Receive a weekly summary and discussion of the top papers of the week by leading researchers in the field.

General General

Correcting data imbalance for semi-supervised COVID-19 detection using X-ray chest images.

In Applied soft computing

A key factor in the fight against viral diseases such as the coronavirus (COVID-19) is the identification of virus carriers as early and quickly as possible, in a cheap and efficient manner. The application of deep learning for image classification of chest X-ray images of COVID-19 patients could become a useful pre-diagnostic detection methodology. However, deep learning architectures require large labelled datasets. This is often a limitation when the subject of research is relatively new as in the case of the virus outbreak, where dealing with small labelled datasets is a challenge. Moreover, in such context, the datasets are also highly imbalanced, with few observations from positive cases of the new disease. In this work we evaluate the performance of the semi-supervised deep learning architecture known as MixMatch with a very limited number of labelled observations and highly imbalanced labelled datasets. We demonstrate the critical impact of data imbalance to the model's accuracy. Therefore, we propose a simple approach for correcting data imbalance, by re-weighting each observation in the loss function, giving a higher weight to the observations corresponding to the under-represented class. For unlabelled observations, we use the pseudo and augmented labels calculated by MixMatch to choose the appropriate weight. The proposed method improved classification accuracy by up to 18%, with respect to the non balanced MixMatch algorithm. We tested our proposed approach with several available datasets using 10, 15 and 20 labelled observations, for binary classification (COVID-19 positive and normal cases). For multi-class classification (COVID-19 positive, pneumonia and normal cases), we tested 30, 50, 70 and 90 labelled observations. Additionally, a new dataset is included among the tested datasets, composed of chest X-ray images of Costa Rican adult patients.

Calderon-Ramirez Saul, Yang Shengxiang, Moemeni Armaghan, Elizondo David, Colreavy-Donnelly Simon, Chavarría-Estrada Luis Fernando, Molina-Cabello Miguel A

2021-Nov

COVID-19, Computer aided diagnosis, Coronavirus, Data imbalance, Semi-supervised learning

General General

Improve teaching with modalities and collaborative groups in an LMS: an analysis of monitoring using visualisation techniques.

In Journal of computing in higher education

Monitoring students in Learning Management Systems (LMS) throughout the teaching-learning process has been shown to be a very effective technique for detecting students at risk. Likewise, the teaching style in the LMS conditions, the type of student behaviours on the platform and the learning outcomes. The main objective of this study was to test the effectiveness of three teaching modalities (all using Online Project-based Learning -OPBL- and Flipped Classroom experiences and differing in the use of virtual laboratories and Intelligent Personal Assistant -IPA-) on Moodle behaviour and student performance taking into account the covariate "collaborative group". Both quantitative and qualitative research methods were used. With regard to the quantitative analysis, differences were found in student behaviour in Moodle and in learning outcomes, with respect to teaching modalities that included virtual laboratories. Similarly, the qualitative study also analysed the behaviour patterns found in each collaborative group in the three teaching modalities studied. The results indicate that the collaborative group homogenises the learning outcomes, but not the behaviour pattern of each member. Future research will address the analysis of collaborative behaviour in LMSs according to different variables (motivation and metacognitive strategies in students, number of members, interactions between students and teacher in the LMS, etc.).

Sáiz-Manzanares María Consuelo, Marticorena-Sánchez Raúl, Rodríguez-Díez Juan José, Rodríguez-Arribas Sandra, Díez-Pastor José Francisco, Ji Yi Peng

2021-Jul-13

Heat map, Machine learning techniques, Monitoring students, Online project-based learning, Self-regulated learning, Visualisation techniques

General General

Fusion of AI techniques to tackle COVID-19 pandemic: models, incidence rates, and future trends.

In Multimedia systems

The COVID-19 pandemic is rapidly spreading across the globe and infected millions of people that take hundreds of thousands of lives. Over the years, the role of Artificial intelligence (AI) has been on the rise as its algorithms are getting more and more accurate and it is thought that its role in strengthening the existing healthcare system will be the most profound. Moreover, the pandemic brought an opportunity to showcase AI and healthcare integration potentials as the current infrastructure worldwide is overwhelmed and crumbling. Due to AI's flexibility and adaptability, it can be used as a tool to tackle COVID-19. Motivated by these facts, in this paper, we surveyed how the AI techniques can handle the COVID-19 pandemic situation and present the merits and demerits of these techniques. This paper presents a comprehensive end-to-end review of all the AI-techniques that can be used to tackle all areas of the pandemic. Further, we systematically discuss the issues of the COVID-19, and based on the literature review, we suggest their potential countermeasures using AI techniques. In the end, we analyze various open research issues and challenges associated with integrating the AI techniques in the COVID-19.

