scholarly journals AImmune: a new blood-based machine learning approach to improving immune profiling analysis on COVID-19 patients

2021 ◽  
Author(s):  
Xi Tom Zhang ◽  
Runpeng Harris Han
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Mononuclear Cells ◽  
Data Sets ◽  
Learning Approaches ◽  
Rna Seq ◽  
Real World Data ◽  
Novel Approach ◽  
Massive Number ◽  
Immune Profiling

A massive number of transcriptomic profiles of blood samples from COVID-19 patients has been produced since pandemic COVID-19 begins, however, these big data from primary studies have not been well integrated by machine learning approaches. Taking advantage of modern machine learning arthrograms, we integrated and collected single cell RNA-seq (scRNA-seq) data from three independent studies, identified genes potentially available for interpretation of severity, and developed a high-performance deep learning-based deconvolution model AImmune that can predict the proportion of seven different immune cells from the bulk RNA-seq results of human peripheral mononuclear cells. This novel approach which can be used for clinical blood testing of COVID-19 on the ground that previous research shows that mRNA alternations in blood-derived PBMCs may serve as a severity indicator. Assessed on real-world data sets, the AImmune model outperformed the most recognized immune profiling model CIBERSORTx. The presented study showed the results obtained by the true scRNA-seq route can be consistently reproduced through the new approach AImmune, indicating a potential replacing the costly scRNA-seq technique for the analysis of circulating blood cells for both clinical and research purposes.

scholarly journals Don’t Overweight Weights: Evaluation of Weighting Strategies for Multi-Task Bioactivity Classification Models

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6959
Author(s):  
Lina Humbeck ◽  
Tobias Morawietz ◽  
Noe Sturm ◽  
Adam Zalewski ◽  
Simon Harnqvist ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Model Performance ◽  
Pharmaceutical Companies ◽  
Data Sets ◽  
Learning Approaches ◽  
Classification Models ◽  
Real World Data ◽  
Robust Model ◽  
Performance Results

Machine learning models predicting the bioactivity of chemical compounds belong nowadays to the standard tools of cheminformaticians and computational medicinal chemists. Multi-task and federated learning are promising machine learning approaches that allow privacy-preserving usage of large amounts of data from diverse sources, which is crucial for achieving good generalization and high-performance results. Using large, real world data sets from six pharmaceutical companies, here we investigate different strategies for averaging weighted task loss functions to train multi-task bioactivity classification models. The weighting strategies shall be suitable for federated learning and ensure that learning efforts are well distributed even if data are diverse. Comparing several approaches using weights that depend on the number of sub-tasks per assay, task size, and class balance, respectively, we find that a simple sub-task weighting approach leads to robust model performance for all investigated data sets and is especially suited for federated learning.

scholarly journals Classification Of Association Item Sets From Large Data Sets Based On User Awareness Using Hybrid

2019 ◽  
Vol 8 (6S) ◽  
pp. 1055-1061
Keyword(s):  
Machine Learning ◽  
Customer Service ◽  
Business Intelligence ◽  
High Performance ◽  
Experimental Result ◽  
Data Sets ◽  
Learning Approaches ◽  
Time Data ◽  
Depth Analysis ◽  
User Awareness

In business intelligence, large number of data to be generated because of increasing data in business applications. Analysis and prediction of data is very aggressive concept to evaluate the results present in data based on decision making analysis. To provide effective analysis of data traditionally some of the machine learning related methods like Clustering, Classification, Neural network based approaches and association rule based approaches were used to explore and analysis of business data. Because of increasing depth analysis of data in business intelligence related applications then above static machine learning approaches were not satisfied to form association between different attributes in real time data sets. So that in this paper, we propose Advanced & Hybrid Machine Learning Approach (AHMLA) for effective data analysis of different associated attributes of high dimensional data. Our proposed approach increase customer service, report generations based on user awareness in business intelligence applications. An experimental result of proposed approach gives better high performance with respect to different parameters with respect to existing approaches

Improving Reliability Estimation for Individual Numeric Predictions: A Machine Learning Approach

2021 ◽  
Author(s):  
Gediminas Adomavicius ◽  
Yaqiong Wang
Keyword(s):  
Machine Learning ◽  
General Purpose ◽  
Reliability Estimation ◽  
Machine Learning Techniques ◽  
Data Sets ◽  
Real World Data ◽  
Learning Techniques ◽  
Reliability Indicator ◽  
Machine Learning Approach ◽  
Prediction Reliability

