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Deep Learning in Mining Biological Data

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Authors : Mufti Mahmud, M. Shamim Kaiser, T. Martin McGinnity, Amir Hussain

Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Categorized in three broad types (i.e. images, signals, and sequences), these data are huge in amount and complex in nature.

Mining such enormous amount of data for pattern recognition is a big challenge and requires sophisticated data-intensive machine learning techniques. Artificial neural network-based learning systems are well known for their pattern recognition capabilities, and lately their deep architectures—known as deep learning (DL)—have been successfully applied to solve many complex pattern recognition problems.

To investigate how DL—especially its different architectures—has contributed and been utilized in the mining of biological data pertaining to those three types, a meta-analysis has been performed and the resulting resources have been critically analysed. Focusing on the use of DL to analyse patterns in data from diverse biological domains, this work investigates different DL architectures’ applications to these data.

This is followed by an exploration of available open access data sources pertaining to the three data types along with popular open-source DL tools applicable to these data. Also, comparative investigations of these tools from qualitative, quantitative, and benchmarking perspectives are provided.

Finally, some open research challenges in using DL to mine biological data are outlined and a number of possible future perspectives are put forward.

URL : Deep Learning in Mining Biological Data

DOI : https://doi.org/10.1007/s12559-020-09773-x

Questionable Research Practices and Open Science in Quantitative Criminology

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Authors : Jason Chinn, Justin Pickett, Simine Vazire, Alex Holcombe

Objectives

Questionable research practices (QRPs) lead to incorrect research results and contribute to irreproducibility in science. Researchers and institutions have proposed open science practices (OSPs) to improve the detectability of QRPs and the credibility of science. We examine the prevalence of QRPs and OSPs in criminology, and researchers’ opinions of those practices.

Methods

We administered an anonymous survey to authors of articles published in criminology journals. Respondents self-reported their own use of 10 QRPs and 5 OSPs. They also estimated the prevalence of use by others, and reported their attitudes toward the practices.

Results

QRPs and OSPs are both common in quantitative criminology, about as common as they are in other fields. Criminologists who responded to our survey support using QRPs in some circumstances, but are even more supportive of using OSPs.

We did not detect a significant relationship between methodological training and either QRP or OSP use.

Support for QRPs is negatively and significantly associated with support for OSPs. Perceived prevalence estimates for some practices resembled a uniform distribution, suggesting criminologists have little knowledge of the proportion of researchers that engage in certain questionable practices.

Conclusions

Most quantitative criminologists in our sample use QRPs, and many use multiple QRPs. The substantial prevalence of QRPs raises questions about the validity and reproducibility of published criminological research.

We found promising levels of OSP use, albeit at levels lagging what researchers endorse. The findings thus suggest that additional reforms are needed to decrease QRP use and increase the use of OSPs.

URL : Questionable Research Practices and Open Science in Quantitative Criminology

DOI : https://doi.org/10.31235/osf.io/bwm7s

Cite Unseen: Theory and Evidence on the Effect of Open Access on Cites to Academic Articles Across the Quality Spectrum

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Authors : Mark J. McCabe, Christopher Snyder

Our previous paper (McCabe and Snyder 2014) contained the provocative result that, despite a positive average effect, open access reduces cites to some articles, in particular those published in lower-tier journals.

We propose a model in which open access leads more readers to acquire the full text, yielding more cites from some, but fewer cites from those who would have cited the article based on superficial knowledge but who refrain once they learn that the article is a bad match.

We test the theory with data for over 200,000 science articles binned by cites received during a pre-study period. Consistent with the theory, the marginal effect of open access is negative for the least-cited articles, positive for the most cited, and generally monotonic for quality levels in between.

Also consistent with the theory is a magnification of these effects for articles placed on PubMed Central, one of the broadest open-access platforms, and the differential pattern of results for cites from insiders versus outsiders to the article’s field.

URL : https://www.nber.org/papers/w28128

The move to open: medical library leadership in scholarly communication

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Author : Chris Shaffer

Over the years, health sciences librarians have been change agents, leading the charge on issues of importance to the profession and the communities we serve. From its founding in 1898 with the Exchange, the Medical Library Association (MLA) has been dedicated to improving access to health information.

In 2003, the Board of Directors published a statement supporting open access to information generated from federally funded scientific and medical research and maintained that having access to timely, relevant, and accurate information is vital to the health of the nation and its education and research programs.