Shah Het, Shah Saiyam, Tanwar Sudeep, Gupta Rajesh, Kumar Neeraj

2021-Jul-13

AI, COVID-19, Deep learning, Healthcare, Machine learning

General General

New but for whom? Discourses of innovation in precision agriculture.

In Agriculture and human values

We describe how the set of tools, practices, and social relations known as "precision agriculture" is defined, promoted, and debated. To do so, we perform a critical discourse analysis of popular and trade press websites. Promoters of precision agriculture champion how big data analytics, automated equipment, and decision-support software will optimize yields in the face of narrow margins and public concern about farming's environmental impacts. At its core, however, the idea of farmers leveraging digital infrastructure in their operations is not new, as agronomic research in this vein has existed for over 30 years. Contemporary discourse in precision ag tends to favour emerging digital technologies themselves over their embeddedness in longstanding precision management approaches. Following several strands of science and technology studies (STS) research, we explore what rhetorical emphasis on technical innovation achieves, and argue that this discourse of novelty is a reinvention of precision agriculture in the context of the growing "smart" agricultural economy. We overview six tensions that remain unresolved in this promotional rhetoric, concerning the definitions, history, goals, adoption, uses, and impacts of precision agriculture. We then synthesize these in a discussion of the extent to which digital tools are believed to displace farmer decision-making and whether digital agriculture addresses the biophysical heterogeneity of farm landscapes or land itself has become an "experimental technology"-a way to advance the general development of artificial intelligence. This discussion ultimately helps us name a larger dilemma: that the smart agricultural economy is perhaps less about supporting land and its stewards than promising future tech and profits.

Duncan Emily, Glaros Alesandros, Ross Dennis Z, Nost Eric

2021-Jul-14

Digital agriculture, Discourse, Innovation, Precision agriculture

General General

Machine Learning for Real-World Evidence Analysis of COVID-19 Pharmacotherapy

ArXiv Preprint

Introduction: Real-world data generated from clinical practice can be used to analyze the real-world evidence (RWE) of COVID-19 pharmacotherapy and validate the results of randomized clinical trials (RCTs). Machine learning (ML) methods are being used in RWE and are promising tools for precision-medicine. In this study, ML methods are applied to study the efficacy of therapies on COVID-19 hospital admissions in the Valencian Region in Spain. Methods: 5244 and 1312 COVID-19 hospital admissions - dated between January 2020 and January 2021 from 10 health departments, were used respectively for training and validation of separate treatment-effect models (TE-ML) for remdesivir, corticosteroids, tocilizumab, lopinavir-ritonavir, azithromycin and chloroquine/hydroxychloroquine. 2390 admissions from 2 additional health departments were reserved as an independent test to analyze retrospectively the survival benefits of therapies in the population selected by the TE-ML models using cox-proportional hazard models. TE-ML models were adjusted using treatment propensity scores to control for pre-treatment confounding variables associated to outcome and further evaluated for futility. ML architecture was based on boosted decision-trees. Results: In the populations identified by the TE-ML models, only Remdesivir and Tocilizumab were significantly associated with an increase in survival time, with hazard ratios of 0.41 (P = 0.04) and 0.21 (P = 0.001), respectively. No survival benefits from chloroquine derivatives, lopinavir-ritonavir and azithromycin were demonstrated. Tools to explain the predictions of TE-ML models are explored at patient-level as potential tools for personalized decision making and precision medicine. Conclusion: ML methods are suitable tools toward RWE analysis of COVID-19 pharmacotherapies. Results obtained reproduce published results on RWE and validate the results from RCTs.

Aurelia Bustos, Patricio Mas_Serrano, Mari L. Boquera, Jose M. Salinas

2021-07-19

General General

Analysis of training and seed bias in small molecules generated with a conditional graph-based variational autoencoder -- Insights for practical AI-driven molecule generation

ArXiv Preprint

The application of deep learning to generative molecule design has shown early promise for accelerating lead series development. However, questions remain concerning how factors like training, dataset, and seed bias impact the technology's utility to medicine and computational chemists. In this work, we analyze the impact of seed and training bias on the output of an activity-conditioned graph-based variational autoencoder (VAE). Leveraging a massive, labeled dataset corresponding to the dopamine D2 receptor, our graph-based generative model is shown to excel in producing desired conditioned activities and favorable unconditioned physical properties in generated molecules. We implement an activity swapping method that allows for the activation, deactivation, or retention of activity of molecular seeds, and we apply independent deep learning classifiers to verify the generative results. Overall, we uncover relationships between noise, molecular seeds, and training set selection across a range of latent-space sampling procedures, providing important insights for practical AI-driven molecule generation.

Seung-gu Kang, Joseph A. Morrone, Jeffrey K. Weber, Wendy D. Cornell

2021-07-19