Nanopublications LDF server

Matches in Nanopublications for { ?s <http://purl.org/dc/terms/abstract> ?o ?g. }

• peerj-cs.189 abstract "The analysis of literary works has experienced a surge in computer-assisted processing. To obtain insights into the community structures and social interactions portrayed in novels, the creation of social networks from novels has gained popularity. Many methods rely on identifying named entities and relations for the construction of these networks, but many of these tools are not specifically created for the literary domain. Furthermore, many of the studies on information extraction from literature typically focus on 19th and early 20th century source material. Because of this, it is unclear if these techniques are as suitable to modern-day literature as they are to those older novels. We present a study in which we evaluate natural language processing tools for the automatic extraction of social networks from novels as well as their network structure. We find that there are no significant differences between old and modern novels but that both are subject to a large amount of variance. Furthermore, we identify several issues that complicate named entity recognition in our set of novels and we present methods to remedy these. We see this work as a step in creating more culturally-aware AI systems." assertion.
• rio.8.e94150 abstract "Beginning in 1995, early Internet pioneers proposed Digital Objects as encapsulations of data and metadata made accessible through persistent identifier resolution services. In recent years, this Digital Object Architecture has been extended to include the FAIR Guiding Principles, resulting in the concept of a FAIR Digital Object (FDO), a minimal, uniform container making any digital resource machine-actionable. Beginning in 2009, nanopublications were independently conceived as a minimal, uniform container making individual semantic assertions and their associated provenance metadata, machine-actionable. These two technologies share the same vision of a data infrastructure, and act as instances of Machine-Actionable Containers (MACs) that make use of minimal uniform standards to enable FAIR operations. Here, we compare the structure and computational behaviors of the existing nanopublication infrastructure, to those in the proposed FAIR Digital Object Framework. Although developed independently there are clear parallels between the vision and the approach of nanopublication and FDOF. We find a remarkable congruence between the currently proposed FDO requirements and the existing nanopublication infrastructure, including several FDO-like qualities already embodied in the nanopublication ecosystem." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170010 abstract "Various approaches and systems have been presented in the context of scholarly communication for what has been called semantic publishing. Closer inspection, however, reveals that these approaches are mostly not about publishing semantic representations, as the name seems to suggest. Rather, they take the processes and outcomes of the current narrative-based publishing system for granted and only work with already published papers. This includes approaches involving semantic annotations, semantic interlinking, semantic integration, and semantic discovery, but with the semantics coming into play only after the publication of the original article. While these are interesting and important approaches, they fall short of providing a vision to transcend the current publishing paradigm. We argue here for taking the term semantic publishing literally and work towards a vision of genuine semantic publishing, where computational tools and algorithms can help us with dealing with the wealth of human knowledge by letting researchers capture their research results with formal semantics from the start, as integral components of their publications. We argue that these semantic components should furthermore cover at least the main claims of the work, that they should originate from the authors themselves, and that they should be fine-grained and light-weight for optimized re-usability and minimized publication overhead. This paper is in fact not just advocating our concept, but is itself a genuine semantic publication, thereby demonstrating and illustrating our points." assertion.
• DS-170004 abstract "Symbolic approaches to Artificial Intelligence (AI) represent things within a domain of knowledge through physical symbols, combine symbols into symbol expressions, and manipulate symbols and symbol expressions through inference processes. While a large part of Data Science relies on statistics and applies statistical approaches to AI, there is an increasing potential for successfully applying symbolic approaches as well. Symbolic representations and symbolic inference are close to human cognitive representations and therefore comprehensible and interpretable; they are widely used to represent data and metadata, and their specific semantic content must be taken into account for analysis of such information; and human communication largely relies on symbols, making symbolic representations a crucial part in the analysis of natural language. Here we discuss the role symbolic representations and inference can play in Data Science, highlight the research challenges from the perspective of the data scientist, and argue that symbolic methods should become a crucial component of the data scientists’ toolbox." assertion.
• DS-170004 abstract "Symbolic approaches to artificial intelligence represent things within a domain of knowledge through physical symbols, combine symbols into symbol expressions and structures, and manipulate symbols and symbol expressions and structures through inference processes. While a large part of Data Science relies on statistics and applies statistical approaches to artificial intelligence, there is an increasing potential for successfully applying symbolic approaches as well. Sym- bolic representations and symbolic inference are close to human cognitive repre- sentations and therefore comprehensible and interpretable; they are widely used to represent data and metadata, and their specific semantic content must be taken into account for analysis of such information; and human communication largely relies on symbols, making symbolic representations a crucial part in the analysis of natu- ral language. Here we discuss the role symbolic representations and inference can play in Data Science, highlight the research challenges from the perspective of the data scientist, and argue that symbolic methods should become a crucial component of the data scientists’ toolbox." assertion.
• DS-170005 abstract "The majority of economic sectors are transformed by the abundance of data. Smart grids, smart cities, smart health, Industry 4.0 impose to domain experts requirements for data science skills in order to respond to their duties and the challenges of the digital society. Business training or replacing domain experts with computer scientists can be costly, limiting for the diversity in business sectors and can lead to sacrifice of invaluable domain knowledge. This paper illustrates experience and lessons learnt from the design and teaching of a novel cross-disciplinary data science course at a postgraduate level in a top-class university. The course design is approached from the perspectives of the constructivism and transformative learning theory. Students are introduced to a guideline for a group research project they need to deliver, which is used as a pedagogical artifact for students to unfold their data science skills as well as reflect within their team their domain and prior knowledge. In contrast to other related courses, the course content illustrated is designed to be self-contained for students of different discipline. Without assuming certain prior programming skills, students from different discipline are qualified to practice data science with open-source tools at all stages: data manipulation, interactive graphical analysis, plotting, machine learning and big data analytics. Quantitative and qualitative evaluation with interviews outlines invaluable lessons learnt." assertion.
• DS-170006 abstract "Stream reasoning studies the application of inference techniques to data characterised by being highly dynamic. It can find application in several settings, from Smart Cities to Industry 4.0, from Internet of Things to Social Media analytics. This year stream reasoning turns ten, and in this article we analyse its growth. In the first part, we trace the main results obtained so far, by presenting the most prominent studies. We start by an overview of the most relevant studies developed in the context of semantic web, and then we extend the analysis to include contributions from adjacent areas, such as database and artificial intelligence. Looking at the past is useful to prepare for the future: in the second part, we present a set of open challenges and issues that stream reasoning will face in the next future." assertion.
• DS-170007 abstract "In modern machine learning, raw data is the preferred input for our models. Where a decade ago data scientists were still engineering features, manually picking out the details we thought salient, they now prefer the data in their raw form. As long as we can assume that all relevant and irrelevant information is present in the input data, we can design deep models that build up intermediate representations to sift out relevant features. However, these models are often domain specific and tailored to the task at hand, and therefore unsuited for learning on heterogeneous knowledge: information of different types and from different domains. If we can develop methods that operate on this form of knowledge, we can dispense with a great deal more ad-hoc feature engineering and train deep models end-to-end in many more domains. To accomplish this, we first need a data model capable of expressing heterogeneous knowledge naturally in various domains, in as usable a form as possible, and satisfying as many use cases as possible. In this position paper, we argue that the knowledge graph is a suitable candidate for this data model. We further describe current research and discuss some of the promises and challenges of this approach." assertion.
