scholarly journals Evaluating recommender systems for AI-driven biomedical informatics

2020 ◽  
Author(s):  
William La Cava ◽  
Heather Williams ◽  
Weixuan Fu ◽  
Steve Vitale ◽  
Durga Srivatsan ◽  
...  
Keyword(s):  
Septic Shock ◽  
Recommender Systems ◽  
Data Science ◽  
Expert Knowledge ◽  
State Of The Art ◽  
Optimal Algorithm ◽  
Supplementary Information ◽  
Biomedical Data ◽  
Classification Problems ◽  
Systems Research

Abstract Motivation Many researchers with domain expertise are unable to easily apply machine learning (ML) to their bioinformatics data due to a lack of ML and/or coding expertise. Methods that have been proposed thus far to automate ML mostly require programming experience as well as expert knowledge to tune and apply the algorithms correctly. Here, we study a method of automating biomedical data science using a web-based AI platform to recommend model choices and conduct experiments. We have two goals in mind: first, to make it easy to construct sophisticated models of biomedical processes; and second, to provide a fully automated AI agent that can choose and conduct promising experiments for the user, based on the user’s experiments as well as prior knowledge. To validate this framework, we conduct an experiment on 165 classification problems, comparing to state-of-the-art, automated approaches. Finally, we use this tool to develop predictive models of septic shock in critical care patients. Results We find that matrix factorization-based recommendation systems outperform metalearning methods for automating ML. This result mirrors the results of earlier recommender systems research in other domains. The proposed AI is competitive with state-of-the-art automated ML methods in terms of choosing optimal algorithm configurations for datasets. In our application to prediction of septic shock, the AI-driven analysis produces a competent ML model (AUROC 0.85±0.02) that performs on par with state-of-the-art deep learning results for this task, with much less computational effort. Availability and implementation PennAI is available free of charge and open-source. It is distributed under the GNU public license (GPL) version 3. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CPS analysis: self-contained validation of biomedical data clustering

2020 ◽  
Vol 36 (11) ◽  
pp. 3516-3521 ◽  
Author(s):  
Lixiang Zhang ◽  
Lin Lin ◽  
Jia Li
Keyword(s):  
Data Clustering ◽  
State Of The Art ◽  
R Package ◽  
Research Community ◽  
Supplementary Information ◽  
Biomedical Data ◽  
Data Generation ◽  
Supplementary Data ◽  
Point Set ◽  
Class Labels

Abstract Motivation Cluster analysis is widely used to identify interesting subgroups in biomedical data. Since true class labels are unknown in the unsupervised setting, it is challenging to validate any cluster obtained computationally, an important problem barely addressed by the research community. Results We have developed a toolkit called covering point set (CPS) analysis to quantify uncertainty at the levels of individual clusters and overall partitions. Functions have been developed to effectively visualize the inherent variation in any cluster for data of high dimension, and provide more comprehensive view on potentially interesting subgroups in the data. Applying to three usage scenarios for biomedical data, we demonstrate that CPS analysis is more effective for evaluating uncertainty of clusters comparing to state-of-the-art measurements. We also showcase how to use CPS analysis to select data generation technologies or visualization methods. Availability and implementation The method is implemented in an R package called OTclust, available on CRAN. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Recommendation Systems: Algorithms, Challenges, Metrics, and Business Opportunities

2020 ◽  
Vol 10 (21) ◽  
pp. 7748
Author(s):  
Zeshan Fayyaz ◽  
Mahsa Ebrahimian ◽  
Dina Nawara ◽  
Ahmed Ibrahim ◽  
Rasha Kashef
Keyword(s):  
Recommender Systems ◽  
Recommendation System ◽  
Information Overload ◽  
State Of The Art ◽  
Recommendation Systems ◽  
Qualitative Evaluation ◽  
Potential Influence ◽  
Systems Research ◽  
Current State

