, we argue and evaluate the most prominent GANs for tabular network data synthesis.

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