• DS-170008 abstract "Modern biomedical research is complex and requires a cross section of experts collaborating using multi-, inter-, or transdisciplinary approaches to address scientific questions. Known as team science, such approaches have become so critical it has given rise to a new field – the science of team science. In biomedical research, data scientists often play a critical role in team-based collaborations. Integration of data scientists into research teams has multiple advantages to the clinical and translational investigator as well as to the data scientist. Clinical and translational investigators benefit from having an invested dedicated collaborator who can assume principal responsibility for essential data-related activities, while the data scientist can build a career developing tools that are relevant and data-driven. Participation in team science, however, can pose challenges. One particular challenge is the ability to appropriately evaluate the data scientist’s scholarly contributions, necessary for promotion. Only a minority of academic health centers have attempted to address this challenge. In order for team science to thrive on academic campuses, leaders of institutions need to hire data science faculty for the purpose of doing team science, with novel systems in place that incentivize the data scientist’s engagement in team science and that allow for appropriate evaluation of performance. Until such systems are adopted at the institutional level, the ability to conduct team science to address modern biomedical research with its increasingly complex data needs will be compromised. Fostering team science on campuses by putting supportive systems in place will benefit not only clinical and translational investigators as well as data scientists, but also the larger academic institution." assertion.
• DS-170009 abstract "Scientists from diverse backgrounds are joining the field of data science. This leads to advances in data science being actualized in the context of many different domains. Conclusions from datasets using innovative algorithms are obvious aspects but advances in data science can take on many different forms such as new methods for data interpretation, new data integration and processing technologies, or as will be the topic of this editorial, data visualization techniques. The parity and complementary relationship between techniques from all domains provide ways to improve discovery although quantifying the contributions to discovery process from each technique can be elusive. The experiences described here come from visualizing life science multi-omics data, but most of the remarks can be associated with visualization methods in general. From the perspective that visualization serves as an important method for shaping data science interpretations, this paper sets out: 1) some of the necessary requirements for visualization tools due to the nature of multi-omics datasets and, 2) some of the difficulties encountered in creating and valorizing new visualization implementations for scientific discovery." assertion.
• DS-170012 abstract "Semantic Publishing involves the use of Web and Semantic Web technologies and standards for the semantic enhancement of a scholarly work so as to improve its discoverability, interactivity, openness and (re-)usability for both humans and machines. Recently, people have suggested that the semantic enhancements of a scholarly work should be undertaken by the authors of that scholarly work, and should be considered as integral parts of the contribution subjected to peer review. However, this requires that the authors should spend additional time and effort adding such semantic annotations, time that they usually do not have available. Thus, the most pragmatic way to facilitate this additional task is to use automated services that create the semantic annotation of authors’ scholarly articles by parsing the content that they have already written, thus reducing the additional time required of the authors to that for checking and validating these semantic annotations. In this article, I propose a generic approach called compositional and iterative semantic enhancement (CISE) that enables the automatic enhancement of scholarly papers with additional semantic annotations in a way that is independent of the markup used for storing scholarly articles and the natural language used for writing their content." assertion.
• DS-190023 abstract "The increasing interest in analysing, describing, and improving the research process requires the development of new forms of scholarly data publication and analysis that integrates lessons and approaches from the field of Semantic Technologies, Science of Science, Digital Libraries, and Artificial Intelligence. This editorial summarises the content of the Special Issue on Scholarly Data Analysis (Semantics, Analytics, Visualisation), which aims to showcase some of the most interesting research efforts in the field. This issue includes an extended version of the best papers of the last two editions of the “Semantics, Analytics, Visualisation: Enhancing Scholarly Dissemination” (SAVE-SD 2017 and 2018) workshop at The Web Conference." assertion.
• DS-190024 abstract "This is an extended, revised version of Philipson (2017). Findability and interoperability of some PIDs, Persistent Identifers, and their compliance with the FAIR data principles are explored, where ARKs, Archival Reource Keys, were added in this version. It is suggested that the wide distribution and findability (e.g. by simple ‘googling’) on the internet may be as important for the usefulness of PIDs as the resolvability of PID URIs – Uniform Resource Identifiers. This version also includes new reasoning about why sometimes PIDs such as DOIs, Digital Object Identifiers, are not used in citations. The prevalence of phenomena such as link rot implies that URIs cannot always be trusted to be persistently resolvable. By contrast, the well distributed, but seldom directly resolvable ISBN, International Standard Book Number, has proved remarkably resilient, with far-reaching persistence, inherent structural meaning and good validatability, through fixed string-length, pattern-recognition, restricted character set and check digit. Examples of regular expressions used for validation of PIDs are supplied or referenced. The suggestion to add context and meaning to PIDs, making them “identify themselves”, through namespace prefixes and object types is more elaborate in this version. Meaning can also be inherent through structural elements, such as well defined, restricted string patterns, that at the same time make PIDs more “validatable”. Concluding this version is a generic, refined model for a PID with these properties, in which namespaces are instrumental as custodians, meaning-givers and validation schema providers. A draft example of a Schematron schema for validation of “new” PIDs in accordance with the proposed model is provided." assertion.
• DS-190020 abstract "Translational research applies findings from basic science to enhance human health and well-being. In translational research projects, academia and industry work together to improve healthcare, often through public-private partnerships. This “translation” is often not easy, because it means that the so-called “valley of death” will need to be crossed: many interesting findings from fundamental research do not result in new treatments, diagnostics and prevention. To cross the valley of death, fundamental researchers need to collaborate with clinical researchers and with industry so that promising results can be implemented in a product. The success of translational research projects often does not depend only on the fundamental science and the applied science, but also on the informatics needed to connect everything: the translational research informatics. This informatics, which includes data management, data stewardship and data governance, enables researchers to store and analyze their ‘big data’ in a meaningful way, and enable application in the clinic. The author has worked on the information technology infrastructure for several translational research projects in oncology for the past nine years, and presents his lessons learned in this paper in the form of ten commandments. These commandments are not only useful for the data managers, but for all involved in a translational research project. Some of the commandments deal with topics that are currently in the spotlight, such as machine readability, the FAIR Guiding Principles and the GDPR regulations. Others are mentioned less in the literature, but are just as crucial for the success of a translational research project." assertion.