Recommender systems are widely used to provide users with recommendations based on their preferences. With the ever-growing volume of information online, recommender systems have been a useful tool to overcome information overload. The utilization of recommender systems cannot be overstated, given its potential influence to ameliorate many over-choice challenges. There are many types of recommendation systems with different methodologies and concepts. Various applications have adopted recommendation systems, including e-commerce, healthcare, transportation, agriculture, and media. This paper provides the current landscape of recommender systems research and identifies directions in the field in various applications. This article provides an overview of the current state of the art in recommendation systems, their types, challenges, limitations, and business adoptions. To assess the quality of a recommendation system, qualitative evaluation metrics are discussed in the paper.

scholarly journals BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images

2020 ◽  
Vol 36 (17) ◽  
pp. 4668-4670
Author(s):  
Tim Scherr ◽  
Karolin Streule ◽  
Andreas Bartschat ◽  
Moritz Böhland ◽  
Johannes Stegmaier ◽  
...  
Keyword(s):  
Expert Knowledge ◽  
State Of The Art ◽  
Supplementary Information ◽  
Bacterial Invasion ◽  
Low Resolution ◽  
Image Labeling ◽  
Detection And Counting ◽  
Software Code ◽  
High Throughput Experiments ◽  
Microscopy Images

Abstract Motivation An automated counting of beads is required for many high-throughput experiments such as studying mimicked bacterial invasion processes. However, state-of-the-art algorithms under- or overestimate the number of beads in low-resolution images. In addition, expert knowledge is needed to adjust parameters. Results In combination with our image labeling tool, BeadNet enables biologists to easily annotate and process their data reducing the expertise required in many existing image analysis pipelines. BeadNet outperforms state-of-the-art-algorithms in terms of missing, added and total amount of beads. Availability and implementation BeadNet (software, code and dataset) is available at https://bitbucket.org/t_scherr/beadnet. The image labeling tool is available at https://bitbucket.org/abartschat/imagelabelingtool. Supplementary information Supplementary data are available at Bioinformatics online.

Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Ferdinand Filip ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
State Of The Art ◽  
Science Methods ◽  
Learning Models ◽  
Diverse Range ◽  
Hybrid Machine ◽  
Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

Survey of the State-of-the-Art Expert/Knowledge Based Systems in Civil Engineering.

1986 ◽  
Author(s):  
Simon S. Kim ◽  
Mary Lou Maher ◽  
Raymond E. Levitt ◽  
Martin F. Rooney ◽  
Thomas J. Siller
Keyword(s):  
Civil Engineering ◽  
Expert Knowledge ◽  
State Of The Art ◽  
The State ◽  
Knowledge Based Systems ◽  
Knowledge Based

scholarly journals Improving Land Cover Classification Using Genetic Programming for Feature Construction

2021 ◽  
Vol 13 (9) ◽  
pp. 1623
Author(s):  
João E. Batista ◽  
Ana I. R. Cabral ◽  
Maria J. P. Vasconcelos ◽  
Leonardo Vanneschi ◽  
Sara Silva
Keyword(s):  
Land Cover ◽  
Genetic Programming ◽  
Satellite Images ◽  
State Of The Art ◽  
Binary Classification ◽  
Feature Construction ◽  
Classification Problems ◽  
Construction Methods ◽  
Box Models

Genetic programming (GP) is a powerful machine learning (ML) algorithm that can produce readable white-box models. Although successfully used for solving an array of problems in different scientific areas, GP is still not well known in the field of remote sensing. The M3GP algorithm, a variant of the standard GP algorithm, performs feature construction by evolving hyperfeatures from the original ones. In this work, we use the M3GP algorithm on several sets of satellite images over different countries to create hyperfeatures from satellite bands to improve the classification of land cover types. We add the evolved hyperfeatures to the reference datasets and observe a significant improvement of the performance of three state-of-the-art ML algorithms (decision trees, random forests, and XGBoost) on multiclass classifications and no significant effect on the binary classifications. We show that adding the M3GP hyperfeatures to the reference datasets brings better results than adding the well-known spectral indices NDVI, NDWI, and NBR. We also compare the performance of the M3GP hyperfeatures in the binary classification problems with those created by other feature construction methods such as FFX and EFS.