At some financial risk, the association made the Journal of the Medical Library Association (JMLA) open access and published the entire archive of JMLA and its predecessor, the Bulletin of the Medical Library Association, in PubMed Central. Nearly two decades later, the promise of open access and open science finally seems to be coming to fruition.

In the 2020 Janet Doe Lecture, Chris Shaffer, AHIP, described the ways that MLA has led the profession, standing behind a shared vision and “walking the walk.” In challenging listeners to embrace open science, he affirmed that, as leaders in improving access to health sciences information since 1898, medical librarians must work in the open science arena to realize our vision “that quality information is essential for improved health.”

URL : The move to open: medical library leadership in scholarly communication

DOI : https://doi.org/10.5195/jmla.2021.1127

An intersectional approach to analyse gender productivity and open access: a bibliometric analysis of the Italian National Research Council

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Authors : Roberta Ruggieri, Fabrizio Pecoraro, Daniela Luzi

Gender equality and Open Access (OA) are priorities within the European Research Area and cross-cutting issues in European research program H2020. Gender and openness are also key elements of responsible research and innovation.

However, despite the common underlying targets of fostering an inclusive, transparent and sustainable research environment, both issues are analysed as independent topics. This paper represents a first exploration of the inter-linkages between gender and OA analysing the scientific production of researchers of the Italian National Research Council under a gender perspective integrated with the different OA publications modes.

A bibliometric analysis was carried out for articles published in the period 2016–2018 and retrieved from the Web of Science. Results are presented constantly analysing CNR scientific production in relation to gender, disciplinary fields and OA publication modes.

These variables are also used when analysing articles that receive financial support. Our results indicate that gender disparities in scientific production still persist particularly in STEM disciplines, while the gender gap is the closest to parity in medical and agricultural sciences.

A positive dynamic toward OA publishing and women’s scientific production is shown when disciplines with well-established open practices are related to articles supported by funds. A slightly higher women’s propensity toward OA is shown when considering Gold OA, or authorships with women in the first and last article by-line position.

The prevalence of Italian funded articles with women’s contributions published in Gold OA journals seems to confirm this tendency, especially if considering the weak enforcement of the Italian OA policies.

URL : An intersectional approach to analyse gender productivity and open access: a bibliometric analysis of the Italian National Research Council

DOI : https://doi.org/10.1007/s11192-020-03802-0

What About Reuse? A Study on the Use of Open Educational Resources in Dutch Higher Education

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Authors : Marjon Baas, Robert Schuwer

Extensive research has taken place over the years to examine the barriers of OER adoption, but little empirical studies has been undertaken to map the amount of OER reuse. The discussion around the actual use of OER, outside the context in which they were developed, remains ongoing.

Previous studies have already shown that searching and evaluating resources are barriers for actual reuse. Hence, in this quantitative survey study we explored teachers’ practices with resources in Higher Education Institutes in the Netherlands. The survey had three runs, each in a different context, with a total of 439 respondents.

The results show that resources that are hard or time-consuming to develop are most often reused from third parties without adaptations. Resources that need to be more context specific are often created by teachers themselves.

To improve our understanding of reuse, follow-up studies must explore reuse with a more qualitative research design in order to explore how these hidden practices of dark reuse look like and how teachers and students benefit of it.

URL : What About Reuse? A Study on the Use of Open Educational Resources in Dutch Higher Education

Original location : https://openpraxis.org/index.php/OpenPraxis/article/view/1139

The Science of Citizen Science

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Authors : Katrin Vohland, Anne Land-Zandstra, Luigi Ceccaroni, Rob Lemmens, Josep Perelló, Marisa Ponti, Roeland Samson, Katherin Wagenknecht

This open access book discusses how the involvement of citizens into scientific endeavors is expected to contribute to solve the big challenges of our time, such as climate change and the loss of biodiversity, growing inequalities within and between societies, and the sustainability turn. The field of citizen science has been growing in recent decades.

Many different stakeholders from scientists to citizens and from policy makers to environmental organisations have been involved in its practice. In addition, many scientists also study citizen science as a research approach and as a way for science and society to interact and collaborate.

This book provides a representation of the practices as well as scientific and societal outcomes in different disciplines. It reflects the contribution of citizen science to societal development, education, or innovation and provides and overview of the field of actors as well as on tools and guidelines.

It serves as an introduction for anyone who wants to get involved in and learn more about the science of citizen science.

URL : The Science of Citizen Science

DOI : https://doi.org/10.1007/978-3-030-58278-4