• DS-190019 abstract "Context: Systematic Reviews (SRs) are means for collecting and synthesizing evidence from the identification and analysis of relevant studies from multiple sources. To this aim, they use a well-defined methodology meant to mitigate the risks of biases and ensure repeatability for later updates. SRs, however, involve significant effort. Goal: The goal of this paper is to introduce a novel methodology that reduces the amount of manual tedious tasks involved in SRs while taking advantage of the value provided by human expertise. Method: Starting from current methodologies for SRs, we replaced the steps of keywording and data extraction with an automatic methodology for generating a domain ontology and classifying the primary studies. This methodology has been applied in the Software Engineering sub-area of Software Architecture and evaluated by human annotators. Results: The result is a novel Expert-Driven Automatic Methodology, EDAM, for assisting researchers in performing SRs. EDAM combines ontology-learning techniques and semantic technologies with the human-in-the-loop. The first (thanks to automation) fosters scalability, objectivity, reproducibility and granularity of the studies; the second allows tailoring to the specific focus of the study at hand and knowledge reuse from domain experts. We evaluated EDAM on the field of Software Architecture against six senior researchers. As a result, we found that the performance of the senior researchers in classifying papers was not statistically significantly different from EDAM. Conclusions: Thanks to automation of the less-creative steps in SRs, our methodology allows researchers to skip the tedious tasks of keywording and manually classifying primary studies, thus freeing effort for the analysis and the discussion." assertion.
• data-science-and-symbolic-ai-synergies-challenges-and-opportunities abstract "Symbolic approaches to artificial intelligence represent things within a domain of knowledge through physical symbols, combine symbols into symbol expressions and structures, and manipulate symbols and symbol expressions and structures through inference processes. While a large part of Data Science relies on statistics and applies statistical approaches to artificial intelligence, there is an increasing potential for successfully applying symbolic approaches as well. Sym- bolic representations and symbolic inference are close to human cognitive repre- sentations and therefore comprehensible and interpretable; they are widely used to represent data and metadata, and their specific semantic content must be taken into account for analysis of such information; and human communication largely relies on symbols, making symbolic representations a crucial part in the analysis of natu- ral language. Here we discuss the role symbolic representations and inference can play in Data Science, highlight the research challenges from the perspective of the data scientist, and argue that symbolic methods should become a crucial component of the data scientists’ toolbox." assertion.
• data-science-and-symbolic-ai-synergies-challenges-and-opportunities-0 abstract "Symbolic approaches to artificial intelligence represent things within a domain of knowledge through physical symbols, combine symbols into symbol ex- pressions, and manipulate symbols and symbol expressionsNN through inference processes. While a large part of Data Science relies on statistics and applies statisti- cal approaches to artificial intelligence, there is an increasing potential for success- fully applying symbolic approaches as well. Symbolic representations and sym- bolic inference are close to human cognitive representations and therefore compre- hensible and interpretable; they are widely used to represent data and metadata, and their specific semantic content must be taken into account for analysis of such in- formation; and human communication largely relies on symbols, making symbolic representations a crucial part in the analysis of natural language. Here we discuss the role symbolic representations and inference can play in Data Science, high- light the research challenges from the perspective of the data scientist, and argue that symbolic methods should become a crucial component of the data scientists’ toolbox." assertion.
• sdata.2016.18 abstract "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community." assertion.
• sdata.2016.18 abstract "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community." assertion.
• sdata.2016.18 abstract "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community." assertion.
• sdata.2016.18 abstract "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community." assertion.
• sdata.2016.18 abstract "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community." assertion.
• sdata.2016.18 abstract "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community." assertion.
• DS-230058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• DS-220058 abstract "Sarcasm is a linguistic phenomenon often indicating a disparity between literal and inferred meanings. Due to its complexity, it is typically difficult to discern it within an online text message. Consequently, in recent years sarcasm detection has received considerable attention from both academia and industry. Nevertheless, the majority of current approaches simply model low-level indicators of sarcasm in various machine learning algorithms. This paper aims to present sarcasm in a new light by utilizing novel indicators in a deep weighted average ensemble-based framework (DWAEF). The novel indicators pertain to exploiting the presence of simile and metaphor in text and detecting the subtle shift in tone at a sentence’s structural level. A graph neural network (GNN) structure is implemented to detect the presence of simile, bidirectional encoder representations from transformers (BERT) embeddings are exploited to detect metaphorical instances and fuzzy logic is employed to account for the shift of tone. To account for the existence of sarcasm, the DWAEF integrates the inputs from the novel indicators. The performance of the framework is evaluated on a self-curated dataset of online text messages. A comparative report between the results acquired using primitive features and those obtained using a combination of primitive features and proposed indicators is provided. The highest accuracy of 92% was achieved after applying DWAEF, the proposed framework which combines the primitive features and novel indicators together as compared to 78.58% obtained using Support Vector Machine (SVM) which was the lowest among all classifiers." assertion.
• gigabyte.99 abstract "In China, 65 types of venomous snakes exist, with the Chinese Cobra Naja atra being prominent and a major cause of snakebites in humans. Furthermore, N. atra is a protected animal in some areas, as it has been listed as vulnerable by the International Union for Conservation of Nature. Recently, due to the medical value of snake venoms, venomics has experienced growing research interest. In particular, genomic resources are crucial for understanding the molecular mechanisms of venom production. Here, we report a highly continuous genome assembly of N. atra, based on a snake sample from Huangshan, Anhui, China. The size of this genome is 1.67 Gb, while its repeat content constitutes 37.8% of the genome. A total of 26,432 functional genes were annotated. This data provides an essential resource for studying venom production in N. atra. It may also provide guidance for the protection of this species." assertion.
• DS-170001 abstract "Computational manipulation of knowledge is an important, and often under-appreciated, aspect of biomedical Data Science. The first Data Science initiative from the US National Institutes of Health was entitled “Big Data to Knowledge (BD2K).” The main emphasis of the more than $200M allocated to that program has been on “Big Data;” the “Knowledge” component has largely been the implicit assumption that the work will lead to new biomedical knowledge. However, there is long-standing and highly productive work in computational knowledge representation and reasoning, and computational processing of knowledge has a role in the world of Data Science. Knowledge-based biomedical Data Science involves the design and implementation of computer systems that act as if they knew about biomedicine. There are many ways in which a computational approach might act as if it knew something: for example, it might be able to answer a natural language question about a biomedical topic, or pass an exam; it might be able to use existing biomedical knowledge to rank or evaluate hypotheses; it might explain or interpret data in light of prior knowledge, either in a Bayesian or other sort of framework. These are all examples of automated reasoning that act on computational representations of knowledge. After a brief survey of existing approaches to knowledge-based data science, this position paper argues that such research is ripe for expansion, and expanded application." assertion.
• DS-170001 abstract "Computational manipulation of knowledge is an important, and often under-appreciated, aspect of biomedical Data Science. The first Data Science initiative from the US National Institutes of Health was entitled “Big Data to Knowledge (BD2K).” The main emphasis of the more than $200M allocated to that program has been on “Big Data;” the “Knowledge” component has largely been the implicit assumption that the work will lead to new biomedical knowledge. However, there is long-standing and highly productive work in computational knowledge representation and reasoning, and computational processing of knowledge has a role in the world of Data Science. Knowledge-based biomedical Data Science involves the design and implementation of computer systems that act as if they knew about biomedicine. There are many ways in which a computational approach might act as if it knew something: for example, it might be able to answer a natural language question about a biomedical topic, or pass an exam; it might be able to use existing biomedical knowledge to rank or evaluate hypotheses; it might explain or interpret data in light of prior knowledge, either in a Bayesian or other sort of framework. These are all examples of automated reasoning that act on computational representations of knowledge. After a brief survey of existing approaches to knowledge-based data science, this position paper argues that such research is ripe for expansion, and expanded application." assertion.