Numerical predictive modeling is widely used in different application domains. Although many modeling techniques have been proposed, and a number of different aggregate accuracy metrics exist for evaluating the overall performance of predictive models, other important aspects, such as the reliability (or confidence and uncertainty) of individual predictions, have been underexplored. We propose to use estimated absolute prediction error as the indicator of individual prediction reliability, which has the benefits of being intuitive and providing highly interpretable information to decision makers, as well as allowing for more precise evaluation of reliability estimation quality. As importantly, the proposed reliability indicator allows the reframing of reliability estimation itself as a canonical numeric prediction problem, which makes the proposed approach general-purpose (i.e., it can work in conjunction with any outcome prediction model), alleviates the need for distributional assumptions, and enables the use of advanced, state-of-the-art machine learning techniques to learn individual prediction reliability patterns directly from data. Extensive experimental results on multiple real-world data sets show that the proposed machine learning-based approach can significantly improve individual prediction reliability estimation as compared with a number of baselines from prior work, especially in more complex predictive scenarios.

scholarly journals Machine learning approaches to calibrate individual-based infectious disease models

2021 ◽  
Author(s):  
Theresa Reiker ◽  
Monica Golumbeanu ◽  
Andrew Shattock ◽  
Lydia Burgert ◽  
Thomas A. Smith ◽  
...  
Keyword(s):  
Machine Learning ◽  
Disease Transmission ◽  
Goodness Of Fit ◽  
Epidemiological Data ◽  
Bayesian Optimization ◽  
Model Complexity ◽  
Learning Approaches ◽  
Dimensional Parameter ◽  
Novel Approach ◽  
Transmission Models

AbstractIndividual-based models have become important tools in the global battle against infectious diseases, yet model complexity can make calibration to biological and epidemiological data challenging. We propose a novel approach to calibrate disease transmission models via a Bayesian optimization framework employing machine learning emulator functions to guide a global search over a multi-objective landscape. We demonstrate our approach by application to an established individual-based model of malaria, optimizing over a high-dimensional parameter space with respect to a portfolio of multiple fitting objectives built from datasets capturing the natural history of malaria transmission and disease progression. Outperforming other calibration methodologies, the new approach quickly reaches an improved final goodness of fit. Per-objective parameter importance and sensitivity diagnostics provided by our approach offer epidemiological insights and enhance trust in predictions through greater interpretability.One Sentence SummaryWe propose a novel, fast, machine learning-based approach to calibrate disease transmission models that outperforms other methodologies

scholarly journals Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM

2019 ◽  
Author(s):  
Marcus Alvarez ◽  
Elior Rahmani ◽  
Brandon Jew ◽  
Kristina M. Garske ◽  
Zong Miao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Types ◽  
Supervised Machine Learning ◽  
Data Sets ◽  
Rna Seq ◽  
Novel Approach ◽  
Single Nucleus ◽  
Downstream Analysis

AbstractSingle-nucleus RNA sequencing (snRNA-seq) measures gene expression in individual nuclei instead of cells, allowing for unbiased cell type characterization in solid tissues. Contrary to single-cell RNA seq (scRNA-seq), we observe that snRNA-seq is commonly subject to contamination by high amounts of extranuclear background RNA, which can lead to identification of spurious cell types in downstream clustering analyses if overlooked. We present a novel approach to remove debris-contaminated droplets in snRNA-seq experiments, called Debris Identification using Expectation Maximization (DIEM). Our likelihood-based approach models the gene expression distribution of debris and cell types, which are estimated using EM. We evaluated DIEM using three snRNA-seq data sets: 1) human differentiating preadipocytes in vitro, 2) fresh mouse brain tissue, and 3) human frozen adipose tissue (AT) from six individuals. All three data sets showed various degrees of extranuclear RNA contamination. We observed that existing methods fail to account for contaminated droplets and led to spurious cell types. When compared to filtering using these state of the art methods, DIEM better removed droplets containing high levels of extranuclear RNA and led to higher quality clusters. Although DIEM was designed for snRNA-seq data, we also successfully applied DIEM to single-cell data. To conclude, our novel method DIEM removes debris-contaminated droplets from single-cell-based data fast and effectively, leading to cleaner downstream analysis. Our code is freely available for use at https://github.com/marcalva/diem.