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Systematic Review of Recommender Systems and Their Applications in Cybersecurity

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 5248
Author(s):  
Aleksandra Pawlicka ◽  
Marek Pawlicki ◽  
Rafał Kozik ◽  
Ryszard S. Choraś
Keyword(s):  
Systematic Review ◽  
Recommender Systems ◽  
Recommender System ◽  
State Of The Art ◽  
The State ◽  
Advantages And Disadvantages ◽  
Comprehensive Survey ◽  
Security Concerns ◽  
Valuable Role

This paper discusses the valuable role recommender systems may play in cybersecurity. First, a comprehensive presentation of recommender system types is presented, as well as their advantages and disadvantages, possible applications and security concerns. Then, the paper collects and presents the state of the art concerning the use of recommender systems in cybersecurity; both the existing solutions and future ideas are presented. The contribution of this paper is two-fold: to date, to the best of our knowledge, there has been no work collecting the applications of recommenders for cybersecurity. Moreover, this paper attempts to complete a comprehensive survey of recommender types, after noticing that other works usually mention two–three types at once and neglect the others.

scholarly journals Evaluation of recent advances in recommender systems on Arabic content

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Mehdi Srifi ◽  
Ahmed Oussous ◽  
Ayoub Ait Lahcen ◽  
Salma Mouline
Keyword(s):  
Recommender Systems ◽  
High Performance ◽  
Large Scale ◽  
State Of The Art ◽  
Experimental Results ◽  
Recent Advances ◽  
Research Gap ◽  
Text Preprocessing

AbstractVarious recommender systems (RSs) have been developed over recent years, and many of them have concentrated on English content. Thus, the majority of RSs from the literature were compared on English content. However, the research investigations about RSs when using contents in other languages such as Arabic are minimal. The researchers still neglect the field of Arabic RSs. Therefore, we aim through this study to fill this research gap by leveraging the benefit of recent advances in the English RSs field. Our main goal is to investigate recent RSs in an Arabic context. For that, we firstly selected five state-of-the-art RSs devoted originally to English content, and then we empirically evaluated their performance on Arabic content. As a result of this work, we first build four publicly available large-scale Arabic datasets for recommendation purposes. Second, various text preprocessing techniques have been provided for preparing the constructed datasets. Third, our investigation derived well-argued conclusions about the usage of modern RSs in the Arabic context. The experimental results proved that these systems ensure high performance when applied to Arabic content.

scholarly journals Robust CNN Compression Framework for Security-Sensitive Embedded Systems

2021 ◽  
Vol 11 (3) ◽  
pp. 1093
Author(s):  
Jeonghyun Lee ◽  
Sangkyun Lee
Keyword(s):  
Embedded Systems ◽  
Optimization Problem ◽  
State Of The Art ◽  
Classification Problems ◽  
Proximal Gradient Method ◽  
Knowledge Distillation ◽  
New Type ◽  
Adversarial Examples ◽  
Adversarial Training ◽  
Memory Efficient

Convolutional neural networks (CNNs) have achieved tremendous success in solving complex classification problems. Motivated by this success, there have been proposed various compression methods for downsizing the CNNs to deploy them on resource-constrained embedded systems. However, a new type of vulnerability of compressed CNNs known as the adversarial examples has been discovered recently, which is critical for security-sensitive systems because the adversarial examples can cause malfunction of CNNs and can be crafted easily in many cases. In this paper, we proposed a compression framework to produce compressed CNNs robust against such adversarial examples. To achieve the goal, our framework uses both pruning and knowledge distillation with adversarial training. We formulate our framework as an optimization problem and provide a solution algorithm based on the proximal gradient method, which is more memory-efficient than the popular ADMM-based compression approaches. In experiments, we show that our framework can improve the trade-off between adversarial robustness and compression rate compared to the existing state-of-the-art adversarial pruning approach.

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