• DS-170001 abstract "Computational manipulation of knowledge is an important, and often under-appreciated, aspect of biomedical Data Science. The first Data Science initiative from the US National Institutes of Health was entitled “Big Data to Knowledge (BD2K).” The main emphasis of the more than $200M allocated to that program has been on “Big Data;” the “Knowledge” component has largely been the implicit assumption that the work will lead to new biomedical knowledge. However, there is long-standing and highly productive work in computational knowledge representation and reasoning, and computational processing of knowledge has a role in the world of Data Science. Knowledge-based biomedical Data Science involves the design and implementation of computer systems that act as if they knew about biomedicine. There are many ways in which a computational approach might act as if it knew something: for example, it might be able to answer a natural language question about a biomedical topic, or pass an exam; it might be able to use existing biomedical knowledge to rank or evaluate hypotheses; it might explain or interpret data in light of prior knowledge, either in a Bayesian or other sort of framework. These are all examples of automated reasoning that act on computational representations of knowledge. After a brief survey of existing approaches to knowledge-based data science, this position paper argues that such research is ripe for expansion, and expanded application." assertion.
• DS-170001 abstract "Computational manipulation of knowledge is an important, and often under-appreciated, aspect of biomedical Data Science. The first Data Science initiative from the US National Institutes of Health was entitled “Big Data to Knowledge (BD2K).” The main emphasis of the more than $200M allocated to that program has been on “Big Data;” the “Knowledge” component has largely been the implicit assumption that the work will lead to new biomedical knowledge. However, there is long-standing and highly productive work in computational knowledge representation and reasoning, and computational processing of knowledge has a role in the world of Data Science. Knowledge-based biomedical Data Science involves the design and implementation of computer systems that act as if they knew about biomedicine. There are many ways in which a computational approach might act as if it knew something: for example, it might be able to answer a natural language question about a biomedical topic, or pass an exam; it might be able to use existing biomedical knowledge to rank or evaluate hypotheses; it might explain or interpret data in light of prior knowledge, either in a Bayesian or other sort of framework. These are all examples of automated reasoning that act on computational representations of knowledge. After a brief survey of existing approaches to knowledge-based data science, this position paper argues that such research is ripe for expansion, and expanded application." assertion.
• DS-170002 abstract "Research on international conflict has mostly focused on explaining events such as the onset or termination of wars, rather than on trying to predict them. Recently, however, forecasts of political phenomena have received growing attention. Predictions of violent events, in particular, have been increasingly accurate using various methods ranging from expert knowledge to quantitative methods and formal modeling. Yet, we know little about the limits of these approaches, even though information about these limits has critical implications for both future research and policy-making. In particular, are our predictive inaccuracies due to limitations of our models, data, or assumptions, in which case improvements should occur incrementally. Or are there aspects of conflicts that will always remain fundamentally unpredictable? After reviewing some of the current approaches to forecasting conflict, I suggest avenues of research that could disentangle the causes of our current predictive failures." assertion.
• DS-170002 abstract "Research on international conflict has mostly focused on explaining events such as the onset or termination of wars, rather than on trying to predict them. Recently, however, forecasts of political phenomena have received growing attention. Predictions of violent events, in particular, have been increasingly accurate using various methods ranging from expert knowledge to quantitative methods and formal modeling. Yet, we know little about the limits of these approaches, even though information about these limits has critical implications for both future research and policy-making. In particular, are our predictive inaccuracies due to limitations of our models, data, or assumptions, in which case improvements should occur incrementally. Or are there aspects of conflicts that will always remain fundamentally unpredictable? After reviewing some of the current approaches to forecasting conflict, I suggest avenues of research that could disentangle the causes of our current predictive failures." assertion.
• DS-170002 abstract "Research on international conflict has mostly focused on explaining events such as the onset or termination of wars, rather than on trying to predict them. Recently, however, forecasts of political phenomena have received growing attention. Predictions of violent events, in particular, have been increasingly accurate using various methods ranging from expert knowledge to quantitative methods and formal modeling. Yet, we know little about the limits of these approaches, even though information about these limits has critical implications for both future research and policy-making. In particular, are our predictive inaccuracies due to limitations of our models, data, or assumptions, in which case improvements should occur incrementally. Or are there aspects of conflicts that will always remain fundamentally unpredictable? After reviewing some of the current approaches to forecasting conflict, I suggest avenues of research that could disentangle the causes of our current predictive failures." assertion.
• DS-170003 abstract "Data science is a young and rapidly expanding field, but one which has already experienced several waves of temporarily-ubiquitous methodological fashions. In this paper we argue that a diversity of ideas and methodologies is crucial for the long term success of the data science community. Towards the goal of a healthy, diverse ecosystem of different statistical models and approaches, we review how ideas spread in the scientific community and the role of incentives in influencing which research ideas scientists pursue. We conclude with suggestions for how universities, research funders and other actors in the data science community can help to maintain a rich, eclectic statistical environment." assertion.
• DS-170003 abstract "Data science is a young and rapidly expanding field, but one which has already experienced several waves of temporarily-ubiquitous methodological fashions. In this paper we argue that a diversity of ideas and methodologies is crucial for the long term success of the data science community. Towards the goal of a healthy, diverse ecosystem of different statistical models and approaches, we review how ideas spread in the scientific community and the role of incentives in influencing which research ideas scientists pursue. We conclude with suggestions for how universities, research funders and other actors in the data science community can help to maintain a rich, eclectic statistical environment." assertion.
• DS-170003 abstract "Data science is a young and rapidly expanding field, but one which has already experienced several waves of temporarily-ubiquitous methodological fashions. In this paper we argue that a diversity of ideas and methodologies is crucial for the long term success of the data science community. Towards the goal of a healthy, diverse ecosystem of different statistical models and approaches, we review how ideas spread in the scientific community and the role of incentives in influencing which research ideas scientists pursue. We conclude with suggestions for how universities, research funders and other actors in the data science community can help to maintain a rich, eclectic statistical environment." assertion.
• DSP4FAIR abstract "Data Stewardship Plan (DSP) templates prompt users to consider various issues but typically have no requirements for actual implementation choices. But as FAIR methodologies mature the DSP will become a more directive “how to” manual for making data FAIR." assertion.
• DSP4FAIR abstract "Data Stewardship Plan (DSP) templates prompt users to consider various issues but typically have no requirements for actual implementation choices. But as FAIR methodologies mature the DSP will become a more directive “how to” manual for making data FAIR." assertion.