scholarly journals Clustering and enhanced classification using a hybrid quantum autoencoder

2021 ◽  
Author(s):  
Maiyuren Srikumar ◽  
Charles Daniel Hill ◽  
Lloyd Hollenberg
Keyword(s):  
Machine Learning ◽  
Supervised Classification ◽  
Quantum Information Theory ◽  
Quantum States ◽  
Data Sets ◽  
New Paradigm ◽  
Novel Approach ◽  
Representational Space ◽  
Quantum Machine Learning ◽  
Pure States

Abstract Quantum machine learning (QML) is a rapidly growing area of research at the intersection of classical machine learning and quantum information theory. One area of considerable interest is the use of QML to learn information contained within quantum states themselves. In this work, we propose a novel approach in which the extraction of information from quantum states is undertaken in a classical representational-space, obtained through the training of a hybrid quantum autoencoder (HQA). Hence, given a set of pure states, this variational QML algorithm learns to identify – and classically represent – their essential distinguishing characteristics, subsequently giving rise to a new paradigm for clustering and semi-supervised classification. The analysis and employment of the HQA model are presented in the context of amplitude encoded states – which in principle can be extended to arbitrary states for the analysis of structure in non-trivial quantum data sets.

scholarly journals Optimising Daily Fantasy Sports Teams with Artificial Intelligence

2020 ◽  
Vol 19 (2) ◽  
pp. 21-35
Author(s):  
Ryan Beal ◽  
Timothy J. Norman ◽  
Sarvapali D. Ramchurn
Keyword(s):  
Real World ◽  
National Football League ◽  
Mixed Integer ◽  
Data Sets ◽  
Fantasy Sports ◽  
Real World Data ◽  
Sports Teams ◽  
Novel Approach ◽  
Four Seasons ◽  
Daily Fantasy Sports

AbstractThis paper outlines a novel approach to optimising teams for Daily Fantasy Sports (DFS) contests. To this end, we propose a number of new models and algorithms to solve the team formation problems posed by DFS. Specifically, we focus on the National Football League (NFL) and predict the performance of real-world players to form the optimal fantasy team using mixed-integer programming. We test our solutions using real-world data-sets from across four seasons (2014-2017). We highlight the advantage that can be gained from using our machine-based methods and show that our solutions outperform existing benchmarks, turning a profit in up to 81.3% of DFS game-weeks over a season.

scholarly journals Environmental Sound Recognition on Embedded Systems: From FPGAs to TPUs

Electronics ◽  
2021 ◽  
Vol 10 (21) ◽  
pp. 2622
Author(s):  
Jurgen Vandendriessche ◽  
Nick Wouters ◽  
Bruno da Silva ◽  
Mimoun Lamrini ◽  
Mohamed Yassin Chkouri ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Machine Learning Techniques ◽  
Sound Recognition ◽  
Learning Approaches ◽  
Environmental Sound ◽  
Embedded Devices ◽  
Power Efficient ◽  
Computationally Intensive ◽  
Environmental Sound Recognition

In recent years, Environmental Sound Recognition (ESR) has become a relevant capability for urban monitoring applications. The techniques for automated sound recognition often rely on machine learning approaches, which have increased in complexity in order to achieve higher accuracy. Nonetheless, such machine learning techniques often have to be deployed on resource and power-constrained embedded devices, which has become a challenge with the adoption of deep learning approaches based on Convolutional Neural Networks (CNNs). Field-Programmable Gate Arrays (FPGAs) are power efficient and highly suitable for computationally intensive algorithms like CNNs. By fully exploiting their parallel nature, they have the potential to accelerate the inference time as compared to other embedded devices. Similarly, dedicated architectures to accelerate Artificial Intelligence (AI) such as Tensor Processing Units (TPUs) promise to deliver high accuracy while achieving high performance. In this work, we evaluate existing tool flows to deploy CNN models on FPGAs as well as on TPU platforms. We propose and adjust several CNN-based sound classifiers to be embedded on such hardware accelerators. The results demonstrate the maturity of the existing tools and how FPGAs can be exploited to outperform TPUs.

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