• s41467-022-29206-7 abstract "A central question concerning natural competence is why orthologs of competence genes are conserved in non-competent bacterial species, suggesting they have a role other than in transformation. Here we show that competence induction in the human pathogen Staphylococcus aureus occurs in response to ROS and host defenses that compromise bacterial respiration during infection. Bacteria cope with reduced respiration by obtaining energy through fermentation instead. Since fermentation is energetically less efficient than respiration, the energy supply must be assured by increasing the glycolytic flux. The induction of natural competence increases the rate of glycolysis in bacteria that are unable to respire via upregulation of DNA- and glucose-uptake systems. A competent-defective mutant showed no such increase in glycolysis, which negatively affects its survival in both mouse and Galleria infection models. Natural competence foster genetic variability and provides S. aureus with additional nutritional and metabolic possibilities, allowing it to proliferate during infection." assertion.
• DS-170011 abstract "Artificial intelligence will play an increasingly more prominent role in scientific research ecosystems, and will become indispensable as more interdisciplinary science questions are tackled. While in recent years computers have propelled science by crunching through data and leading to a data science revolution, qualitatively different scientific advances will result from advanced intelligent technologies for crunching through knowledge and ideas. We propose seven principles for developing thoughtful artificial intelligence, which will turn intelligent systems into partners for scientists. We present a personal perspective on a research agenda for thoughtful artificial intelligence, and discuss its potential for data science and scientific discovery." assertion.
• DS-170011 abstract "Artificial intelligence will play an increasingly more prominent role in scientific research ecosystems, and will become indispensable as more interdisciplinary science questions are tackled. While in recent years computers have propelled science by crunching through data and leading to a data science revolution, qualitatively different scientific advances will result from advanced intelligent technologies for crunching through knowledge and ideas. We propose seven principles for developing thoughtful artificial intelligence, which will turn intelligent systems into partners for scientists. We present a personal perspective on a research agenda for thoughtful artificial intelligence, and discuss its potential for data science and scientific discovery." assertion.
• DS-170011 abstract "Artificial intelligence will play an increasingly more prominent role in scientific research ecosystems, and will become indispensable as more interdisciplinary science questions are tackled. While in recent years computers have propelled science by crunching through data and leading to a data science revolution, qualitatively different scientific advances will result from advanced intelligent technologies for crunching through knowledge and ideas. We propose seven principles for developing thoughtful artificial intelligence, which will turn intelligent systems into partners for scientists. We present a personal perspective on a research agenda for thoughtful artificial intelligence, and discuss its potential for data science and scientific discovery." assertion.
• DS-170011 abstract "Artificial intelligence will play an increasingly more prominent role in scientific research ecosystems, and will become indispensable as more interdisciplinary science questions are tackled. While in recent years computers have propelled science by crunching through data and leading to a data science revolution, qualitatively different scientific advances will result from advanced intelligent technologies for crunching through knowledge and ideas. We propose seven principles for developing thoughtful artificial intelligence, which will turn intelligent systems into partners for scientists. We present a personal perspective on a research agenda for thoughtful artificial intelligence, and discuss its potential for data science and scientific discovery." assertion.
• access.2023.3269660 abstract "Topic modeling comprises a set of machine learning algorithms that allow topics to be extracted from a collection of documents. These algorithms have been widely used in many areas, such as identifying dominant topics in scientific research. However, works addressing such problems focus on identifying static topics, providing snapshots that cannot show how those topics evolve. Aiming to close this gap, in this article, we describe an approach for dynamic article set analysis and classification. This is accomplished by querying open data of notable scientific databases via representational state transfers. After that, we enforce data management practices with a dynamic topic modeling approach on the associated metadata available. As a result, we identify research trends for a given field at specific instants and the referred terminology trends evolution throughout the years. It was possible to detect the associated lexical variation over time in published content, ultimately determining the so-called “hot topics” in arbitrary instants and how they correlate." assertion.
• access.2023.3269660 abstract "Topic modeling comprises a set of machine learning algorithms that allow topics to be extracted from a collection of documents. These algorithms have been widely used in many areas, such as identifying dominant topics in scientific research. However, works addressing such problems focus on identifying static topics, providing snapshots that cannot show how those topics evolve. Aiming to close this gap, in this article, we describe an approach for dynamic article set analysis and classification. This is accomplished by querying open data of notable scientific databases via representational state transfers. After that, we enforce data management practices with a dynamic topic modeling approach on the associated metadata available. As a result, we identify research trends for a given field at specific instants and the referred terminology trends evolution throughout the years. It was possible to detect the associated lexical variation over time in published content, ultimately determining the so-called “hot topics” in arbitrary instants and how they correlate." assertion.
• DS-240059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• DS-240059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• DS-240059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• DS-240059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• DS-240059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• DS-240059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• peerj-cs.387 abstract "While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing." assertion.
• peerj-cs.387 abstract "While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing." assertion.
• peerj-cs.387 abstract "While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing." assertion.
• peerj-cs.387 abstract "While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing." assertion.
• peerj-cs.387 abstract "While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing." assertion.
• peerj-cs.387 abstract "While the publication of Linked Data has become increasingly common, the process tends to be a relatively complicated and heavy-weight one. Linked Data is typically published by centralized entities in the form of larger dataset releases, which has the downside that there is a central bottleneck in the form of the organization or individual responsible for the releases. Moreover, certain kinds of data entries, in particular those with subjective or original content, currently do not fit into any existing dataset and are therefore more difficult to publish. To address these problems, we present here an approach to use nanopublications and a decentralized network of services to allow users to directly publish small Linked Data statements through a simple and user-friendly interface, called Nanobench, powered by semantic templates that are themselves published as nanopublications. The published nanopublications are cryptographically verifiable and can be queried through a redundant and decentralized network of services, based on the grlc API generator and a new quad extension of Triple Pattern Fragments. We show here that these two kinds of services are complementary and together allow us to query nanopublications in a reliable and efficient manner. We also show that Nanobench makes it indeed very easy for users to publish Linked Data statements, even for those who have no prior experience in Linked Data publishing." assertion.
• 34979 abstract "Background: In the poorly studied field of physician suicide, various factors can contribute to misinformation or information distortion, which in turn can influence evidence-based policies and prevention of suicide in this unique population. Objective: The aim of this paper is to use nanopublications as a scientific publishing approach to establish a citation network of claims in peer-reviewed publications about the rate of suicide among US physicians. Methods: A list of articles from a previously published scoping literature review on physician suicide was used to identify those articles that commented on or investigated suicidal behaviors of physician populations, including students, postgraduate trainees, and practicing physicians. The included articles were from peer-reviewed publications and asserted a claim about the annual rate of physician suicide. Manual data extraction was performed to collect article (or resource) type, title, authors, digital object identifier or URI, publication year, claim (about annual physician suicide rate), data of last access of the article (eg, for a webpage), and citations supporting the claim. Additional articles, websites, or other links were only added to the set of claims if they were cited by a peer-reviewed article already included in the data set. A nanopublication was created for each article or resource using Nanobench with an investigator-developed literature-based claim nanopublication template. Results: A set of 49 claims concerning the rate of US physician suicide was represented as nanopublications. Analysis of the claim network revealed that (1) the network is not fully connected, (2) no single primary source of the claim could be identified, and (3) all end-point citations had a claim with no further citation, had no apparent claim, or could not be accessed to verify the claim. The nanopublication strategy also enabled the capture of variant claims published on a website. Conclusions: Nanopublications remain to be adopted in broader scientific publishing in medicine, especially in publishing about physician mental health and suicide. This proof-of-concept study highlights an opportunity for more coordinated research efforts in the subject of physician suicide. Our work integrates these various claims and enables the verification of nonauthoritative assertions, thereby better equipping researchers to advance evidence-based knowledge and to make informed statements in the advocacy of physician suicide prevention. Representing physician suicide rate claims as nanopublications can be extended and improved in future work." assertion.
• peerj-cs.1038 abstract "Understanding the complexity of restricted research data is vitally important in the current new era of Open Science. While the FAIR Guiding Principles have been introduced to help researchers to make data Findable, Accessible, Interoperable and Reusable, it is still unclear how the notions of FAIR and Openness can be applied in the context of restricted data. Many methods have been proposed in support of the implementation of the principles, but there is yet no consensus among the scientific community as to the suitable mechanisms of making restricted data FAIR. We present here a systematic literature review to identify the methods applied by scientists when researching restricted data in a FAIR-compliant manner in the context of the FAIR principles. Through the employment of a descriptive and iterative study design, we aim to answer the following three questions: (1) What methods have been proposed to apply the FAIR principles to restricted data?, (2) How can the relevant aspects of the methods proposed be categorized?, (3) What is the maturity of the methods proposed in applying the FAIR principles to restricted data?. After analysis of the 40 included publications, we noticed that the methods found, reflect the stages of the Data Life Cycle, and can be divided into the following Classes: Data Collection, Metadata Representation, Data Processing, Anonymization, Data Publication, Data Usage and Post Data Usage. We observed that a large number of publications used 'Access Control' and 'Usage and License Terms' methods, while others such as 'Embargo on Data Release' and the use of 'Synthetic Data' were used in fewer instances. In conclusion, we are presenting the first extensive literature review on the methods applied to confidential data in the context of FAIR, providing a comprehensive conceptual framework for future research on restricted access data." assertion.
• s13326-024-00310-5 abstract "Background: In today's landscape of data management, the importance of knowledge graphs and ontologies is escalating as critical mechanisms aligned with the FAIR Guiding Principles—ensuring data and metadata are Findable, Accessible, Interoperable, and Reusable. We discuss three challenges that may hinder the effective exploitation of the full potential of FAIR knowledge graphs. Results: We introduce "semantic units" as a conceptual solution, although currently exemplified only in a limited prototype. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs by adding another layer of triples on top of the conventional data layer. Semantic units and their subgraphs are represented by their own resource that instantiates a corresponding semantic unit class. We distinguish statement and compound units as basic categories of semantic units. A statement unit is the smallest, independent proposition that is semantically meaningful for a human reader. Depending on the relation of its underlying proposition, it consists of one or more triples. Organizing a knowledge graph into statement units results in a partition of the graph, with each triple belonging to exactly one statement unit. A compound unit, on the other hand, is a semantically meaningful collection of statement and compound units that form larger subgraphs. Some semantic units organize the graph into different levels of representational granularity, others orthogonally into different types of granularity trees or different frames of reference, structuring and organizing the knowledge graph into partially overlapping, partially enclosed subgraphs, each of which can be referenced by its own resource. Conclusions: Semantic units, applicable in RDF/OWL and labeled property graphs, offer support for making statements about statements and facilitate graph-alignment, subgraph-matching, knowledge graph profiling, and for management of access restrictions to sensitive data. Additionally, we argue that organizing the graph into semantic units promotes the differentiation of ontological and discursive information, and that it also supports the differentiation of multiple frames of reference within the graph." assertion.
• 3360901.3364434 abstract "Scientific publishing seems to be at a turning point. Its paradigm has stayed basically the same for 300 years but is now challenged by the increasing volume of articles that makes it very hard for scientists to stay up to date in their respective fields. In fact, many have pointed out serious flaws of current scientific publishing practices, including the lack of accuracy and efficiency of the reviewing process. To address some of these problems, we apply here the general principles of the Web and the Semantic Web to scientific publishing, focusing on the reviewing process. We want to determine if a fine-grained model of the scientific publishing workflow can help us make the reviewing processes better organized and more accurate, by ensuring that review comments are created with formal links and semantics from the start. Our contributions include a novel model called Linkflows that allows for such detailed and semantically rich representations of reviews and the reviewing processes. We evaluate our approach on a manually curated dataset from several recent Computer Science journals and conferences that come with open peer reviews. We gathered ground-truth data by contacting the original reviewers and asking them to categorize their own review comments according to our model. Comparing this ground truth to answers provided by model experts, peers, and automated techniques confirms that our approach of formally capturing the reviewers' intentions from the start prevents substantial discrepancies compared to when this information is later extracted from the plain-text comments. In general, our analysis shows that our model is well understood and easy to apply, and it revealed the semantic properties of such review comments." assertion.
• 3360901.3364434 abstract "Scientific publishing seems to be at a turning point. Its paradigm has stayed basically the same for 300 years but is now challenged by the increasing volume of articles that makes it very hard for scientists to stay up to date in their respective fields. In fact, many have pointed out serious flaws of current scientific publishing practices, including the lack of accuracy and efficiency of the reviewing process. To address some of these problems, we apply here the general principles of the Web and the Semantic Web to scientific publishing, focusing on the reviewing process. We want to determine if a fine-grained model of the scientific publishing workflow can help us make the reviewing processes better organized and more accurate, by ensuring that review comments are created with formal links and semantics from the start. Our contributions include a novel model called Linkflows that allows for such detailed and semantically rich representations of reviews and the reviewing processes. We evaluate our approach on a manually curated dataset from several recent Computer Science journals and conferences that come with open peer reviews. We gathered ground-truth data by contacting the original reviewers and asking them to categorize their own review comments according to our model. Comparing this ground truth to answers provided by model experts, peers, and automated techniques confirms that our approach of formally capturing the reviewers' intentions from the start prevents substantial discrepancies compared to when this information is later extracted from the plain-text comments. In general, our analysis shows that our model is well understood and easy to apply, and it revealed the semantic properties of such review comments." assertion.
• SSW240006 abstract "Traditional dataset retrieval systems rely on metadata for indexing, rather than on the underlying data values. However, high-quality metadata creation and enrichment often require manual annotations, which is a labour-intensive and challenging process to automate. In this study, we propose a method to support metadata enrichment using topic annotations generated by three Large Language Models (LLMs): ChatGPT-3.5, GoogleBard, and GoogleGemini. Our analysis focuses on classifying column headers based on domain-specific topics from the Consortium of European Social Science Data Archives (CESSDA), a Linked Data controlled vocabulary. Our approach operates in a zero-shot setting, integrating the controlled topic vocabulary directly within the input prompt. This integration serves as a Large Context Windows approach, with the aim of improving the results of the topic classification task. We evaluated the performance of the LLMs in terms of internal consistency, inter-machine alignment, and agreement with human classification. Additionally, we investigate the impact of contextual information (i.e., dataset description) on the classification outcomes. Our findings suggest that ChatGPT and GoogleGemini outperform GoogleBard in terms of internal consistency as well as LLM-human-agreement. Interestingly, we found that contextual information had no significant impact on LLM performance. This work proposes a novel approach that leverages LLMs for topic classification of column headers using a controlled vocabulary, presenting a practical application of LLMs and Large Context Windows within the Semantic Web domain. This approach has the potential to facilitate automated metadata enrichment, thereby enhancing dataset retrieval and the Findability, Accessibility, Interoperability, and Reusability (FAIR) of research data on the Web." assertion.
• 3460210.3493561 abstract "The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the life sciences, computer science, and the social sciences. Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the "super-pattern". We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door on the longer run for allowing researchers to express their high-level scientific findings in a manner they can be automatically interpreted. This in turn will allow for automated consistency checking, question answering, aggregation, and much more." assertion.
• 3460210.3493561 abstract "The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the life sciences, computer science, and the social sciences. Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the "super-pattern". We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door on the longer run for allowing researchers to express their high-level scientific findings in a manner they can be automatically interpreted. This in turn will allow for automated consistency checking, question answering, aggregation, and much more." assertion.
• 978-3-030-61244-3_7 abstract "Scientific publishing is the means by which we communicate and share scientific knowledge, but this process currently often lacks transparency and machine-interpretable representations. Scientific articles are published in long coarse-grained text with complicated structures, and they are optimized for human readers and not for automated means of organization and access. Peer reviewing is the main method of quality assessment, but these peer reviews are nowadays rarely published and their own complicated structure and linking to the respective articles is not accessible. In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent in a semantic way the elements of publications, their assessments, as well as the involved processes, actors, and provenance in general. To evaluate our approach, we present a dataset of 627 nanopublications representing an interlinked network of the elements of articles (such as individual paragraphs) and their reviews (such as individual review comments). Focusing on the specific scenario of editors performing a meta-review, we introduce seven competency questions and show how they can be executed as SPARQL queries. We then present a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful to answer their competency questions. In summary, we demonstrate that a unified and semantic publication model based on nanopublications can make scientific communication more effective and user-friendly." assertion.
• 978-3-319-67468-1_3 abstract "The number of scientific articles has grown rapidly over the years and there are no signs that this growth will slow down in the near future. Because of this, it becomes increasingly difficult to keep up with the latest developments in a scientific field. To address this problem, we present here an approach to help researchers learn about the latest developments and findings by extracting in a normalized form core claims from scientific articles. This normalized representation is a controlled natural language of English sentences called AIDA, which has been proposed in previous work as a method to formally structure and organize scientific findings and discourse. We show how such AIDA sentences can be automatically extracted by detecting the core claim of an article, checking for AIDA compliance, and – if necessary – transforming it into a compliant sentence. While our algorithm is still far from perfect, our results indicate that the different steps are feasible and they support the claim that AIDA sentences might be a promising approach to improve scientific communication in the future." assertion.
• 978-1-61499-904-1-52 abstract "Scientific communication still mainly relies on natural language written in scientific papers, which makes the described knowledge very difficult to access with automatic means. We can therefore only make limited use of formal knowledge organization methods to support researchers and other interested parties with features such as automatic aggregations, fact checking, consistency checking, question answering, and powerful semantic search. Existing approaches to solve this problem by improving the scientific communication methods have either very restricted coverage, require formal logic skills on the side of the researchers, or depend on unreliable machine learning for the formalization of knowledge. Here, I propose an approach to this problem that is general, intuitive, and flexible. It is based on a unique kind of controlled natural language, called AIDA, consisting of English sentences that are atomic, independent, declarative, and absolute. Such sentences can then serve as nodes in a network of scientific claims linked to publications, researchers, and domain elements. I present here some small studies on preliminary applications of this language. The results indicate that it is well accepted by users and provides a good basis for the creation of a knowledge graph of scientific findings." assertion.
• 978-3-319-67256-4_23 abstract "Climate change, vaccination, abortion, Trump: Many topics are surrounded by fierce controversies. The nature of such heated debates and their elements have been studied extensively in the social science literature. More recently, various computational approaches to controversy analysis have appeared, using new data sources such as Wikipedia, which help us now better understand these phenomena. However, compared to what social sciences have discovered about such debates, the existing computational approaches mostly focus on just a few of the many important aspects around the concept of controversies. In order to link the two strands, we provide and evaluate here a controversy model that is both, rooted in the findings of the social science literature and at the same time strongly linked to computational methods. We show how this model can lead to computational controversy analytics that have full coverage over all the crucial aspects that make up a controversy." assertion.
• 3587259.3627559 abstract "In response to the increasing volume of research data being generated, more and more data portals have been designed to facilitate data findability and accessibility. However, a significant portion of this data remains confidential or restricted due to its sensitive nature, such as patient data or census microdata. While maintaining confidentiality prohibits its public release, the emergence of portals supporting rich metadata can help enable researchers to at least discover the existence of restricted access data, empowering them to assess the suitability of the data before requesting access. Existing standards, such as CSV on the Web and RDF Data Cube, have been adopted to facilitate data management, integration, and re-use of data on the Web. However, the current landscape still lacks adequate standards not only to effectively describe restricted access data while preserving confidentiality but also to facilitate its discovery. In this work, we investigate the relationship between the structural, statistical, and semantic elements of restricted access tabular data, and we explore how such relationship can be formally modeled in a way that is Findable, Accessible, Interoperable, and Reusable. We introduce the DataSet-Variable Ontology (DSV), that by combining CSV on the Web and RDF Data Cube standards, leveraging semantic technologies and Linked Data principles, and introducing variable-level metadata, aims to capture high-quality metadata to support the management and re-use of restricted access data on the Web. As evaluation, we conducted a case study where we applied DSV to four different datasets from different statistical governmental agencies. We employed a set of competency questions to assess the ontology's ability to support knowledge discovery and data exploration. By describing high-quality metadata, both at the dataset- and variable levels, while maintaining data privacy, this novel ontology facilitates data interoperability, discovery, and re-use and it empowers researchers to manage, integrate, and analyze complex restricted access data sources." assertion.
• cor.2012.0026 abstract "In this paper, we present Coral, an interface in which complex corpus queries can be expressed in a controlled subset of natural English. With the help of a predictive editor, users can compose queries and submit them to the Coral system, which then automatically translates them into formal AQL statements. We give an overview of the controlled natural language developed for Coral and describe the functionalities of the predictive editor provided for it. We also report on a user experiment in which the system was evaluated. The results show that, with Coral, corpora of annotated texts can be queried more easily and more quickly than with the existing ANNIS interface. Our system demonstrates that complex corpora can be accessed without the need to learn a complicated, formal query language." assertion.
• coli_a_00168 abstract "What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions." assertion.
• f1000research.54159.1 abstract "Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future." assertion.
• DS-230059 abstract "Measuring data drift is essential in machine learning applications where model scoring (evaluation) is done on data samples that differ from those used in training. The Kullback-Leibler divergence is a common measure of shifted probability distributions, for which discretized versions are invented to deal with binned or categorical data. We present the Unstable Population Indicator, a robust, flexible and numerically stable, discretized implementation of Jeffrey's divergence, along with an implementation in a Python package that can deal with continuous, discrete, ordinal and nominal data in a variety of popular data types. We show the numerical and statistical properties in controlled experiments. It is not advised to employ a common cut-off to distinguish stable from unstable populations, but rather to let that cut-off depend on the use case." assertion.
• DS-240063 abstract "Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and high-dimensional systems is challenging because these transitions are rare events, and isolating the relevant species in experiments is difficult. Most of the time, the system remains near a local minimum, with rare, large fluctuations leading to transitions between minima. The probability of such transitions decreases exponentially with the height of the energy barrier, making the system's dynamics highly sensitive to the calculated energy barriers. This work aims to formulate the problem of finding the minimum energy barrier between two stable states in the system's state space as a cost-minimization problem. It is proposed to solve this problem using reinforcement learning algorithms. The exploratory nature of reinforcement learning agents enables efficient sampling and determination of the minimum energy barrier for transitions." assertion.
• DS-240063 abstract "Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and high-dimensional systems is challenging because these transitions are rare events, and isolating the relevant species in experiments is difficult. Most of the time, the system remains near a local minimum, with rare, large fluctuations leading to transitions between minima. The probability of such transitions decreases exponentially with the height of the energy barrier, making the system's dynamics highly sensitive to the calculated energy barriers. This work aims to formulate the problem of finding the minimum energy barrier between two stable states in the system's state space as a cost-minimization problem. It is proposed to solve this problem using reinforcement learning algorithms. The exploratory nature of reinforcement learning agents enables efficient sampling and determination of the minimum energy barrier for transitions." assertion.
• DS-240063 abstract "Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and high-dimensional systems is challenging because these transitions are rare events, and isolating the relevant species in experiments is difficult. Most of the time, the system remains near a local minimum, with rare, large fluctuations leading to transitions between minima. The probability of such transitions decreases exponentially with the height of the energy barrier, making the system's dynamics highly sensitive to the calculated energy barriers. This work aims to formulate the problem of finding the minimum energy barrier between two stable states in the system's state space as a cost-minimization problem. It is proposed to solve this problem using reinforcement learning algorithms. The exploratory nature of reinforcement learning agents enables efficient sampling and determination of the minimum energy barrier for transitions." assertion.
• DS-240063 abstract "Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems. Precisely determining the transition pathways in complex and high-dimensional systems is challenging because these transitions are rare events, and isolating the relevant species in experiments is difficult. Most of the time, the system remains near a local minimum, with rare, large fluctuations leading to transitions between minima. The probability of such transitions decreases exponentially with the height of the energy barrier, making the system's dynamics highly sensitive to the calculated energy barriers. This work aims to formulate the problem of finding the minimum energy barrier between two stable states in the system's state space as a cost-minimization problem. It is proposed to solve this problem using reinforcement learning algorithms. The exploratory nature of reinforcement learning agents enables efficient sampling and determination of the minimum energy barrier for transitions." assertion.
• COLI_a_00168 abstract "What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions." assertion.
• COLI_a_00168 abstract "What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions." assertion.
• COLI_a_00168 abstract "What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions." assertion.
• COLI_a_00168 abstract "What is here called controlled natural language (CNL) has traditionally been given many different names. Especially during the last four decades, a wide variety of such languages have been designed. They are applied to improve communication among humans, to improve translation, or to provide natural and intuitive representations for formal notations. Despite the apparent differences, it seems sensible to put all these languages under the same umbrella. To bring order to the variety of languages, a general classification scheme is presented here. A comprehensive survey of existing English-based CNLs is given, listing and describing 100 languages from 1930 until today. Classification of these languages reveals that they form a single scattered cloud filling the conceptual space between natural languages such as English on the one end and formal languages such as propositional logic on the other. The goal of this article is to provide a common terminology and a common model for CNL, to contribute to the understanding of their general nature, to provide a starting point for researchers interested in the area, and to help developers to make design decisions." assertion.
• 11799511_7 abstract "Linking the biomedical literature to other data resources is notoriously difficult and requires text mining. Text mining aims to automatically extract facts from literature. Since authors write in natural language, text mining is a great natural language processing challenge, which is far from being solved. We propose an alternative: If authors and editors summarize the main facts in a controlled natural language, text mining will become easier and more powerful. To demonstrate this approach, we use the language Attempto Controlled English (ACE). We define a simple model to capture the main aspects of protein interactions. To evaluate our approach, we collected a dataset of 459 paragraph headings about protein interaction from literature. 56% of these headings can be represented exactly in ACE and another 23% partially. These results indicate that our approach is feasible." assertion.
• 11799511_7 abstract "Linking the biomedical literature to other data resources is notoriously difficult and requires text mining. Text mining aims to automatically extract facts from literature. Since authors write in natural language, text mining is a great natural language processing challenge, which is far from being solved. We propose an alternative: If authors and editors summarize the main facts in a controlled natural language, text mining will become easier and more powerful. To demonstrate this approach, we use the language Attempto Controlled English (ACE). We define a simple model to capture the main aspects of protein interactions. To evaluate our approach, we collected a dataset of 459 paragraph headings about protein interaction from literature. 56% of these headings can be represented exactly in ACE and another 23% partially. These results indicate that our approach is feasible." assertion.
• arXiv.0807.4618 abstract "We present AceWiki, a prototype of a new kind of semantic wiki using the controlled natural language Attempto Controlled English (ACE) for representing its content. ACE is a subset of English with a restricted grammar and a formal semantics. The use of ACE has two important advantages over existing semantic wikis. First, we can improve the usability and achieve a shallow learning curve. Second, ACE is more expressive than the formal languages of existing semantic wikis. Our evaluation shows that people who are not familiar with the formal foundations of the Semantic Web are able to deal with AceWiki after a very short learning phase and without the help of an expert." assertion.
• arXiv.0807.4618 abstract "We present AceWiki, a prototype of a new kind of semantic wiki using the controlled natural language Attempto Controlled English (ACE) for representing its content. ACE is a subset of English with a restricted grammar and a formal semantics. The use of ACE has two important advantages over existing semantic wikis. First, we can improve the usability and achieve a shallow learning curve. Second, ACE is more expressive than the formal languages of existing semantic wikis. Our evaluation shows that people who are not familiar with the formal foundations of the Semantic Web are able to deal with AceWiki after a very short learning phase and without the help of an expert." assertion.